Contacts of the strand formed by residues 663 - 667 (chain B) in PDB entry 5X61


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 HIS 663 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580B  MET*     3.8     2.9    +      -       -      +
    655B  PRO*     4.1    17.8    -      -       +      +
    656B  LYS      4.1    14.4    -      -       -      +
    657B  HIS*     3.1    30.1    +      -       -      +
    658B  THR*     4.8     2.5    -      -       -      -
    661B  GLY*     3.8    21.5    +      -       -      -
    662B  ARG*     1.3    77.9    -      -       -      +
    664B  TYR*     1.3    58.2    +      -       -      +
    674B  VAL*     3.5    27.7    -      -       +      +
    675B  GLY      3.2    10.2    +      -       -      -
    676B  ARG*     3.6    26.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 664 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580B  MET*     3.3    34.5    -      -       +      +
    581B  TYR*     4.4     1.3    -      -       -      +
    582B  LEU*     3.6    42.4    -      -       +      +
    654B  TRP*     5.0     1.3    -      -       -      +
    655B  PRO*     5.5     1.3    -      -       -      -
    663B  HIS*     1.3    73.3    -      -       -      +
    665B  LEU*     1.3    62.9    +      -       -      +
    666B  GLU*     4.3    12.6    -      -       +      -
    673B  PHE*     3.9    16.2    -      +       -      -
    674B  VAL*     3.3    10.1    -      -       -      +
    675B  GLY*     3.0    59.4    +      -       -      -
    676B  ARG      3.4    13.5    -      -       -      -
    677B  GLY      3.5     5.6    -      -       -      +
    678B  PRO*     3.5    28.8    -      -       +      +
    806B  SO4      4.5     7.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 665 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    580B  MET      3.0     7.7    +      -       -      -
    581B  TYR*     3.3     7.3    -      -       -      +
    582B  LEU      3.0    18.7    +      -       -      -
    628B  LYS*     5.8     1.3    -      -       -      +
    632B  TYR*     3.6    28.9    -      -       +      +
    652B  PRO*     5.0     4.3    -      -       +      -
    653B  GLU      3.8    15.7    -      -       -      +
    654B  TRP*     3.7    51.5    -      -       +      +
    655B  PRO*     5.0     0.2    -      -       +      -
    664B  TYR*     1.3    74.4    -      -       -      +
    666B  GLU*     1.3    72.1    +      -       -      +
    667B  LEU*     3.5     9.0    +      -       +      +
    672B  SER*     4.0    18.6    -      -       -      +
    673B  PHE      3.9    13.9    -      -       -      +
    674B  VAL*     4.2     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 666 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    582B  LEU*     3.4     8.3    -      -       +      +
    584B  THR*     3.1    42.5    +      -       +      +
    628B  LYS*     5.6     2.9    +      -       -      -
    664B  TYR*     3.9    10.9    +      -       +      -
    665B  LEU*     1.3    83.7    -      -       -      +
    667B  LEU*     1.3    58.8    +      -       -      +
    671B  THR*     3.3    40.1    +      -       +      +
    672B  SER*     4.9     1.6    -      -       -      -
    673B  PHE*     3.0    42.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 667 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    581B  TYR*     3.6    32.5    -      -       +      -
    582B  LEU      2.7    13.4    +      -       -      +
    583B  TYR*     3.9    17.0    -      -       +      -
    584B  THR*     3.3    18.8    +      -       -      -
    585B  HIS      3.7     2.3    +      -       -      -
    625B  PHE*     3.2    21.4    -      -       +      -
    628B  LYS*     5.2     6.7    -      -       -      +
    629B  ILE*     4.3    13.7    -      -       +      -
    632B  TYR*     3.7    32.5    -      -       +      -
    633B  TRP*     3.9    23.6    -      -       +      -
    654B  TRP*     4.6     1.8    -      -       +      -
    665B  LEU*     3.9    22.9    -      -       +      +
    666B  GLU*     1.3    71.1    -      -       -      +
    668B  GLY*     1.3    57.8    +      -       -      +
----------------------------------------------------------
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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