Contacts of the strand formed by residues 53 - 60 (chain L) in PDB entry 1N34


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 ARG 53 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520A    A      4.6     0.6    +      -       -      -
    521A    G      3.3    36.1    +      -       +      +
    522A    C      3.5    14.1    -      -       -      +
    523A    A      2.7    37.1    -      -       -      +
     42L  THR*     2.9    19.9    -      -       -      +
     43L  VAL*     3.5    15.9    +      -       -      +
     45L  PRO*     3.1    24.2    -      -       -      +
     49L  ASN*     4.8     0.6    -      -       -      +
     50L  SER      4.6     2.4    -      -       -      -
     51L  ALA*     3.6    11.0    +      -       +      +
     52L  LEU*     1.3    75.3    -      -       -      +
     54L  LYS*     1.3    64.9    +      -       +      +
     55L  VAL*     4.0     0.9    +      -       -      +
     69L  TYR*     3.2    33.2    -      -       +      +
     92L  ASP*     2.7    37.4    +      -       -      +
     93L  LEU*     3.5    29.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 54 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520A    A      4.0    11.9    +      -       -      -
    521A    G      2.6    45.9    +      -       -      +
     40L  VAL      5.9     0.2    -      -       -      +
     41L  ARG      4.5     7.6    -      -       -      +
     42L  THR*     5.3     3.4    -      -       +      +
     52L  LEU*     2.7    30.0    +      -       -      +
     53L  ARG*     1.3    78.9    -      -       +      +
     55L  VAL*     1.3    55.8    +      -       -      +
     69L  TYR*     3.5     3.4    -      -       -      +
     70L  ILE*     2.7    64.8    +      -       +      +
     72L  GLY      5.0     3.6    -      -       -      +
     73L  GLU      4.4     4.0    -      -       -      +
     75L  HIS*     3.6    28.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 55 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39L  VAL      4.5     0.2    -      -       -      +
     40L  VAL      3.7     9.4    -      -       -      -
     41L  ARG      3.7    18.6    +      -       -      +
     42L  THR*     5.1     0.6    -      -       -      +
     43L  VAL*     4.9    15.3    -      -       +      -
     53L  ARG      4.0     2.0    +      -       -      +
     54L  LYS*     1.3    71.0    -      -       -      +
     56L  ALA*     1.3    75.1    +      -       -      +
     67L  THR*     3.6    32.3    -      -       +      +
     68L  ALA      2.8    17.3    -      -       -      +
     69L  TYR*     3.3    38.1    -      -       +      -
     70L  ILE*     3.1     7.1    -      -       -      +
     93L  LEU*     4.1     7.6    -      -       +      -
     96L  VAL*     3.7    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 56 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37L  CYS*     3.7    29.2    -      -       -      -
     39L  VAL      3.6     7.9    -      -       -      +
     40L  VAL*     4.4     7.6    -      -       +      -
     55L  VAL*     1.3    79.0    -      -       -      +
     57L  LYS*     1.3    65.1    +      -       -      +
     58L  VAL*     3.1     7.5    -      -       +      +
     68L  ALA      2.7    36.3    +      -       -      +
     70L  ILE*     4.0     7.8    -      -       +      +
     77L  LEU*     5.1     1.1    -      -       +      -
    100L  ILE*     4.4     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 57 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1412A    C      3.7    21.3    +      -       -      -
     37L  CYS*     3.3     1.6    -      -       -      +
     38L  THR*     2.8    44.8    +      -       +      -
     39L  VAL*     2.9    30.8    +      -       +      +
     56L  ALA*     1.3    73.5    -      -       -      +
     58L  VAL*     1.3    57.9    +      -       -      +
     59L  ARG*     6.0     4.3    -      -       -      +
     65L  GLU*     5.8     5.3    +      -       +      +
     66L  VAL*     3.1    13.2    -      -       -      +
     67L  THR*     3.2    28.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35L  GLY*     3.4    13.9    -      -       -      +
     36L  VAL      2.9    37.0    -      -       -      +
     37L  CYS*     4.1    13.7    -      -       -      -
     38L  THR*     4.8     1.3    -      -       -      -
     56L  ALA*     3.1    20.0    -      -       +      +
     57L  LYS*     1.3    76.9    -      -       -      +
     59L  ARG*     1.3    59.3    +      -       -      +
     60L  LEU*     3.1    29.8    -      -       +      +
     65L  GLU*     3.4     3.0    -      -       -      -
     66L  VAL*     2.6    23.2    +      -       +      +
     68L  ALA*     4.0    18.2    -      -       +      -
     83L  VAL*     4.0    16.6    -      -       +      -
     85L  ILE*     5.2     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 59 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35L  GLY*     3.0     3.5    -      -       -      -
     36L  VAL*     2.4    57.4    +      -       +      +
     37L  CYS      5.6     0.2    -      -       -      +
     38L  THR*     4.0    23.7    +      -       -      +
     57L  LYS*     6.0     3.8    -      -       -      +
     58L  VAL*     1.3    66.8    -      -       -      +
     60L  LEU*     1.3    68.1    +      -       -      +
     61L  THR*     4.8     0.3    -      -       -      +
     63L  GLY*     4.9     4.0    -      -       -      -
     64L  TYR      3.5    14.1    -      -       -      -
     65L  GLU*     3.0    31.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 60 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26L  ALA*     5.2     3.8    -      -       -      +
     33L  ARG*     4.1     8.5    -      -       +      +
     34L  ARG      3.3    18.6    -      -       -      +
     35L  GLY*     4.4     3.1    -      -       -      -
     58L  VAL*     3.1    22.9    -      -       +      +
     59L  ARG*     1.3    80.6    -      -       -      +
     61L  THR*     1.3    60.1    +      -       -      +
     62L  SER*     2.9    29.2    +      -       -      +
     63L  GLY*     3.2    11.8    +      -       -      -
     64L  TYR*     2.8    27.1    +      -       +      +
     65L  GLU      3.7     0.2    -      -       -      +
     66L  VAL*     3.5    26.9    -      -       +      +
     85L  ILE*     3.2    33.0    -      -       +      -
     98L  TYR*     6.4     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