Contacts of the strand formed by residues 272 - 282 (chain A) in PDB entry 4H3T


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 ALA 272 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  GLU      3.8     0.2    -      -       -      +
    268A  ARG*     3.5     2.5    -      -       -      -
    269A  ARG*     2.8    41.6    +      -       +      +
    271A  ASP*     1.4    84.7    +      -       -      +
    273A  ILE*     1.3    62.6    -      -       -      +
    274A  VAL*     3.9    14.7    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 273 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  MSE      4.0    37.7    -      -       +      -
      6A  HIS      3.8    22.9    -      -       -      +
      7A  PHE*     5.9     1.1    -      -       +      -
    102A  PHE*     3.6    27.6    -      -       +      -
    154A  PRO*     3.2    25.9    -      -       +      +
    266A  PRO*     4.0     7.9    -      -       +      -
    267A  GLU      3.6     3.8    -      -       -      +
    268A  ARG*     3.5    40.4    -      -       -      +
    271A  ASP      4.0     1.0    +      -       -      +
    272A  ALA*     1.3    72.3    -      -       -      +
    274A  VAL*     1.3    68.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 274 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  ALA*     3.9    19.3    -      -       +      -
    152A  LEU      3.4    14.6    -      -       -      +
    153A  SER*     5.1     2.7    -      -       -      -
    154A  PRO*     4.7     0.9    -      -       -      -
    266A  PRO*     3.3     5.5    -      -       -      +
    267A  GLU*     2.8    39.5    +      -       +      +
    269A  ARG*     3.6    38.6    -      -       +      +
    272A  ALA*     4.5    14.4    -      -       +      +
    273A  ILE*     1.3    80.4    -      -       -      +
    275A  VAL*     1.3    63.2    +      -       -      +
    276A  PRO*     3.6     4.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 275 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  PHE*     3.8    31.6    -      -       +      -
    125A  ALA*     3.1    17.8    -      -       +      +
    151A  ALA*     4.1     1.3    -      -       -      -
    152A  LEU*     2.8    36.2    +      -       +      +
    153A  SER      4.6     2.9    -      -       -      +
    154A  PRO*     4.6     1.3    -      -       +      -
    157A  ALA*     3.9    23.3    -      -       +      -
    264A  LEU*     3.9    27.1    -      -       +      -
    265A  PHE      4.2     5.4    -      -       -      +
    266A  PRO*     4.5     1.6    -      -       +      -
    274A  VAL*     1.3    78.9    -      -       -      +
    276A  PRO*     1.3    59.1    -      -       -      +
    277A  ARG      3.5    20.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 276 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  THR*     3.3    11.6    -      -       -      +
    125A  ALA*     2.8    20.5    +      -       +      -
    149A  GLU      5.9     1.1    -      -       -      +
    151A  ALA*     3.9    13.0    -      -       +      -
    265A  PHE      3.3    18.6    -      -       -      +
    267A  GLU*     3.7    28.5    -      -       +      +
    269A  ARG*     3.6    19.3    -      -       -      +
    274A  VAL*     3.6    11.4    -      -       +      +
    275A  VAL*     1.3    85.5    -      -       -      +
    277A  ARG*     1.3    69.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 277 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  VAL*     3.8    28.8    -      -       +      +
    123A  LYS      3.3    12.3    -      -       -      +
    124A  THR*     4.7     6.7    -      -       +      -
    125A  ALA*     3.7     2.9    -      -       -      +
    265A  PHE*     3.0    59.5    +      -       +      +
    275A  VAL*     3.5     8.6    -      -       -      +
    276A  PRO*     1.3    95.1    -      -       +      +
    278A  VAL*     1.4    65.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 278 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  VAL*     3.6     1.0    -      -       -      +
    123A  LYS*     2.8    35.1    +      -       +      +
    124A  THR      3.8     8.7    -      -       -      +
    125A  ALA*     4.0     8.7    -      -       +      -
    127A  SER*     3.3    26.9    -      -       -      +
    128A  LEU*     4.3    11.4    -      -       +      -
    262A  ILE*     3.8    22.7    -      -       +      -
    263A  ARG      3.3    15.7    -      -       -      +
    264A  LEU*     3.9    16.4    -      -       +      -
    265A  PHE*     3.9     6.0    -      -       -      -
    277A  ARG*     1.4    75.5    -      -       -      +
    279A  LEU*     1.3    61.6    +      -       -      +
    280A  ILE*     3.8    17.0    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  LEU*     3.8    22.4    -      -       +      +
    115A  GLU*     3.5    37.2    -      -       -      -
    116A  PRO*     3.5    10.5    -      -       +      -
    121A  GLY*     3.7    18.2    -      -       -      +
    122A  VAL*     4.2     4.9    -      -       +      +
    174A  THR*     3.6    31.9    -      -       +      -
    261A  ARG      3.7     0.6    -      -       -      +
    262A  ILE*     3.2     9.0    -      -       -      +
    263A  ARG*     2.9    31.9    +      -       +      +
    265A  PHE*     3.9    15.7    -      -       +      -
    278A  VAL*     1.3    73.6    -      -       -      +
    280A  ILE*     1.3    61.1    +      -       -      +
    281A  CYS*     3.8    12.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  GLY      5.3     1.2    +      -       -      -
    123A  LYS*     6.2     1.2    -      -       -      +
    127A  SER*     4.0    21.1    -      -       -      +
    128A  LEU*     3.9    18.4    -      -       +      -
    164A  ARG*     3.6    31.0    -      -       +      +
    172A  ASP*     3.9    37.1    -      -       +      +
    174A  THR*     3.5    21.1    +      -       -      -
    260A  ARG*     4.5     4.3    -      -       -      -
    261A  ARG      3.6     2.2    -      -       -      -
    262A  ILE*     4.1    20.6    -      -       +      -
    278A  VAL*     3.8    16.2    -      -       +      -
    279A  LEU*     1.3    81.6    -      -       -      +
    281A  CYS*     1.3    62.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  LEU*     4.2     3.6    -      -       -      -
    172A  ASP      3.7     7.0    -      -       -      -
    174A  THR*     3.5    23.8    -      -       -      +
    176A  ALA*     3.8    27.8    -      -       +      +
    260A  ARG*     3.3    13.8    -      -       -      +
    261A  ARG*     2.8    40.8    +      -       +      +
    279A  LEU*     3.8    29.2    -      -       -      -
    280A  ILE*     1.3    76.8    -      -       -      +
    282A  ALA*     1.3    62.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  ASP      3.5     7.5    +      -       -      -
    174A  THR      4.5     1.4    +      -       -      -
    179A  ASN*     5.5     1.9    +      -       -      +
    187A  ASP*     3.4    27.7    +      -       +      +
    189A  PRO*     3.7    18.4    -      -       +      -
    241A  PRO      4.8     2.9    -      -       -      +
    243A  ARG*     3.5    35.7    -      -       -      +
    260A  ARG*     4.4     1.1    -      -       -      +
    261A  ARG*     3.4    15.2    -      -       -      +
    281A  CYS*     1.3    77.7    -      -       -      +
    283A  GLY*     1.3    59.3    +      -       -      +
----------------------------------------------------------
 Back to top of page


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