Contacts of the strand formed by residues 313 - 316 (chain A) in PDB entry 1D1T


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 THR 313 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  LEU*     5.0     0.4    -      -       -      +
    286A  TYR      6.0     0.2    -      -       -      -
    287A  GLY      2.9     8.3    +      -       -      +
    288A  THR*     3.2    19.3    +      -       +      +
    289A  SER*     2.8    28.6    +      -       -      -
    311A  GLY      3.5     4.0    +      -       -      -
    312A  ARG*     1.3    74.9    -      -       -      +
    314A  TRP*     1.3    61.1    +      -       -      +
    315A  LYS*     4.1    17.3    -      -       +      +
    313B  THR*     3.5    29.6    -      -       +      -
    314B  TRP      3.5     3.1    -      -       -      +
    315B  LYS*     3.8    24.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275A  MET*     4.5    16.0    +      -       +      -
    276A  ILE*     5.2     1.6    -      -       +      -
    279A  LEU*     3.8    30.3    -      -       +      +
    289A  SER*     3.3    31.3    +      -       -      -
    291A  VAL*     3.3    21.0    -      -       +      +
    301A  LEU*     3.8    24.5    -      -       +      -
    303A  TYR*     3.7    32.3    -      +       +      -
    308A  LEU*     3.8    14.1    -      -       +      -
    313A  THR*     1.3    74.9    -      -       -      +
    315A  LYS*     1.3    59.4    +      -       -      +
    303B  TYR*     3.0    31.4    -      +       -      -
    308B  LEU*     3.4    20.3    -      -       +      +
    314B  TRP*     2.6    61.1    +      +       +      +
----------------------------------------------------------
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Residues in contact with LYS 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  THR*     3.2    42.5    +      -       +      +
    187A  GLY*     5.4     0.2    -      -       -      -
    188A  LYS*     5.3     7.1    -      -       -      +
    288A  THR*     4.2    12.3    -      -       +      +
    289A  SER      3.1     9.4    +      -       -      +
    290A  VAL*     3.4    10.8    -      -       +      -
    291A  VAL*     2.8    32.7    +      -       -      +
    313A  THR*     4.1    18.8    -      -       +      +
    314A  TRP*     1.3    75.6    -      -       -      +
    316A  GLY*     1.3    56.8    +      -       -      +
    308B  LEU*     3.8     6.5    -      -       -      -
    311B  GLY      4.7     3.1    -      -       -      +
    312B  ARG      3.3    12.8    -      -       -      +
    313B  THR*     3.3    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  THR*     3.4    18.7    -      -       -      +
    291A  VAL*     3.5     8.5    -      -       -      -
    315A  LYS*     1.3    78.0    -      -       -      +
    317A  CYS*     1.3    62.1    +      -       -      -
    308B  LEU*     3.3    29.6    +      -       -      +
    309B  PHE*     3.5    11.9    -      -       -      -
    311B  GLY*     4.1    12.0    -      -       -      +
    312B  ARG      3.5     3.2    +      -       -      -
----------------------------------------------------------
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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