Contacts of the strand formed by residues 1217 - 1220 (chain A) in PDB entry 3AVR


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 LEU1217 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    968A  THR      3.9     0.3    -      -       -      +
    969A  VAL*     3.6     2.5    -      -       -      +
    970A  ILE*     2.8    60.0    +      -       +      -
    973A  LEU*     3.3    37.5    -      -       +      -
   1106A  LEU*     4.8     0.4    -      -       +      -
   1110A  VAL*     4.3    23.6    -      -       +      -
   1155A  VAL*     3.6    26.7    -      -       +      -
   1156A  ASN      3.3    10.5    -      -       -      +
   1157A  ILE*     3.8    11.7    -      -       +      -
   1215A  GLY      3.8     1.4    +      -       -      -
   1216A  ASP*     1.3    73.4    -      -       -      +
   1218A  VAL*     1.3    77.1    +      -       -      +
   1219A  TRP*     3.8     9.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    967A  VAL*     3.8    23.8    -      -       +      -
    968A  THR      3.7     2.9    -      -       -      +
    969A  VAL*     4.4     3.8    -      -       +      -
   1154A  SER      3.5     2.3    -      -       -      +
   1155A  VAL*     3.5     5.2    -      -       -      -
   1156A  ASN*     2.8    35.3    +      -       -      +
   1166A  TRP*     3.8    35.2    -      -       +      -
   1210A  PHE*     3.6    27.1    -      -       +      -
   1212A  GLN*     3.5    30.1    -      -       +      +
   1217A  LEU*     1.3    76.5    -      -       -      +
   1219A  TRP*     1.3    61.7    -      -       -      +
   1220A  ILE*     3.9     6.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP1219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    957A  HIS*     5.4     0.9    -      +       -      -
    960A  CYS*     3.1    41.6    +      -       +      -
    961A  THR*     3.9    19.1    -      -       +      -
    967A  VAL*     3.3     5.9    -      -       -      +
    968A  THR*     2.9    46.6    +      -       -      +
    970A  ILE*     5.4     0.2    -      -       +      -
   1109A  PHE*     3.5    39.5    -      +       -      -
   1110A  VAL*     3.8    18.6    -      -       +      -
   1153A  CYS*     3.6    23.3    -      -       +      -
   1154A  SER      3.5     4.9    -      -       -      -
   1155A  VAL*     3.9    10.3    -      -       +      -
   1217A  LEU*     3.8     8.4    -      -       +      +
   1218A  VAL*     1.3    73.2    -      -       -      +
   1220A  ILE*     1.3    60.9    +      -       -      +
   1221A  ASN*     3.6    21.1    +      -       +      +
   1241A  VAL*     3.4    26.2    -      -       +      -
   1243A  PRO*     3.9     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    966A  PRO      4.2     1.1    -      -       -      -
    967A  VAL*     3.8    22.4    -      -       +      -
   1148A  GLU*     4.8     5.4    -      -       +      -
   1153A  CYS*     3.2     8.0    -      -       -      +
   1154A  SER*     2.9    50.7    +      -       -      +
   1156A  ASN*     6.3     0.2    -      -       +      -
   1166A  TRP*     3.7    34.8    -      -       +      -
   1168A  VAL*     4.0     9.4    -      -       +      -
   1218A  VAL*     3.9     3.4    -      -       +      +
   1219A  TRP*     1.3    71.3    -      -       -      +
   1221A  ASN*     1.3    74.3    +      -       -      +
   1224A  THR*     3.7    15.0    -      -       +      +
   1226A  HIS*     3.7    34.5    -      -       +      +
----------------------------------------------------------
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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