Contacts of the strand formed by residues 118 - 123 (chain A) in PDB entry 2XCV


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 LEU 118 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  LEU*     4.1    23.1    -      -       +      -
    111A  LYS      3.8     3.4    -      -       -      -
    112A  VAL*     4.6     6.1    -      -       +      -
    116A  GLY      4.1     3.1    -      -       -      +
    117A  ASN*     1.3    69.3    -      -       -      +
    119A  LEU*     1.3    66.7    +      -       -      +
    120A  VAL      4.8     5.6    -      -       -      +
    121A  CYS*     4.2    11.7    -      -       +      -
    133A  THR*     4.5     9.9    -      -       +      -
    137A  TYR*     3.8    32.5    -      -       +      -
    140A  LYS*     3.1    30.4    +      -       +      +
    141A  PHE*     3.7    21.8    -      -       -      +
    142A  ILE*     3.8    24.9    -      -       +      -
    446A  ARG*     4.2     9.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  LYS*     2.6    21.0    +      -       +      +
    112A  VAL      4.0    17.3    -      -       -      +
    113A  ASP*     3.9    13.9    -      -       +      +
    117A  ASN      4.1     4.7    -      -       -      +
    118A  LEU*     1.3    77.0    -      -       -      +
    120A  VAL*     1.3    66.9    +      -       +      +
    443A  SER*     4.0    27.3    +      -       -      +
    446A  ARG*     3.8    66.6    -      -       +      +
    447A  GLN      4.1     5.8    -      -       -      +
    448A  THR*     4.1    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  LEU      4.5     0.2    -      -       -      -
    110A  LEU*     3.3     7.3    -      -       -      +
    111A  LYS*     3.0    54.7    +      -       +      +
    118A  LEU*     4.8     3.1    -      -       -      +
    119A  LEU*     1.3    87.6    +      -       +      +
    121A  CYS*     1.3    65.5    +      -       -      +
    127A  PHE*     3.7    35.7    -      -       +      -
    431A  ASP*     5.5     2.5    -      -       -      +
    436A  MET      5.2     1.8    -      -       -      +
    437A  MET*     4.0    17.7    -      -       +      +
    443A  SER*     4.5     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  ASN*     3.9    23.1    -      -       -      -
    109A  LEU      3.6     3.4    -      -       -      -
    110A  LEU*     3.5    23.1    -      -       +      -
    118A  LEU*     4.2     6.3    -      -       +      -
    120A  VAL*     1.3    79.2    -      -       -      +
    122A  ALA*     1.3    56.4    +      -       -      +
    127A  PHE*     3.6     4.7    -      -       -      +
    128A  ILE*     2.8    54.0    +      -       -      +
    133A  THR*     4.1    22.4    -      -       +      -
    136A  GLN*     5.5     0.4    -      -       -      -
    137A  TYR*     4.1     9.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  PHE*     4.9     0.4    -      -       +      -
    107A  GLY      4.5     0.2    -      -       -      +
    108A  ASN*     3.4     5.5    -      -       -      -
    109A  LEU*     3.0    35.8    +      -       +      +
    120A  VAL*     4.3     0.4    -      -       -      +
    121A  CYS*     1.3    74.1    -      -       -      +
    123A  HIS*     1.3    58.2    +      -       -      +
    124A  GLY      4.0    14.7    +      -       -      +
    126A  ASN      3.4     7.2    -      -       -      +
    127A  PHE*     3.9    16.6    -      -       +      -
    128A  ILE*     4.7     0.2    -      -       -      -
    437A  MET*     3.2    33.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  TYR      3.4    15.6    +      -       -      -
    107A  GLY      3.3     8.3    +      -       -      -
    108A  ASN*     3.0    22.9    +      -       -      +
    122A  ALA*     1.3    70.3    -      -       -      +
    124A  GLY*     1.3    62.4    +      -       -      +
    125A  PHE      3.2     0.3    +      -       -      -
    126A  ASN*     2.9    31.9    +      -       +      +
    128A  ILE*     4.1    18.5    -      -       +      +
    136A  GLN*     5.8     1.7    +      -       -      -
    169A  VAL*     3.5    17.4    -      -       +      +
    173A  THR*     4.1    15.6    +      -       +      +
    194A  TYR*     3.1    31.3    +      +       -      -
----------------------------------------------------------
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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