Contacts of the strand formed by residues 443 - 448 (chain D) 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 443 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400D  VAL*     4.0    15.7    -      -       +      -
    401D  TYR      3.5    30.1    -      -       -      +
    402D  PRO*     3.6    10.3    -      -       +      -
    403D  PHE*     3.2    10.8    -      -       -      -
    438D  ASP*     2.9    38.0    +      -       +      +
    441D  ARG*     3.7    28.7    -      -       +      +
    442D  ASN*     1.3    78.0    -      -       -      +
    444D  VAL*     1.3    64.0    +      -       -      +
    445D  ARG*     3.8    14.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 444 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401D  TYR*     2.9    49.4    +      -       +      +
    403D  PHE*     3.5    24.7    -      -       +      -
    407D  VAL*     3.6    24.5    -      -       +      -
    409D  VAL*     4.3     4.0    -      -       +      -
    421D  LEU*     4.2    23.3    -      -       +      -
    422D  ALA*     4.6     5.6    -      -       +      -
    435D  VAL*     4.1    20.2    -      -       +      -
    436D  GLU      3.8     4.0    -      -       -      +
    437D  VAL*     4.4     6.5    -      -       +      +
    443D  VAL*     1.3    71.6    -      -       -      +
    445D  ARG*     1.3    69.4    +      -       -      +
    446D  VAL*     4.6     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 445 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202D  VAL*     5.4     2.0    -      -       -      -
    204D  LEU*     4.1    27.0    -      -       -      +
    396D  VAL*     5.4     6.2    -      -       -      +
    398D  ALA*     4.6    15.3    -      -       +      -
    399D  ARG      3.3     5.2    -      -       -      +
    400D  VAL*     3.6    27.1    -      -       +      +
    435D  VAL*     3.6     0.5    -      -       -      -
    436D  GLU*     2.9    75.4    +      -       +      +
    437D  VAL      5.5     0.2    -      -       -      -
    438D  ASP*     3.1    40.6    +      -       -      +
    441D  ARG*     3.5    14.8    -      -       -      +
    443D  VAL*     3.8    11.9    +      -       +      +
    444D  VAL*     1.3    75.3    -      -       -      +
    446D  VAL*     1.3    65.1    +      -       -      +
    447D  VAL*     4.0     2.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 446 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398D  ALA*     3.2     4.1    -      -       -      -
    399D  ARG*     2.9    32.1    +      -       -      +
    401D  TYR*     4.1    26.5    -      -       +      -
    415D  VAL*     4.2     5.6    -      -       +      -
    421D  LEU*     4.3    13.0    -      -       +      -
    429D  SER*     4.1     7.9    -      -       -      +
    431D  VAL*     3.6    23.6    -      -       +      -
    433D  GLY*     3.7    26.0    -      -       -      +
    434D  ARG      3.5     2.5    -      -       -      -
    435D  VAL*     4.1    19.5    -      -       +      -
    444D  VAL*     4.6     1.8    -      -       +      -
    445D  ARG*     1.3    78.9    -      -       -      +
    447D  VAL*     1.3    60.4    +      -       -      +
    448D  GLU*     3.5     2.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 447 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163D  TYR      4.0    20.2    -      -       -      +
    164D  GLY*     4.5     8.5    -      -       -      -
    165D  LYS      5.2     1.1    -      -       -      +
    166D  GLN*     5.2     5.6    -      -       +      +
    396D  VAL*     3.6    19.7    -      -       +      -
    397D  LYS      3.4    16.2    -      -       -      +
    398D  ALA*     3.7    10.1    -      -       +      -
    433D  GLY*     3.1     1.7    -      -       -      -
    434D  ARG*     2.9    43.0    +      -       +      +
    436D  GLU*     3.5    28.7    -      -       +      +
    445D  ARG*     5.2     2.0    -      -       +      +
    446D  VAL*     1.3    72.7    -      -       -      +
    448D  GLU*     1.3    66.4    +      -       -      +
    449D  SER*     3.0     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 448 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160D  GLU      4.7     0.9    -      -       -      +
    164D  GLY*     3.3    18.5    -      -       -      -
    165D  LYS      4.6     0.5    +      -       -      -
    397D  LYS*     3.3    52.6    +      -       +      +
    398D  ALA*     4.3     9.4    -      -       -      +
    399D  ARG*     2.9    37.6    +      -       +      -
    431D  VAL*     4.3    21.6    -      -       +      +
    432D  TYR      3.6     8.3    -      -       -      +
    446D  VAL      4.4     0.4    -      -       -      +
    447D  VAL*     1.3    69.6    -      -       -      +
    449D  SER*     1.3    62.5    +      -       -      +
    450D  TYR*     6.0     0.2    -      -       -      -
----------------------------------------------------------
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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