Contacts of the strand formed by residues 284 - 295 (chain 2) 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 ARG 284 (chain 2).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     502  PHE*     3.3     4.2    -      -       -      +
     512  LEU*     3.0    31.4    +      -       +      +
    1172  THR*     2.7    29.1    +      -       -      +
    1182  GLU*     3.4    10.8    -      -       -      +
    1192  VAL*     4.1    14.0    -      -       +      +
    1202  ILE*     3.9     4.7    -      -       -      -
    1502  HIS*     5.1     5.7    -      -       -      +
    1512  PHE      3.8    14.3    +      -       -      +
    1522  PHE*     3.9    21.0    -      -       -      +
    2632  ALA*     3.6    12.1    -      -       +      -
    2642  VAL      4.1     0.2    +      -       -      -
    2652  ASP*     2.5    54.9    +      -       -      +
    2822  LEU      3.6     0.2    +      -       -      -
    2832  PRO*     1.3    74.3    -      -       -      +
    2852  TYR*     1.3    62.1    +      -       -      +
    2862  PHE*     3.3    32.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 285 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     482  GLU*     2.7    30.2    +      -       +      -
     492  CYS      4.4     5.8    -      -       -      -
     502  PHE*     4.1     5.2    -      -       +      -
    1162  LYS*     3.5    14.9    -      -       +      +
    1172  THR*     2.6    37.9    +      -       -      -
    1182  GLU*     2.9    18.6    +      -       +      +
    1202  ILE*     3.8    16.5    -      -       +      +
    2842  ARG*     1.3    71.4    -      -       -      +
    2862  PHE*     1.3    72.4    +      -       -      +
    2872  LYS*     3.4    35.7    -      -       +      +
    2123  PRO*     3.3    35.9    +      -       +      -
    2133  SER*     3.3    31.2    -      -       -      -
    3296  GLU*     5.3     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 286 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     472  VAL      4.3     0.9    -      -       -      -
     482  GLU*     3.3     5.2    -      -       -      -
     492  CYS*     3.2    51.4    +      -       -      +
     502  PHE*     4.4     1.3    -      -       -      -
     512  LEU*     4.1     9.9    -      -       +      -
    1152  VAL*     4.3     9.4    -      -       +      -
    1162  LYS      3.3     4.9    -      -       -      -
    1172  THR*     4.4     2.0    -      -       -      -
    1522  PHE*     3.6    25.1    -      +       +      -
    1542  VAL*     4.0    16.4    -      -       +      -
    2612  VAL*     3.7    31.9    -      -       +      -
    2622  SER      3.9     3.6    -      -       -      -
    2632  ALA*     3.8    12.1    -      -       +      -
    2842  ARG*     3.3    40.8    -      -       +      -
    2852  TYR*     1.3    85.6    -      -       -      +
    2872  LYS*     1.3    64.0    +      -       -      +
    2882  ILE*     3.9     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 287 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     462  GLU*     3.5    40.1    +      -       +      -
     472  VAL      3.3     6.1    -      -       -      +
     482  GLU*     3.8    16.1    +      -       +      -
    1142  THR*     3.3     2.3    -      -       -      +
    1152  VAL*     3.1     5.4    -      -       -      +
    1162  LYS*     2.8    64.5    +      -       +      +
    2852  TYR*     3.4    30.7    +      -       +      +
    2862  PHE*     1.3    75.3    -      -       -      +
    2882  ILE*     1.3    65.4    +      -       -      +
    2892  THR*     4.2     5.9    +      -       -      +
    2163  GLU*     4.7    16.4    +      -       -      +
    2473  GLU*     5.8     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 288 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     452  THR      3.8     0.5    -      -       -      +
     462  GLU*     3.5     2.6    -      -       -      -
     472  VAL*     2.9    41.0    +      -       +      +
     492  CYS*     4.6     4.9    -      -       -      -
     932  ILE*     5.0     2.5    -      -       +      -
    1122  ALA*     4.1    11.7    -      -       +      -
    1142  THR      3.2     7.4    -      -       -      +
    1152  VAL*     4.1    14.6    -      -       +      -
    1542  VAL*     4.4    11.7    -      -       +      -
    2442  LEU*     5.0     0.2    -      -       +      -
    2592  LEU*     3.9    21.3    -      -       +      -
    2612  VAL*     3.9    27.4    -      -       +      -
    2862  PHE*     3.9    15.3    -      -       +      -
    2872  LYS*     1.3    75.4    -      -       -      +
    2892  THR*     1.3    67.6    +      -       -      +
    2902  LEU*     3.6    29.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 289 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     442  PHE*     4.3    16.4    -      -       +      -
     452  THR      3.4    11.0    -      -       -      +
     462  GLU*     4.0    20.1    -      -       +      +
    1132  VAL*     3.0    33.7    +      -       +      +
    1142  THR*     3.0    36.9    +      -       +      +
    2872  LYS*     4.2     6.1    +      -       -      +
    2882  ILE*     1.3    75.7    -      -       -      +
    2902  LEU*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 290 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     352  LEU*     5.7     1.1    -      -       +      -
     442  PHE*     2.8    25.6    -      -       -      +
     452  THR*     2.8    22.7    +      -       -      +
     472  VAL*     4.2    19.3    -      -       +      -
     952  LEU*     4.1    23.3    -      -       +      -
    1102  TRP*     3.8    20.4    -      -       +      -
    1112  GLU*     3.2     7.4    -      -       -      +
    1122  ALA*     3.2    38.1    -      -       +      -
    1132  VAL*     5.7     0.2    -      -       -      -
    2542  CYS*     5.1     0.9    -      -       -      -
    2592  LEU*     3.9    25.8    -      -       +      -
    2882  ILE*     3.6    10.8    -      -       +      +
    2892  THR*     1.3    78.5    -      -       -      +
    2912  ARG*     1.3    61.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 291 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     432  SER      4.4     2.5    -      -       -      +
     442  PHE*     4.1    12.1    -      -       +      -
    1102  TRP*     3.5    10.1    -      -       -      -
    1112  GLU*     2.7    77.8    +      -       +      +
    1132  VAL*     3.3    20.6    -      -       +      +
    2452  LEU*     3.9    16.3    -      -       -      +
    2492  GLY      3.3    17.0    +      -       -      -
    2902  LEU*     1.3    75.8    -      -       -      +
    2922  LYS*     1.3    71.0    +      -       -      +
    2932  ARG*     3.4     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 292 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     181  LYS*     4.8    11.1    -      -       -      +
     392  THR*     3.0    36.5    +      -       -      +
     402  GLY      2.6    31.9    +      -       -      +
     412  VAL*     3.4    23.8    +      -       -      +
     432  SER*     3.8    14.6    +      -       -      +
     982  ILE*     4.2    24.1    -      -       +      +
    1082  LEU*     4.0    22.3    -      -       +      +
    1092  MET      3.9     3.1    -      -       -      -
    1102  TRP*     4.2    23.1    -      -       +      -
    2912  ARG*     1.3    80.7    -      -       -      +
    2932  ARG*     1.3    61.3    +      -       -      +
    2942  SER      4.0     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 293 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     211  VAL*     3.4    35.1    -      -       -      +
    1082  LEU*     3.2     5.9    -      -       -      -
    1092  MET*     2.8    44.8    +      -       -      +
    1112  GLU*     2.4    65.6    +      -       +      +
    2482  GLN      4.4     2.6    +      -       -      -
    2492  GLY      2.9    20.2    +      -       -      -
    2502  VAL*     3.5    16.7    -      -       -      +
    2532  LEU*     4.2    15.9    -      -       +      -
    2912  ARG*     3.4    11.1    +      -       -      +
    2922  LYS*     1.3    72.9    -      -       -      +
    2942  SER*     1.3    80.2    +      -       -      +
    2952  VAL*     3.7     7.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 294 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     171  PRO*     4.3     8.3    -      -       -      +
     181  LYS*     2.7    39.5    +      -       -      +
     191  GLU      4.4     1.6    -      -       -      -
     201  PRO*     3.6    28.1    -      -       -      +
     211  VAL*     4.8     0.5    +      -       -      +
    1062  ASN*     4.6     2.8    +      -       -      -
    1072  ILE      3.7     7.5    +      -       -      -
    1082  LEU*     3.5    16.0    -      -       -      +
    2922  LYS      4.0     1.0    +      -       -      -
    2932  ARG*     1.3    88.6    +      -       -      +
    2952  VAL*     1.3    64.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 295 (chain 2). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     201  PRO*     3.4    17.6    -      -       -      +
    1052  GLY      4.9     0.7    -      -       -      +
    1062  ASN*     5.3     0.7    -      -       -      -
    1072  ILE*     3.0    44.3    +      -       +      +
    1092  MET*     3.2    45.1    -      -       +      -
    2532  LEU*     4.2    14.1    -      -       +      -
    2932  ARG*     4.0    20.6    -      -       +      +
    2942  SER*     1.3    80.0    +      -       -      +
    2962  LYS*     1.3    68.9    -      -       -      +
    3056  LEU*     6.4     0.2    -      -       +      -
----------------------------------------------------------
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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