Contacts of the strand formed by residues 1106 - 1109 (chain D) in PDB entry 5D4E


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 VAL1106 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1103D  HIS      4.7     1.1    -      -       -      +
   1104D  GLU      3.4     8.6    +      -       -      +
   1105D  ILE*     1.3    79.2    -      -       -      +
   1107D  VAL*     1.3    71.3    +      -       -      +
   1108D  ARG*     3.2    30.0    +      -       +      +
   1199D  GLY*     3.5     5.4    -      -       -      -
   1200D  VAL      3.4    16.8    +      -       -      -
   1218D  GLY*     3.4    23.6    -      -       -      +
   1219D  GLU      3.3    17.3    -      -       -      +
   1220D  ALA*     3.8    13.0    -      -       +      -
   1221D  VAL*     4.3     2.9    -      -       -      +
   1462D  LEU*     4.6     9.4    -      -       +      -
   1473D  PRO      4.0    12.1    -      -       -      +
   1474D  ALA*     3.8    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1107 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1106D  VAL*     1.3    72.6    -      -       -      +
   1108D  ARG*     1.3    59.3    +      -       -      +
   1109D  GLU      3.6    18.2    -      -       -      +
   1200D  VAL*     3.2    24.7    -      -       +      +
   1201D  CYS      4.6     0.7    -      -       -      +
   1202D  GLN*     3.8    16.4    -      -       +      +
   1205D  TYR*     4.8     0.4    -      -       +      -
   1215D  VAL*     4.3    20.2    -      -       +      -
   1216D  SER      4.4     0.4    -      -       -      +
   1217D  ILE*     3.4    19.0    -      -       +      +
   1218D  GLY*     2.8    35.4    +      -       -      +
   1219D  GLU      3.0    19.3    +      -       -      +
   1221D  VAL*     3.8    19.7    -      -       +      -
   1478D  SER*     5.1     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG1108 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1104D  GLU      2.9    18.2    +      -       -      -
   1106D  VAL*     3.2    26.8    +      -       +      +
   1107D  VAL*     1.3    73.7    -      -       -      +
   1109D  GLU*     1.3    63.7    +      -       +      +
   1196D  THR*     4.5    10.3    -      -       +      -
   1197D  ARG      3.9    11.9    -      -       -      -
   1198D  TYR*     2.2    48.8    +      -       -      +
   1200D  VAL      3.3     4.9    +      -       -      -
   1217D  ILE*     3.8     8.3    -      -       -      +
   1460D  ILE*     3.1    35.3    +      -       -      +
   1461D  GLY*     4.9     0.8    -      -       -      -
   1473D  PRO*     4.2    19.0    +      -       -      +
   1478D  SER*     5.9     2.0    -      -       -      -
   1480D  PHE*     4.7     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1109 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1107D  VAL*     3.6     5.9    -      -       -      +
   1108D  ARG*     1.3    82.2    -      -       -      +
   1110D  ALA*     1.3    60.6    +      -       -      +
   1111D  ASP      3.7    14.7    -      -       -      +
   1112D  CYS*     3.3    16.2    -      -       -      +
   1196D  THR*     3.1    41.3    +      -       +      +
   1200D  VAL      4.4     0.2    +      -       -      -
   1201D  CYS*     3.4     9.8    -      -       +      -
   1202D  GLN*     2.9    23.0    +      -       -      +
   1217D  ILE*     3.6    12.2    -      -       -      +
   1480D  PHE*     5.4     3.1    -      -       -      -
----------------------------------------------------------
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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