Contacts of the strand formed by residues 27 - 33 (chain A) in PDB entry 1V1A


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 27 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  PRO*     4.0    11.4    -      -       -      +
     17A  GLN*     3.6    39.2    +      -       +      +
     25A  LYS*     3.6     6.1    -      -       -      +
     26A  ARG*     1.3    82.0    -      -       +      +
     28A  LEU*     1.3    74.0    +      -       -      +
     17B  GLN*     3.6    31.0    -      -       -      +
     27B  LEU*     4.2    12.8    -      -       +      -
     28B  LEU      3.3    27.8    -      -       -      +
     29B  GLU*     4.0     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LEU*     4.2    30.5    -      -       +      -
     15A  VAL      3.6     6.7    -      -       -      +
     16A  PRO*     3.8    21.5    -      -       +      -
     17A  GLN*     5.6     0.2    -      -       -      -
     22A  LEU*     3.9    23.3    -      -       +      -
     25A  LYS*     4.8     2.2    -      -       +      -
     27A  LEU*     1.3    84.3    -      -       -      +
     29A  GLU*     1.3    61.9    +      -       -      +
     30A  VAL*     3.8     2.3    +      -       -      +
     90A  LEU*     4.6    11.7    -      -       +      -
     14B  LEU*     3.7    28.7    -      -       +      -
     27B  LEU*     3.4     7.7    -      -       -      -
     28B  LEU*     2.8    37.6    +      -       +      +
     30B  VAL*     3.7    12.8    -      -       +      -
     61B  LEU*     6.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ALA      3.4     1.6    -      -       -      +
     14A  LEU*     3.2     7.4    -      -       -      -
     15A  VAL*     2.7    42.2    +      -       -      +
     16A  PRO      4.3     5.5    -      -       -      +
     17A  GLN*     3.8    25.7    +      -       +      +
     28A  LEU*     1.3    72.0    -      -       -      +
     30A  VAL*     1.3    61.2    +      -       -      +
     31A  TYR*     3.0    38.2    +      -       +      +
     93A  TYR*     5.4     0.2    +      -       -      -
    285A  ARG*     3.1    34.2    +      -       -      +
     26B  ARG      3.7     5.6    -      -       -      +
     27B  LEU*     3.5    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  VAL*     3.9    23.3    -      -       +      -
     13A  ALA      3.6     2.0    -      -       -      -
     14A  LEU*     4.4     5.4    -      -       +      -
     28A  LEU      4.0     2.2    -      -       -      +
     29A  GLU*     1.3    75.5    -      -       -      +
     31A  TYR*     1.3    73.7    +      -       -      +
     61A  LEU*     4.9     5.2    -      -       +      -
     64A  MET*     3.9    26.1    -      -       +      +
     25B  LYS      4.4     1.8    -      -       -      +
     26B  ARG*     3.2    46.3    +      -       -      +
     27B  LEU      3.8     2.9    -      -       -      +
     28B  LEU*     3.8    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  VAL*     3.4     9.4    -      -       -      +
     13A  ALA*     2.8    44.6    +      -       +      +
     15A  VAL*     3.5    23.8    -      -       +      -
     29A  GLU*     3.0    44.4    +      -       +      +
     30A  VAL*     1.3    81.2    -      -       -      +
     32A  VAL*     1.3    64.5    +      -       -      +
     64A  MET*     5.7     0.9    -      -       -      -
    285A  ARG*     3.4    16.4    -      -       +      +
    286A  GLY*     3.3    34.8    -      -       -      -
    287A  ASP*     4.4     5.4    -      -       -      +
    289A  GLU*     3.6    33.4    -      -       +      +
     26B  ARG*     5.8     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU      3.9     5.6    -      -       -      +
     12A  VAL*     4.9     2.0    -      -       +      +
     31A  TYR*     1.3    74.4    -      -       -      +
     33A  GLY*     1.3    61.6    +      -       -      +
     37A  VAL*     4.2    18.8    -      -       +      -
     64A  MET*     3.8    29.2    -      -       +      +
     65A  VAL*     4.3    20.2    -      -       +      +
     68A  ARG*     3.7    42.0    -      -       +      +
     69A  LEU*     5.7     0.7    -      -       +      -
    287A  ASP*     3.8     6.2    -      -       -      +
    288A  HIS*     2.9    29.4    +      -       +      -
    289A  GLU*     4.6     6.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     2.7    27.2    +      -       -      -
     12A  VAL*     4.6     0.2    -      -       -      +
     13A  ALA*     4.6     1.8    -      -       -      +
     31A  TYR      3.7     2.6    +      -       -      -
     32A  VAL*     1.3    75.3    -      -       -      +
     34A  GLY*     1.3    63.1    +      -       -      -
     37A  VAL*     3.1    25.3    -      -       -      +
     38A  ASN*     3.6     7.6    -      -       -      -
    287A  ASP*     3.3    20.4    -      -       -      -
----------------------------------------------------------
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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