Contacts of the strand formed by residues 128 - 132 (chain H) in PDB entry 3V4V


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 SER 128 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  PRO      5.1     0.7    -      -       -      -
    127H  PRO*     1.3    75.9    -      -       -      +
    129H  VAL*     1.3    61.2    +      -       -      +
    130H  TYR*     3.2    40.6    +      -       -      -
    149H  LEU      3.7     0.2    -      -       -      +
    151H  LYS*     2.9    33.2    +      -       -      +
    152H  GLY      4.9     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 129 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127H  PRO*     5.1     0.9    -      -       +      -
    128H  SER*     1.3    74.1    -      -       -      +
    130H  TYR*     1.3    74.0    +      -       -      +
    131H  PRO*     4.1     0.4    -      -       -      +
    148H  CYS*     3.7    29.2    -      -       -      -
    149H  LEU      3.3     6.1    -      -       -      +
    150H  VAL*     4.2    10.1    -      -       +      -
    203H  CYS*     4.6     2.9    -      -       -      +
    205H  VAL*     3.7    28.0    -      -       +      -
    214H  VAL*     4.0    23.8    -      -       +      +
    216H  LYS*     3.2    44.7    -      -       +      +
    128L  GLU*     5.1     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 130 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  SER*     3.2    47.5    +      -       -      -
    129H  VAL*     1.3    80.1    -      -       -      +
    131H  PRO*     1.3    67.7    -      -       -      +
    132H  LEU*     4.0     0.8    -      -       +      +
    149H  LEU*     2.7    56.0    +      -       +      +
    151H  LYS*     4.3    18.8    -      -       +      -
    126L  SER*     3.9    15.0    -      -       -      -
    128L  GLU*     3.3    52.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 131 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  VAL      4.1     0.2    -      -       -      +
    130H  TYR*     1.3    89.2    -      -       -      +
    132H  LEU*     1.3    66.7    +      -       -      +
    133H  ALA      4.2     0.8    +      -       -      -
    147H  GLY      4.7     4.9    -      -       -      +
    148H  CYS*     4.8     5.8    -      -       -      -
    216H  LYS*     3.5    37.0    -      -       +      -
    217H  LYS*     4.5     8.5    -      -       -      +
    218H  ILE*     3.5    32.8    -      -       +      -
    126L  SER*     3.7    25.6    +      -       -      +
    128L  GLU*     4.1     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 132 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130H  TYR*     4.0     8.1    -      -       +      +
    131H  PRO*     1.3    83.8    -      -       -      +
    133H  ALA*     1.3    63.3    +      -       -      +
    146H  LEU*     4.0     4.9    -      -       -      +
    147H  GLY*     3.2    37.2    +      -       -      +
    148H  CYS      3.7    26.9    -      -       -      +
    149H  LEU*     4.0    19.5    -      -       +      -
    186H  SER*     5.3     6.1    -      -       -      -
    187H  SER      5.2     0.9    -      -       -      +
    218H  ILE*     4.6     1.2    -      -       -      +
    123L  PHE*     4.1    40.9    -      -       +      +
    124L  PRO      4.3    11.7    -      -       -      +
    125L  PRO*     5.8     0.4    -      -       +      -
    126L  SER*     5.3     5.2    -      -       -      +
----------------------------------------------------------
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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