Contacts of the strand formed by residues 38 - 55 (chain E) in PDB entry 2N0A


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with LEU 38 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  VAL*     5.1     0.4    -      -       -      -
     38D  LEU*     3.6    32.3    -      -       +      +
     35E  GLU*     3.3    28.7    -      -       +      +
     37E  VAL*     1.3    81.5    -      -       -      +
     39E  TYR*     1.3    65.2    +      -       -      +
     40E  VAL*     4.2     7.2    -      -       +      -
     35F  GLU*     4.1     9.6    -      -       -      +
     37F  VAL      3.2     6.1    +      -       -      -
     38F  LEU*     3.6    27.4    -      -       +      -
     39F  TYR      3.0    27.5    +      -       -      +
     40F  VAL*     5.6     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 39 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  LEU      3.0     8.8    +      -       -      +
     39D  TYR*     3.4    52.8    -      +       +      -
     40D  VAL      3.0    25.6    +      -       -      +
     42D  SER*     3.9     8.2    +      -       -      +
     37E  VAL*     3.5    24.5    -      -       +      -
     38E  LEU*     1.3    76.7    -      -       -      +
     40E  VAL*     1.3    64.0    -      -       -      +
     42E  SER*     4.0    14.1    -      -       -      +
     37F  VAL*     4.0     5.2    -      -       -      +
     39F  TYR*     3.4    51.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 40 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  LEU*     5.6     1.6    -      -       +      +
     40D  VAL*     3.3    26.5    -      -       +      +
     38E  LEU*     5.1     7.0    -      -       +      -
     39E  TYR*     1.3    83.3    -      -       -      +
     41E  GLY*     1.3    72.0    +      -       -      +
     42E  SER*     4.3     0.6    +      -       -      -
     39F  TYR      3.0    10.0    +      -       -      +
     40F  VAL*     3.3    23.7    -      -       +      +
     41F  GLY      3.2    14.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 41 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  VAL      3.2     3.4    +      -       -      -
     41D  GLY*     2.9    21.6    +      -       -      -
     39E  TYR      4.3     0.2    -      -       -      -
     40E  VAL*     1.3    72.2    -      -       -      +
     42E  SER*     1.3    56.5    +      -       -      +
     43E  LYS*     5.3     3.8    -      -       -      -
     41F  GLY*     2.9    33.0    +      -       -      -
     42F  SER      3.3     1.7    +      -       -      +
     43F  LYS*     4.8     7.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 42 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  GLY      3.3     5.3    +      -       -      -
     42D  SER*     3.4    13.7    +      -       -      -
     43D  LYS      3.1    23.7    +      -       -      +
     39E  TYR*     4.0    21.1    -      -       -      -
     40E  VAL      3.9     2.3    +      -       -      -
     41E  GLY*     1.3    79.0    +      -       -      +
     43E  LYS*     1.3    67.9    +      -       -      +
     44E  THR*     4.2     4.7    -      -       -      -
     39F  TYR*     3.9    20.6    +      -       -      +
     42F  SER*     3.4    16.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 43 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  GLY      4.8     7.9    +      -       -      -
     43D  LYS*     3.0    48.5    -      -       +      +
     41E  GLY*     5.3     2.4    -      -       -      -
     42E  SER*     1.3    83.1    +      -       -      +
     44E  THR*     1.3    64.4    +      -       -      +
     45E  LYS*     5.2     6.3    -      -       -      -
     42F  SER      3.1     7.2    +      -       -      +
     43F  LYS*     3.0    41.6    -      -       +      +
     44F  THR*     2.9    29.1    +      -       -      +
     45F  LYS*     4.8    13.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 44 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43D  LYS      2.9    17.4    +      -       -      +
     44D  THR*     4.5    16.2    -      -       +      -
     45D  LYS      3.1    23.7    +      -       -      +
     46D  GLU*     5.7     2.5    -      -       +      +
     42E  SER*     4.2     4.9    -      -       -      -
     43E  LYS*     1.3    76.7    +      -       -      +
     45E  LYS*     1.3    69.0    +      -       -      +
     46E  GLU*     4.3    20.4    -      -       +      +
     44F  THR*     3.4    18.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 45 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43D  LYS*     4.8    10.9    -      -       -      +
     45D  LYS*     3.3    47.0    -      -       +      +
     43E  LYS*     5.2     8.3    -      -       -      -
     44E  THR*     1.3    80.9    +      -       -      +
     46E  GLU*     1.3    66.5    +      -       -      +
     47E  GLY      4.3     0.4    -      -       -      -
     48E  VAL*     4.4    17.0    -      -       +      -
     44F  THR      3.1     6.9    +      -       -      +
     45F  LYS*     3.3    38.8    -      -       +      +
     46F  GLU*     3.0    24.5    +      -       -      +
     48F  VAL*     4.5    10.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 46 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  LYS      3.0    10.2    +      -       -      +
     46D  GLU*     3.3    27.0    -      -       +      +
     47D  GLY      3.1    15.1    +      -       -      -
     80D  LYS*     2.8    40.8    +      -       +      +
     44E  THR*     4.3    18.1    -      -       +      +
     45E  LYS*     1.3    80.9    -      -       -      +
     47E  GLY*     1.3    68.2    +      -       -      +
     48E  VAL*     4.3     1.0    -      -       -      +
     80E  LYS*     5.7     0.2    -      -       -      -
     44F  THR*     5.7     2.4    -      -       +      +
     46F  GLU*     3.3    33.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 47 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47D  GLY*     3.0    33.5    +      -       -      -
     48D  VAL      3.2     1.6    +      -       -      -
     78D  ALA*     3.7     4.1    -      -       -      +
     79D  GLN      3.9    23.6    -      -       -      -
     80D  LYS*     5.4     4.1    -      -       -      +
     46E  GLU*     1.3    70.0    -      -       -      +
     48E  VAL*     1.3    59.4    +      -       -      +
     78E  ALA*     3.9     6.1    -      -       -      -
     46F  GLU      3.1     4.0    +      -       -      -
     47F  GLY*     3.0    19.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 48 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  LYS*     4.5    15.3    -      -       +      +
     47D  GLY      4.7     0.7    -      -       -      +
     48D  VAL*     3.3    29.8    -      -       +      +
     78D  ALA*     4.6     0.2    -      -       -      -
     45E  LYS*     4.4    17.0    -      -       +      -
     46E  GLU      4.2    16.6    -      -       -      +
     47E  GLY*     1.3    81.0    -      -       -      +
     49E  VAL*     1.3    70.9    +      -       -      +
     50E  HIS*     5.8     2.0    -      -       +      -
     78E  ALA*     3.5     5.3    -      -       -      +
     47F  GLY      3.2     5.7    +      -       -      -
     48F  VAL*     3.3    20.4    -      -       +      +
     49F  VAL      3.1    23.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 49 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48D  VAL      3.1     5.0    +      -       -      +
     49D  VAL*     3.3    22.1    -      -       +      -
     50D  HIS*     3.1    22.5    +      -       -      +
     76D  ALA*     3.9     9.2    -      -       +      -
     77D  VAL      3.2    34.8    -      -       -      +
     78D  ALA*     3.9     2.0    -      -       +      +
     48E  VAL*     1.3    78.7    -      -       -      +
     50E  HIS*     1.3    67.0    +      -       -      +
     76E  ALA*     3.3    41.5    -      -       +      +
     78E  ALA*     4.3     0.7    -      -       +      -
     49F  VAL*     3.3    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 50 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50D  HIS*     3.2    47.6    +      +       +      +
     52D  VAL*     5.1     0.7    -      -       +      -
     48E  VAL*     5.8     3.1    -      -       +      -
     49E  VAL*     1.3    82.1    -      -       -      +
     51E  GLY*     1.3    61.9    +      -       -      +
     52E  VAL*     2.9    28.7    -      -       +      +
     76E  ALA*     5.2     0.4    -      -       -      +
     49F  VAL      3.1     5.8    +      -       -      +
     50F  HIS*     3.2    40.5    +      +       +      +
     51F  GLY      3.1    22.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 51 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50D  HIS      3.1     8.2    +      -       -      +
     51D  GLY*     3.3     7.0    -      -       -      -
     52D  VAL      3.1    23.4    +      -       -      +
     74D  VAL*     4.8     9.0    -      -       -      +
     76D  ALA*     5.4     3.8    -      -       -      +
     49E  VAL*     4.4     2.6    -      -       -      +
     50E  HIS*     1.3    73.0    -      -       -      +
     52E  VAL*     1.3    65.1    +      -       -      +
     74E  VAL*     4.7    14.1    -      -       -      -
     76E  ALA*     5.4     5.2    -      -       -      -
     51F  GLY      3.3     9.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 52 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52D  VAL*     3.5    22.9    -      -       +      +
     50E  HIS*     2.9    34.8    -      -       +      +
     51E  GLY*     1.3    75.0    -      -       -      +
     53E  ALA*     1.3    63.1    +      -       -      +
     54E  THR*     4.5    11.9    -      -       -      +
     74E  VAL*     5.2     4.1    -      -       -      +
     50F  HIS*     5.1     0.7    -      -       +      -
     51F  GLY      3.1     6.5    +      -       -      +
     52F  VAL*     3.5    21.1    -      -       +      +
     53F  ALA*     2.9    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 53 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52D  VAL      2.9    10.8    +      -       -      +
     53D  ALA*     3.3    11.7    -      -       +      +
     54D  THR*     3.1    24.1    +      -       -      +
     73D  GLY      5.8     0.4    -      -       -      +
     74D  VAL*     5.4     0.4    -      -       +      -
     52E  VAL*     1.3    74.5    -      -       -      +
     54E  THR*     1.3    63.9    +      -       -      +
     55E  VAL*     4.3     6.5    -      -       +      -
     73E  GLY*     6.0     1.8    -      -       -      -
     74E  VAL*     3.8    26.9    -      -       +      +
     53F  ALA*     3.3    10.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 54 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54D  THR*     3.6    20.9    +      -       +      +
     52E  VAL*     4.5    10.9    -      -       -      +
     53E  ALA*     1.3    75.2    +      -       -      +
     55E  VAL*     1.3    72.4    +      -       -      +
     56E  ALA*     5.1     1.6    -      -       +      +
     53F  ALA      3.1    11.4    +      -       -      +
     54F  THR*     3.6    17.0    +      -       +      -
     55F  VAL*     2.9    29.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 55 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54D  THR*     2.9    17.7    +      -       -      +
     55D  VAL*     3.4    17.9    -      -       +      -
     56D  ALA*     3.1    23.9    +      -       -      +
     53E  ALA*     5.2     5.6    -      -       +      -
     54E  THR*     1.3    85.5    -      -       -      +
     56E  ALA*     1.3    61.9    +      -       -      +
     57E  GLU      3.6    18.8    -      -       -      +
     58E  LYS      5.4     0.9    -      -       -      -
     59E  THR*     4.8    18.8    -      -       +      -
     55F  VAL*     3.4    24.0    -      -       +      +
     57F  GLU      5.3     1.1    -      -       -      +
     59F  THR*     6.5     0.4    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il