Contacts of the strand formed by residues 513 - 517 (chain M) in PDB entry 4G7H


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 VAL 513 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497M  ALA*     4.4     6.5    -      -       +      -
    501M  THR*     4.1    16.2    -      -       +      -
    508M  ILE*     3.8    29.8    -      -       +      -
    510M  ALA*     4.4     5.4    -      -       +      +
    512M  ARG*     1.3    77.7    -      -       -      +
    514M  VAL*     1.3    69.5    +      -       -      +
    515M  ALA*     4.4     1.3    -      -       +      -
    522M  VAL      3.6     0.5    -      -       -      +
    523M  ILE*     3.4     8.1    -      -       -      +
    524M  VAL*     2.9    49.0    +      -       +      +
    526M  PRO*     4.2    13.5    -      -       +      -
    529M  VAL*     3.6    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 514 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497M  ALA*     3.5     3.1    -      -       -      +
    498M  GLN*     2.8    39.4    +      -       +      +
    500M  ASN*     5.7     2.7    -      -       -      +
    501M  THR*     4.1     8.3    -      -       +      +
    512M  ARG      5.5     0.9    -      -       -      +
    513M  VAL*     1.3    76.1    -      -       -      +
    515M  ALA*     1.3    61.4    +      -       -      +
    521M  PRO*     5.6     0.4    -      -       +      -
    522M  VAL      3.8     7.2    -      -       -      +
    523M  ILE*     4.3    15.9    -      -       +      -
   1068N  LEU*     3.6    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 515 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    495M  THR*     3.8    22.2    -      -       +      -
    496M  ILE      3.2    21.3    -      -       -      +
    497M  ALA*     3.8     4.3    -      -       +      -
    498M  GLN*     4.5     1.8    -      -       -      +
    513M  VAL*     3.7    10.7    +      -       +      -
    514M  VAL*     1.3    77.1    -      -       -      +
    516M  ARG*     1.3    66.7    +      -       -      +
    521M  PRO*     3.5     4.9    -      -       -      +
    522M  VAL*     2.9    40.3    +      -       +      +
    524M  VAL*     4.5     3.4    -      -       +      -
    529M  VAL*     5.4     0.4    -      -       +      -
   1068N  LEU*     4.7     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 516 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    432M  ARG      5.0     1.2    +      -       -      -
    435M  TYR*     3.2    47.8    +      -       -      +
    471M  TYR*     2.9    35.4    +      -       -      -
    491M  GLU*     3.2    21.7    +      -       -      -
    494M  TYR      3.6     2.4    -      -       -      +
    495M  THR*     3.4     5.0    -      -       -      -
    496M  ILE*     2.9    43.8    +      -       +      +
    498M  GLN*     4.0     9.3    -      -       -      +
    515M  ALA*     1.3    79.0    -      -       -      +
    517M  ARG*     1.3    61.9    +      -       -      +
    518M  LYS      4.1     0.4    -      -       -      -
    519M  GLY*     4.2    30.0    -      -       -      +
    520M  GLU      3.4     6.1    -      -       -      +
    522M  VAL*     4.6     0.2    -      -       -      -
    533M  ASP*     3.8     5.7    +      -       -      -
   1068N  LEU*     3.8    31.6    -      -       +      -
   1071N  PHE*     6.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 517 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    492M  ASP      5.7     0.2    -      -       -      -
    494M  TYR      4.1     7.2    -      -       -      +
    495M  THR*     2.8    35.0    +      -       +      +
    516M  ARG*     1.3    75.4    -      -       -      +
    518M  LYS*     1.3    73.4    +      -       +      +
    520M  GLU*     3.1    27.1    +      -       +      +
    522M  VAL*     4.3    19.8    -      -       +      +
    524M  VAL*     3.4    26.0    -      -       -      +
    528M  GLU*     2.9    34.4    +      -       -      +
----------------------------------------------------------
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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