Contacts of the strand formed by residues 1238 - 1244 (chain A) in PDB entry 6A5T


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 LEU1238 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1197A  LEU      3.5     1.4    -      -       -      +
   1198A  GLU*     3.1     7.0    -      -       -      +
   1199A  LEU*     2.7    47.7    +      -       +      +
   1201A  ARG*     3.5    41.1    -      -       +      +
   1204A  MET*     3.4    33.0    -      -       +      -
   1211A  MET*     3.5    37.2    -      -       +      -
   1231A  SER*     5.2     0.2    -      -       -      -
   1232A  GLU      4.8     3.8    -      -       -      +
   1233A  ASP*     4.0    21.1    -      -       -      +
   1235A  ALA*     4.8     1.1    -      -       -      +
   1237A  LYS*     1.3    71.6    -      -       -      +
   1239A  ILE*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1168A  ASP*     4.5     4.9    -      -       -      +
   1196A  ARG*     3.1    61.7    -      -       +      +
   1197A  LEU      3.5     1.1    -      -       -      +
   1198A  GLU*     3.9    15.5    -      -       +      -
   1211A  MET*     4.3     4.9    -      -       -      +
   1230A  TRP*     4.1     0.9    -      -       -      -
   1231A  SER*     3.3    35.2    +      -       -      +
   1235A  ALA*     5.7     0.7    -      -       +      -
   1237A  LYS*     2.9    35.2    +      -       +      +
   1238A  LEU*     1.3    78.8    -      -       -      +
   1240A  ILE*     1.3    72.5    +      -       -      +
   1241A  ARG*     3.7    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1145A  LEU*     5.7     0.7    -      -       +      -
   1196A  ARG*     3.0     9.2    -      -       -      +
   1197A  LEU*     2.9    54.8    +      -       +      +
   1199A  LEU*     3.5    31.4    -      -       +      -
   1211A  MET*     4.5    10.5    -      -       -      +
   1214A  VAL*     4.9    10.1    -      -       +      -
   1215A  ALA*     5.3     4.7    -      -       +      +
   1218A  ILE*     4.3    23.8    -      -       +      -
   1228A  VAL*     5.0     5.2    -      -       +      -
   1229A  MET      3.7    10.8    -      -       -      +
   1230A  TRP*     4.7     7.9    -      -       +      -
   1239A  ILE*     1.3    79.7    -      -       -      +
   1241A  ARG*     1.3    64.9    +      -       -      +
   1242A  CYS*     4.0    20.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG1241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1155A  TYR*     5.8     0.4    -      -       -      +
   1157A  ASP*     4.1    12.9    +      -       -      -
   1163A  THR*     4.5    12.3    +      -       -      -
   1165A  ILE*     4.7     3.8    -      -       -      +
   1168A  ASP*     2.2    43.6    +      -       -      +
   1172A  VAL*     4.1    15.7    -      -       -      +
   1176A  PHE*     6.1     1.6    -      -       -      -
   1194A  LEU*     3.2    36.6    -      -       +      +
   1195A  LEU      3.3     4.0    -      -       -      -
   1196A  ARG*     3.4    22.0    -      -       +      +
   1227A  PHE*     4.8     0.5    -      -       -      -
   1229A  MET*     2.8    72.6    +      -       -      +
   1231A  SER*     5.4     8.7    -      -       -      +
   1239A  ILE*     3.7    17.7    -      -       +      -
   1240A  ILE*     1.3    79.0    -      -       -      +
   1242A  CYS*     1.3    61.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS1242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1193A  TRP      4.0     0.5    -      -       -      +
   1194A  LEU*     3.1     7.7    -      -       -      +
   1195A  LEU*     2.9    45.8    +      -       +      +
   1197A  LEU*     6.2     0.9    -      -       -      -
   1218A  ILE*     5.2     3.4    -      -       -      -
   1226A  LEU*     3.5    35.2    -      -       +      -
   1227A  PHE      3.1     7.2    -      -       -      -
   1228A  VAL*     4.5    11.0    -      -       -      -
   1240A  ILE*     4.0    21.3    -      -       -      -
   1241A  ARG*     1.3    80.6    -      -       -      +
   1243A  ARG*     1.3    64.3    +      -       -      +
   1263A  LEU*     5.5     0.7    -      -       -      +
   1270A  MET*     4.9    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG1243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1157A  ASP*     3.2    45.4    +      -       -      +
   1158A  PRO      5.9     0.2    -      -       -      -
   1159A  ASP      4.5     5.3    +      -       -      -
   1160A  PRO*     4.7    16.5    -      -       -      +
   1176A  PHE*     5.3     5.3    -      -       -      -
   1190A  GLN*     5.8     8.8    -      -       +      +
   1191A  SER      3.5    26.9    +      -       -      +
   1192A  PRO*     4.1     3.8    +      -       -      +
   1193A  TRP      4.9     2.0    -      -       -      -
   1194A  LEU*     3.6    19.4    -      -       +      +
   1226A  LEU*     3.0     9.7    -      -       -      +
   1227A  PHE*     2.8    62.9    +      -       +      -
   1229A  MET*     4.8    10.1    -      -       -      +
   1242A  CYS*     1.3    77.2    -      -       -      +
   1244A  VAL*     1.3    67.0    +      -       -      +
   1245A  ILE*     3.8     0.4    -      -       +      +
   1263A  LEU*     6.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1190A  GLN*     4.1     2.6    -      -       -      -
   1191A  SER*     3.1    48.1    +      -       -      +
   1193A  TRP*     5.0     2.7    +      -       +      +
   1225A  ASP      3.8     8.1    -      -       -      +
   1226A  LEU*     4.2     2.2    -      -       +      -
   1243A  ARG*     1.3    74.9    -      -       -      +
   1245A  ILE*     1.3    75.5    +      -       -      +
   1259A  GLU*     5.4     4.0    -      -       +      +
   1262A  MET*     4.3    24.7    -      -       -      -
   1263A  LEU*     3.9    33.0    -      -       +      -
   1266A  ILE*     3.9    18.8    -      -       +      -
----------------------------------------------------------
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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