Contacts of the strand formed by residues 1026 - 1032 (chain A) in PDB entry 4UHW


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 ALA1026 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1024A  GLY      4.4     0.4    -      -       -      +
   1025A  GLN*     1.3    78.4    -      -       -      +
   1027A  ALA*     1.3    62.1    +      -       -      +
   1083A  ALA*     6.1     3.1    -      -       -      +
   1084A  ASN      6.1     0.2    -      -       -      +
   1094A  LEU*     3.5    41.1    -      -       +      +
   1095A  ASN*     3.9    15.5    -      -       -      +
   1098A  ALA*     3.4     2.6    -      -       -      +
   1141A  TYR*     3.5     6.7    -      -       -      -
   1142A  PHE*     2.8    36.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA1027 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1026A  ALA*     1.3    77.4    -      -       -      +
   1028A  ALA*     1.3    60.8    +      -       -      +
   1042A  HIS*     3.4     5.5    -      -       -      +
   1043A  GLY*     3.3    25.2    +      -       -      +
   1080A  VAL*     3.6    20.5    -      -       +      +
   1081A  PRO*     5.0     8.1    -      -       +      +
   1083A  ALA*     5.9     3.3    -      -       +      +
   1095A  ASN*     3.6     2.5    +      -       -      +
   1098A  ALA*     3.8     3.8    -      -       -      -
   1139A  VAL*     5.3     4.3    -      -       +      -
   1140A  GLY      3.3    12.1    -      -       -      +
   1141A  TYR*     4.1    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA1028 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1027A  ALA*     1.3    76.1    -      -       -      +
   1029A  LEU*     1.3    62.7    +      -       -      +
   1030A  VAL*     5.1     3.8    -      -       +      -
   1041A  THR      3.2    14.6    -      -       -      +
   1042A  HIS*     3.9     2.9    -      -       +      +
   1080A  VAL*     4.1     5.2    -      -       -      -
   1098A  ALA*     3.9    16.4    -      -       +      +
   1099A  VAL*     3.7    30.3    -      -       +      +
   1102A  ALA*     5.2     0.4    -      -       -      -
   1139A  VAL*     3.4     8.8    -      -       -      +
   1140A  GLY      2.9    27.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1029 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1028A  ALA*     1.3    75.0    -      -       -      +
   1030A  VAL*     1.3    62.9    +      -       -      +
   1031A  HIS*     3.7    34.6    -      -       +      +
   1039A  LEU      3.9     1.4    -      -       -      +
   1040A  VAL*     3.5     3.1    -      -       -      -
   1041A  THR*     2.8    42.3    +      -       +      +
   1079A  THR*     3.9    34.1    -      -       +      +
   1080A  VAL*     4.2     5.4    -      -       +      -
   1137A  SER*     4.2     7.0    -      -       -      +
   1138A  ALA      3.6     8.5    -      -       -      +
   1139A  VAL*     3.9    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1030 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1028A  ALA*     5.1     2.5    -      -       +      -
   1029A  LEU*     1.3    80.3    -      -       -      +
   1031A  HIS*     1.3    65.8    +      -       -      +
   1032A  ILE*     5.0     0.4    -      -       +      -
   1038A  VAL*     3.8    25.4    -      -       +      -
   1039A  LEU      3.6     3.1    -      -       -      +
   1040A  VAL*     4.0    18.8    -      -       +      -
   1059A  VAL*     5.5     1.3    -      -       +      -
   1063A  LEU*     4.8     8.1    -      -       +      -
   1099A  VAL*     4.6     7.2    -      -       +      +
   1102A  ALA*     3.5    21.5    -      -       +      -
   1103A  CYS*     4.8     8.7    -      -       -      -
   1106A  LEU*     3.6    25.8    -      -       +      +
   1136A  LEU      3.7     1.4    -      -       -      +
   1137A  SER*     3.3     3.8    -      -       -      -
   1138A  ALA      2.9    40.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS1031 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1029A  LEU*     3.7    35.1    -      -       +      +
   1030A  VAL*     1.3    72.8    -      -       -      +
   1032A  ILE*     1.3    65.4    +      -       -      +
   1033A  TYR*     3.8    35.7    -      +       +      -
   1038A  VAL*     3.4     9.9    -      -       -      +
   1039A  LEU*     3.0    44.6    +      -       +      +
   1136A  LEU      3.5     3.8    -      -       -      +
   1137A  SER*     2.8    32.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE1032 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1031A  HIS*     1.3    77.1    -      -       -      +
   1033A  TYR*     1.3    76.6    +      -       -      +
   1034A  LEU*     4.7     1.4    -      -       -      +
   1036A  GLY*     4.1    15.9    -      -       -      +
   1037A  SER      3.7     3.1    -      -       -      +
   1038A  VAL*     4.0    12.3    -      -       +      -
   1063A  LEU*     4.6     7.4    -      -       +      -
   1106A  LEU*     4.1    24.5    -      -       +      -
   1110A  LEU*     4.2    11.4    -      -       +      -
   1122A  TRP*     3.6    33.9    -      -       +      -
   1126A  ALA*     4.0    17.7    -      -       +      -
   1136A  LEU*     2.9    44.4    +      -       +      +
----------------------------------------------------------
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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