Contacts of the strand formed by residues 1077 - 1081 (chain J) in PDB entry 6ALG


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 ALA1077 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1037J  PHE      4.0     0.3    -      -       -      -
   1038J  THR*     2.5    50.1    +      -       -      +
   1040J  MET*     4.1     2.5    -      -       -      +
   1075J  ARG      4.2     2.9    -      -       -      +
   1076J  PRO*     1.3    75.0    -      -       -      +
   1078J  LEU*     1.3    66.7    +      -       -      +
   1098J  GLN*     4.8     6.5    -      -       +      -
   1099J  TYR      3.0    24.2    -      -       -      +
   1100J  PHE*     3.9    19.3    -      -       +      +
   1101J  LEU*     4.5     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1078 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1035J  VAL*     3.7    17.9    -      -       +      -
   1036J  ARG      4.2     3.1    -      -       -      +
   1037J  PHE*     3.6    34.1    -      -       +      -
   1040J  MET*     3.7    17.5    -      -       +      -
   1077J  ALA*     1.3    73.4    -      -       -      +
   1079J  LYS*     1.3    59.0    +      -       -      +
   1080J  ILE*     5.4     0.9    -      -       +      -
   1099J  TYR*     2.8    47.8    +      -       +      +
   1101J  LEU*     3.8    27.1    -      -       +      -
   1107J  VAL*     5.6     6.3    -      -       +      -
   1109J  LEU      6.1     0.4    -      -       -      +
   1121J  LEU*     3.9    47.1    -      -       +      +
   1122J  ALA*     5.2     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1079 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1034J  PHE      4.1     0.3    -      -       -      +
   1035J  VAL*     4.2     1.6    -      -       -      +
   1036J  ARG*     3.5    44.0    +      -       -      +
   1038J  THR*     4.1    18.1    -      -       +      +
   1077J  ALA      4.1     0.8    +      -       -      -
   1078J  LEU*     1.3    71.7    -      -       -      +
   1080J  ILE*     1.3    70.9    +      -       -      +
   1081J  VAL*     3.5     6.9    +      -       -      +
   1087J  ASP*     3.5    31.2    +      -       -      +
   1096J  PRO*     4.2    16.6    -      -       +      +
   1097J  ALA      3.4    21.5    -      -       -      +
   1098J  GLN*     3.9    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1080 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1029J  THR*     3.8    17.0    -      -       +      -
   1031J  VAL*     3.8    22.2    -      -       +      +
   1032J  SER      3.4    33.7    -      -       -      +
   1033J  GLY      4.2     0.2    -      -       -      +
   1034J  PHE      3.6     5.6    -      -       -      +
   1035J  VAL*     3.7    27.6    -      -       +      -
   1078J  LEU      5.3     0.4    -      -       -      +
   1079J  LYS*     1.3    79.6    -      -       -      +
   1081J  VAL*     1.3    67.0    +      -       -      +
   1087J  ASP*     4.5     1.2    -      -       -      +
   1088J  VAL*     3.6    20.6    +      -       +      +
   1096J  PRO*     6.2     0.2    -      -       -      +
   1097J  ALA*     3.8     7.7    +      -       +      +
   1099J  TYR*     4.0    23.1    -      -       +      +
   1115J  ILE*     3.8    16.4    -      -       +      -
   1121J  LEU*     4.4     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1081 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1033J  GLY*     3.2     4.3    -      -       -      -
   1034J  PHE*     2.5    52.0    +      -       +      +
   1036J  ARG*     3.4    47.1    -      -       +      +
   1079J  LYS*     3.5     4.9    +      -       -      +
   1080J  ILE*     1.3    77.6    -      -       -      +
   1082J  ASP*     1.3    64.3    +      -       -      +
   1085J  GLY*     4.2     6.7    -      -       -      +
   1086J  ASN      3.5    14.1    -      -       -      +
   1087J  ASP*     3.3    26.9    -      -       -      +
   1088J  VAL*     3.7    10.5    -      -       -      -
----------------------------------------------------------
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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