Contacts of the strand formed by residues 258 - 266 (chain 4) in PDB entry 1SVA


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 258 (chain 4).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     924  ARG*     3.4    39.4    +      -       -      -
     934  ILE      3.2     6.5    -      -       -      -
     944  PRO*     4.2     0.2    -      -       -      -
     954  LEU*     4.5     0.9    -      -       -      -
    1564  GLY      4.0     1.6    -      -       -      +
    2544  CYS*     3.2    24.2    -      -       -      +
    2564  ALA*     2.5    19.8    +      -       -      +
    2574  ASP*     1.3    80.6    +      -       -      +
    2594  LEU*     1.3    61.8    +      -       -      +
    2604  TYR*     3.5    26.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 259 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     474  VAL*     5.6     3.6    -      -       +      -
     914  ALA      3.8     0.2    -      -       -      +
     924  ARG*     3.1     6.8    -      -       -      +
     934  ILE*     2.5    60.8    +      -       +      +
     954  LEU*     4.1     9.2    -      -       +      -
    1124  ALA*     5.0     5.6    -      -       +      -
    1544  VAL*     4.6     8.7    -      -       +      -
    1554  GLY      3.4    17.9    -      -       -      +
    2544  CYS*     4.1    12.6    -      -       -      -
    2584  SER*     1.3    74.4    -      -       -      +
    2604  TYR*     1.3    76.0    +      -       -      +
    2614  VAL*     4.8     0.2    -      -       +      -
    2884  ILE*     3.8    32.1    -      -       +      -
    2904  LEU*     3.9    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 260 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     904  VAL*     5.4     7.9    -      -       +      -
     914  ALA      3.6     5.8    -      -       -      +
     924  ARG*     4.1    23.7    -      -       +      -
    1534  ALA      3.8     0.7    -      -       -      +
    1544  VAL*     3.3     6.4    -      -       -      -
    1554  GLY      2.9    47.5    +      -       -      +
    1564  GLY      3.8     3.8    -      -       -      -
    1574  GLU*     3.4    30.0    -      -       -      +
    1584  PRO*     3.5    39.7    -      -       +      +
    1594  LEU      5.4     1.1    -      -       -      +
    1974  LEU      5.9     0.7    -      -       -      -
    2564  ALA*     4.9     8.7    -      -       +      +
    2584  SER*     3.5    32.5    +      -       -      -
    2594  LEU*     1.3    77.1    -      -       -      +
    2614  VAL*     1.3    66.0    +      -       -      +
    2624  SER*     4.6     4.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 261 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     494  CYS*     4.7     6.3    -      -       -      -
     514  LEU*     3.9    15.2    -      -       +      +
     904  VAL*     3.4     4.0    -      -       -      +
     914  ALA*     3.0    34.8    +      -       +      +
     934  ILE*     4.3    18.4    -      -       +      -
    1534  ALA      3.5     4.3    -      -       -      +
    1544  VAL*     4.9     1.3    -      -       +      -
    2594  LEU*     4.8     1.8    -      -       +      -
    2604  TYR*     1.3    81.5    -      -       -      +
    2624  SER*     1.3    66.4    +      -       -      +
    2864  PHE*     3.3    42.2    -      -       +      -
    2884  ILE*     3.9    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 262 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     514  LEU*     4.2     1.1    -      -       -      -
     884  TYR*     5.9     0.2    -      -       -      -
     894  SER      3.2    13.5    -      -       -      -
     904  VAL*     4.2     5.0    -      -       -      +
    1514  PHE*     4.5     3.1    -      -       -      -
    1524  PHE*     3.1     3.8    -      -       -      +
    1534  ALA*     2.8    44.3    +      -       -      +
    1594  LEU*     4.4    18.3    +      -       -      +
    1974  LEU*     4.1    20.6    -      -       -      -
    2604  TYR*     4.6     4.2    +      -       -      +
    2614  VAL*     1.3    84.3    +      -       -      +
    2634  ALA*     1.3    62.9    +      -       -      +
    2864  PHE*     4.1     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 263 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     514  LEU*     4.3     7.8    -      -       +      +
     884  TYR*     4.2     0.7    -      -       -      +
     894  SER*     3.2    28.3    +      -       -      +
    1514  PHE*     3.1    16.3    -      -       -      +
    1524  PHE*     3.6     2.5    -      -       +      +
    2624  SER*     1.3    79.0    -      -       -      +
    2644  VAL*     1.3    72.7    +      -       -      +
    2654  ASP*     4.3     4.5    -      -       -      +
    2844  ARG*     3.6    30.5    -      -       +      -
    2864  PHE*     4.0     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 264 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     554  MET*     6.2     0.2    -      -       -      -
     874  CYS      4.8     3.4    -      -       -      +
     884  TYR*     3.3    39.0    -      -       +      -
     894  SER*     5.3     3.6    -      -       -      -
    1494  PHE*     3.8    16.4    -      -       +      -
    1504  HIS*     3.1     2.9    -      -       -      -
    1514  PHE*     2.7    38.3    +      -       +      -
    2054  VAL*     3.5    22.2    -      -       +      -
    2634  ALA*     1.3    85.6    -      -       -      +
    2654  ASP*     1.3    68.6    +      -       -      +
    2664  ILE*     3.2    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 265 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     534  PRO*     5.6     5.2    -      -       +      +
     554  MET*     4.4     2.5    -      -       -      -
    1194  VAL*     3.4    15.5    -      -       +      +
    1494  PHE      3.4     0.4    -      -       -      -
    1504  HIS*     2.9    29.9    +      -       +      +
    2634  ALA*     4.3     1.2    -      -       -      +
    2644  VAL*     1.3    84.1    +      -       -      +
    2664  ILE*     1.3    62.9    +      -       -      +
    2674  CYS*     2.8    12.8    +      -       -      -
    2814  GLY*     3.2    19.2    -      -       -      -
    2824  LEU      3.6    24.1    -      -       -      +
    2844  ARG*     2.6    43.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 266 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1263  LEU*     4.8    11.7    -      -       +      -
     554  MET*     3.4    26.2    -      -       +      -
     864  PRO*     4.7     7.6    -      -       +      -
    1474  SER      3.8     9.9    -      -       -      +
    1484  ASN*     3.1     3.3    -      -       -      +
    1494  PHE*     2.7    39.2    +      -       +      +
    1504  HIS*     3.2     3.3    -      -       -      -
    2054  VAL*     4.5    13.9    -      -       +      -
    2644  VAL*     3.2    28.9    -      -       +      -
    2654  ASP*     1.3    70.0    -      -       -      +
    2674  CYS*     1.3    60.2    +      -       -      +
    2684  GLY      3.4    14.6    -      -       -      +
    2794  TRP*     3.4    36.6    -      -       +      -
----------------------------------------------------------
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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