Contacts of the strand formed by residues 35 - 42 (chain B) in PDB entry 3NCF


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 ASN 35 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  PRO*     3.5     2.1    -      -       -      +
     34B  THR*     1.3    89.9    -      -       -      +
     36B  TYR*     1.3    89.1    +      -       -      +
     37B  SER*     5.6     1.4    +      -       -      -
     81B  ALA*     3.4     5.0    -      -       -      +
     82B  THR*     2.8    46.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  PRO*     4.4     9.0    -      -       +      -
     24B  TRP*     3.5    42.4    -      +       +      -
     26B  PRO*     3.1    34.4    -      -       +      +
     33B  PRO*     3.4    21.1    -      -       +      +
     35B  ASN*     1.3    94.9    +      -       -      +
     37B  SER*     1.3    61.8    +      -       -      +
     38B  LEU      4.3     0.2    -      -       -      -
     50B  GLU*     5.2     0.2    -      -       -      +
     54B  TYR*     4.1    10.8    +      -       +      -
     60B  ASN*     3.2    26.9    +      -       -      -
     79B  VAL*     4.1     6.7    -      -       +      -
     80B  ASN*     3.1    17.0    -      -       -      -
     81B  ALA*     3.7    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ASN*     5.6     1.2    +      -       -      -
     36B  TYR*     1.3    75.5    +      -       -      +
     38B  LEU*     1.3    60.4    +      -       -      +
     39B  THR*     3.9     9.7    +      -       -      +
     50B  GLU*     2.9    23.6    +      -       -      -
     54B  TYR*     3.3     2.9    -      -       -      -
     78B  MET      3.8     0.9    -      -       -      +
     79B  VAL*     3.3     4.1    -      -       -      -
     80B  ASN*     2.8    57.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  ILE*     4.0    25.4    -      -       +      -
     22B  CYS*     5.0     4.5    -      -       +      -
     24B  TRP*     4.1    26.0    -      -       +      -
     37B  SER*     1.3    73.6    -      -       -      +
     39B  THR*     1.3    70.5    +      -       -      +
     40B  TYR*     4.1    12.8    -      -       +      -
     50B  GLU*     3.6     1.4    -      -       -      +
     51B  CYS*     2.9    35.6    +      -       +      -
     54B  TYR*     2.7    14.5    +      -       -      +
     62B  CYS*     4.0    32.1    -      -       +      -
     64B  PHE*     4.1    13.7    -      -       +      -
     77B  MET*     4.4    14.1    -      -       +      -
     78B  MET      3.4    10.1    -      -       -      +
     79B  VAL*     4.2     3.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  SER*     3.9    15.6    +      -       -      +
     38B  LEU*     1.3    81.1    -      -       -      +
     40B  TYR*     1.3    63.3    +      -       -      +
     48B  MET*     4.3    24.0    -      -       +      +
     49B  HIS      3.2    14.1    -      -       -      +
     50B  GLU*     4.5     7.6    -      -       +      -
     77B  MET*     3.4     0.9    -      -       -      +
     78B  MET*     2.8    54.3    +      -       -      +
     80B  ASN*     5.4     6.5    +      -       -      +
     89B  PHE*     6.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  LEU*     4.1     8.1    -      -       +      -
     39B  THR*     1.3    78.0    -      -       -      +
     41B  HIS*     1.3    72.1    +      -       -      +
     42B  ARG*     4.0    14.8    -      -       -      -
     48B  MET*     3.7     3.5    -      -       -      +
     49B  HIS*     2.9    74.3    +      +       +      +
     50B  GLU      3.7    16.6    +      -       -      -
     51B  CYS*     4.0     1.6    -      -       -      -
     52B  PRO*     4.6     0.9    -      -       -      +
     64B  PHE*     3.6    29.7    -      +       -      -
     68B  TYR*     4.0    24.8    +      -       -      +
     75B  TYR*     3.8    23.1    -      +       -      -
     76B  ILE      3.0    15.5    -      -       -      +
     77B  MET*     3.6    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  ILE*     6.0     1.8    -      -       +      -
     40B  TYR*     1.3    82.2    -      -       -      +
     42B  ARG*     1.3    69.1    +      -       -      +
     45B  GLU      4.4     8.9    +      -       -      +
     46B  THR*     5.0     3.1    -      -       -      +
     47B  LEU      3.1    26.9    -      -       -      +
     48B  MET*     4.4    12.1    -      -       +      -
     49B  HIS*     4.8     1.6    -      -       -      -
     75B  TYR*     3.7     1.4    -      -       -      -
     76B  ILE*     2.7    75.8    +      -       +      +
     92B  GLU*     4.4     7.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  TYR*     4.0    12.1    -      -       +      -
     41B  HIS*     1.3    80.6    +      -       -      +
     43B  GLU*     1.3    64.3    +      -       -      +
     44B  GLY      3.5     0.2    +      -       -      -
     45B  GLU*     3.3    46.3    +      -       -      +
     47B  LEU      4.8     1.0    +      -       -      -
     49B  HIS*     4.9     4.7    -      -       +      +
     68B  TYR*     4.0     8.5    +      -       -      +
     70B  SER*     2.5    31.1    +      -       -      -
     73B  ARG*     3.4    48.3    -      -       -      +
     74B  THR      3.4     5.8    +      -       -      +
     75B  TYR*     3.1    58.7    +      -       -      -
     76B  ILE*     4.2     3.1    -      -       -      -
----------------------------------------------------------
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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