Contacts of the strand formed by residues 2124 - 2129 (chain B) in PDB entry 1V9P


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 VAL2124 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2082B  MET*     3.0    17.1    -      -       -      +
   2122B  LEU      3.0    19.3    -      -       -      +
   2123B  SER*     1.3    73.0    -      -       -      +
   2125B  ASN*     1.3    67.4    +      -       -      +
   2126B  LEU*     4.2    17.3    -      -       +      -
   2137B  ALA      3.5    14.4    -      -       -      +
   2138B  THR*     4.5     3.6    -      -       +      -
   2139B  ARG      4.3     0.7    -      -       -      +
   2148B  VAL*     5.3     0.4    -      -       +      -
   2152B  LEU*     4.3     7.2    -      -       +      -
   2172B  ARG*     4.1     1.7    -      -       -      -
   2173B  GLY*     3.4    32.1    +      -       -      +
   2174B  GLU      4.0     4.3    -      -       -      +
   2175B  VAL*     3.9    23.1    -      -       +      +
   2208B  LEU*     3.9    24.5    -      -       +      -
   2225B  PHE*     4.9     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN2125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2078B  HIS*     4.2    14.5    +      -       +      -
   2079B  PRO*     4.9     2.9    -      -       -      +
   2082B  MET*     3.6    15.7    -      -       -      +
   2124B  VAL*     1.3    82.1    -      -       -      +
   2126B  LEU*     1.3    69.2    +      -       -      +
   2127B  TYR*     4.5     4.3    +      -       -      +
   2135B  PHE*     3.9     4.9    -      -       -      +
   2136B  GLY*     3.4     2.3    -      -       -      -
   2137B  ALA*     3.1    30.9    +      -       -      +
   2170B  GLU*     3.1    21.2    +      -       -      +
   2171B  VAL      3.5     6.3    -      -       -      -
   2172B  ARG*     2.4    48.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU2126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2124B  VAL*     4.2    11.7    -      -       +      -
   2125B  ASN*     1.3    90.1    -      -       -      +
   2127B  TYR*     1.3    60.3    +      -       -      +
   2128B  TYR*     3.4    34.8    -      -       +      +
   2133B  LEU*     4.0    11.9    -      -       +      -
   2135B  PHE      3.8     3.1    -      -       -      -
   2136B  GLY*     4.7     0.4    -      -       -      -
   2152B  LEU*     3.7    29.8    -      -       +      -
   2158B  ILE*     3.4    20.2    -      -       +      -
   2170B  GLU*     3.6     3.1    -      -       -      -
   2171B  VAL*     2.8    36.8    +      -       +      +
   2225B  PHE*     3.4    31.4    -      -       +      -
   2252B  PHE*     4.3     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR2127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2079B  PRO*     3.7    30.1    -      -       +      -
   2125B  ASN*     4.7     3.8    -      -       -      +
   2126B  LEU*     1.3    73.5    -      -       -      +
   2128B  TYR*     1.3    63.8    +      -       -      +
   2129B  GLU*     2.6    47.9    +      -       +      +
   2133B  LEU*     3.4     2.0    -      -       -      +
   2134B  VAL*     2.7    45.1    +      -       +      -
   2135B  PHE*     3.2    42.2    +      +       +      +
   2168B  ARG*     2.6    36.2    +      -       +      +
   2169B  LEU      3.7    16.8    -      -       -      -
   2170B  GLU*     4.8     4.7    -      -       +      -
   2230B  LEU*     5.6     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR2128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2126B  LEU*     3.4    29.8    -      -       +      +
   2127B  TYR*     1.3    80.2    -      -       -      +
   2129B  GLU*     1.3    65.0    +      -       -      +
   2131B  GLY*     3.7    19.7    -      -       -      -
   2132B  VAL      2.9     8.5    -      -       -      +
   2133B  LEU*     3.3    34.5    -      -       +      +
   2159B  PRO*     2.9    29.1    +      -       -      +
   2160B  ARG      3.9     3.4    -      -       -      -
   2162B  LEU*     3.8    18.8    -      -       +      -
   2165B  VAL*     5.8     0.2    -      -       +      -
   2166B  PRO      5.9     0.2    -      -       -      -
   2167B  ASP      3.7     0.4    -      -       -      +
   2168B  ARG*     3.7     3.1    -      -       -      -
   2169B  LEU*     3.0    40.0    +      -       +      +
   2171B  VAL*     3.8    10.8    -      -       +      -
   2252B  PHE*     3.0    39.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLU2129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2007B  ARG*     3.1    38.6    +      -       -      +
   2011B  ASN*     3.3    20.0    +      -       -      +
   2127B  TYR*     2.6    47.9    +      -       +      +
   2128B  TYR*     1.3    71.9    -      -       -      +
   2130B  GLU*     1.3    68.4    +      -       +      +
   2131B  GLY      2.9     4.5    -      -       -      -
   2132B  VAL*     2.6    30.3    +      -       -      +
   2134B  VAL*     3.8     9.7    -      -       +      +
   2167B  ASP      3.3     4.5    -      -       -      +
   2168B  ARG*     3.3    15.0    +      -       +      +
----------------------------------------------------------
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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