Contacts of the strand formed by residues 1113 - 1115 (chain B) in PDB entry 5M64


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 THR1113 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  PRO*     4.9    14.1    -      -       +      +
     74A  GLY      4.5     9.9    -      -       -      +
     75A  HIS*     4.8     2.3    +      -       -      -
   1102B  SER*     3.2    37.1    +      -       -      +
   1104B  CYS*     5.9     2.7    -      -       -      -
   1107B  CYS*     6.2     0.4    -      -       -      -
   1109B  SER*     5.2     4.5    +      -       -      -
   1110B  ILE*     3.5    22.4    -      -       -      +
   1111B  LEU      4.4     4.6    -      -       -      +
   1112B  THR*     1.3    82.0    -      -       -      +
   1114B  GLN*     1.3    63.3    +      -       -      +
   1115B  GLN      4.2     0.3    +      -       -      -
   1126B  VAL*     4.1     4.9    -      -       -      +
   1127B  CYS      2.5    23.8    +      -       -      -
   1128B  CYS*     4.1    14.0    -      -       -      +
   1173B  THR*     4.5     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN1114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  ALA*     5.5     0.2    -      -       -      +
     73A  PRO*     6.0     0.4    -      -       -      -
     75A  HIS*     4.6     7.2    -      -       +      +
   1112B  THR      3.7     0.2    +      -       -      -
   1113B  THR*     1.3    76.1    -      -       -      +
   1115B  GLN*     1.3    60.0    +      -       -      +
   1116B  SER*     3.6     8.5    -      -       -      +
   1126B  VAL*     3.5     7.7    -      -       -      +
   1127B  CYS      2.8    43.0    +      -       -      +
   1128B  CYS*     4.0     0.2    -      -       -      +
   1129B  ARG*     3.0    67.4    -      -       +      +
   1159B  TRP*     3.1    30.5    -      -       +      -
   1161B  ASP*     4.6     5.3    -      -       -      +
   1167B  PHE*     3.3    23.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN1115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  CYS*     3.0    32.4    -      -       +      +
     67A  LEU*     3.7    27.8    -      -       +      -
     71A  PHE      5.2     1.6    -      -       -      +
     73A  PRO*     4.6    19.8    -      -       +      +
     75A  HIS*     4.7     5.9    -      -       -      -
   1113B  THR      4.2     0.8    +      -       -      -
   1114B  GLN*     1.3    70.7    -      -       -      +
   1116B  SER*     1.3    64.2    +      -       -      +
   1118B  PRO*     6.0     0.3    -      -       -      +
   1124B  SER*     4.7     5.2    +      -       -      -
   1125B  THR      3.5    25.0    +      -       -      +
   1126B  VAL*     3.4    26.5    +      -       -      +
----------------------------------------------------------
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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