Contacts of the strand formed by residues 301 - 310 (chain A) in PDB entry 2WIN


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 301 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253A  ILE*     3.3     7.4    -      -       -      +
    254A  GLN*     2.8    60.5    +      -       -      +
    299A  GLY      5.3     0.7    -      -       -      -
    300A  LYS*     1.3    77.7    -      -       -      +
    302A  LEU*     1.3    63.9    -      -       -      +
    323A  GLY*     4.1    16.1    +      -       -      -
    324A  ILE      3.1    16.6    -      -       -      -
    325A  PRO*     4.7     1.3    -      -       -      -
    326A  ILE*     4.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 302 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  TYR*     4.5    13.5    -      -       +      -
    229A  LEU*     3.7    28.5    -      -       +      -
    251A  PHE*     5.8     2.2    -      -       +      -
    252A  GLY      3.3     7.6    -      -       -      +
    253A  ILE*     3.5    31.4    -      -       +      -
    280A  LEU*     4.7     9.0    -      -       +      -
    285A  LEU*     4.0    25.1    -      -       +      -
    301A  SER*     1.3    74.7    -      -       -      +
    303A  TYR*     1.3    62.4    +      -       -      +
    323A  GLY      3.6     4.1    +      -       -      -
    324A  ILE*     2.8    46.1    +      -       +      +
    326A  ILE*     3.6    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 303 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250A  ILE*     3.9     2.4    -      -       +      +
    251A  PHE*     3.4    12.4    -      -       -      +
    252A  GLY*     3.1    49.9    +      -       -      -
    253A  ILE      3.7    10.5    -      -       -      -
    254A  GLN*     4.4     5.6    -      -       +      +
    259A  ARG*     3.7    48.1    -      -       +      +
    261A  SER*     3.7    28.4    +      -       -      -
    302A  LEU*     1.3    76.0    -      -       -      +
    304A  VAL*     1.3    66.0    +      -       -      +
    305A  SER*     5.0     8.5    -      -       -      -
    320A  GLU*     4.0    16.4    -      -       -      +
    321A  ARG      3.2    11.0    -      -       -      +
    322A  SER*     3.8    19.3    -      -       -      -
    323A  GLY      4.8     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  VAL*     4.5    10.9    -      -       +      +
    216A  PRO*     5.3     0.2    -      -       +      -
    229A  LEU*     4.8     0.9    -      -       +      -
    231A  VAL*     3.9    28.3    -      -       +      -
    233A  ILE*     5.1     0.2    -      -       +      -
    249A  VAL*     3.5    28.5    -      -       +      -
    250A  ILE      3.5     3.8    -      -       -      +
    251A  PHE*     3.5    27.8    -      -       +      -
    303A  TYR*     1.3    73.9    -      -       -      +
    305A  SER*     1.3    64.9    +      -       -      +
    306A  ALA      4.0     0.2    -      -       -      -
    320A  GLU*     3.1     8.5    -      -       -      +
    321A  ARG*     2.7    44.4    +      -       +      +
    324A  ILE*     4.1    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 305 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  PHE      3.4     5.7    -      -       -      +
    249A  VAL*     4.3     0.7    -      -       -      -
    250A  ILE*     2.9    50.4    +      -       -      +
    303A  TYR*     4.1     8.7    +      -       -      -
    304A  VAL*     1.3    73.8    -      -       -      +
    306A  ALA*     1.3    62.6    +      -       -      +
    307A  THR*     4.8     3.3    +      -       -      -
    318A  GLN*     6.0     1.0    -      -       -      +
    319A  ALA      3.7    10.4    +      -       -      -
    320A  GLU*     4.4    12.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 306 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  VAL*     4.6     8.7    -      -       +      -
    214A  VAL*     3.8    27.1    -      -       +      +
    233A  ILE*     4.3    21.8    -      -       +      -
    247A  ALA*     5.4     1.3    -      -       +      -
    248A  PHE      3.4     5.6    -      -       -      +
    249A  VAL*     4.1     7.9    -      -       +      +
    304A  VAL      4.0     1.6    +      -       -      -
    305A  SER*     1.3    74.4    +      -       -      +
    307A  THR*     1.3    70.9    +      -       -      +
    308A  VAL*     4.3     0.9    -      -       +      -
    318A  GLN*     3.5     2.3    -      -       -      +
    319A  ALA*     3.1    31.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 307 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247A  ALA*     3.3     1.6    -      -       -      -
    248A  PHE*     2.8    55.8    +      -       +      +
    305A  SER*     4.8     4.2    +      -       -      -
    306A  ALA*     1.3    83.1    +      -       -      +
    308A  VAL*     1.3    60.4    +      -       -      +
    309A  ILE*     4.7     5.4    -      -       +      -
    316A  MET*     3.5    37.7    -      -       +      -
    317A  VAL      3.4     6.7    -      -       -      +
    318A  GLN*     3.6    18.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 308 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  PHE*     3.8    26.7    -      -       +      -
    212A  VAL*     3.7    31.0    -      -       +      -
    233A  ILE*     4.3     7.0    -      -       +      -
    235A  ALA*     4.4    13.0    -      -       +      -
    243A  VAL*     4.7     8.7    -      -       +      -
    245A  GLY*     5.0     1.3    -      -       -      -
    246A  THR      3.6    11.9    -      -       -      +
    247A  ALA*     3.7    18.8    -      -       +      +
    271A  ILE*     4.6     8.3    -      -       +      -
    307A  THR*     1.3    74.5    -      -       -      +
    309A  ILE*     1.3    72.9    +      -       -      +
    316A  MET*     3.6     2.3    -      -       -      +
    317A  VAL      3.0    29.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 309 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  GLY*     4.3     0.9    -      -       -      -
    246A  THR*     2.8    37.5    +      -       -      +
    248A  PHE*     4.2    24.5    -      -       +      -
    307A  THR*     4.6     5.8    -      -       +      +
    308A  VAL*     1.3    81.2    -      -       -      +
    310A  LEU*     1.3    77.3    +      -       -      +
    313A  GLY*     4.2    13.0    -      -       -      -
    315A  ASP      4.0    11.0    -      -       -      +
    316A  MET*     4.0    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 310 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  SER*     4.4     5.8    -      -       -      +
    210A  PHE*     3.8    27.1    -      -       +      -
    237A  PHE*     4.4    17.5    -      -       +      -
    243A  VAL*     3.5    31.9    -      -       +      -
    244A  GLU      3.8     8.3    -      -       -      +
    245A  GLY*     4.1     0.2    -      -       -      -
    308A  VAL*     4.3     0.4    -      -       +      -
    309A  ILE*     1.3    85.7    -      -       -      +
    311A  HIS*     1.3    60.3    +      -       -      +
    312A  SER*     2.9    22.4    -      -       -      +
    313A  GLY*     3.0    17.2    +      -       -      +
    314A  SER*     5.1     2.0    -      -       -      -
    315A  ASP*     3.7    32.4    +      -       +      +
    828B  VAL*     6.1     0.7    -      -       +      -
    830B  TYR*     4.5     7.9    -      -       -      +
----------------------------------------------------------
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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