Contacts of the strand formed by residues 214 - 219 (chain A) in PDB entry 1A1O


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 214 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  GLU*     5.3     4.0    +      -       -      -
    213A  ILE*     1.3    78.2    +      -       -      +
    215A  LEU*     1.3    66.7    +      -       -      +
    216A  THR*     4.3    14.4    -      -       -      +
    260A  HIS      3.4     1.5    -      -       -      +
    261A  VAL*     3.4     5.9    -      -       -      -
    262A  GLN*     2.9    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  CYS*     3.9     8.3    -      -       +      +
    205A  ALA*     4.0    16.2    -      -       +      -
    213A  ILE*     4.4     4.7    -      -       +      +
    214A  THR*     1.3    76.6    -      -       -      +
    216A  THR*     1.3    63.7    +      -       -      +
    228A  THR*     5.4     1.6    -      -       -      +
    230A  LEU*     3.9    20.4    -      -       +      +
    243A  LYS*     3.8    41.2    -      -       +      +
    244A  TRP*     3.8    17.9    -      -       -      +
    245A  ALA*     3.9    18.8    -      -       +      +
    259A  CYS*     4.6     7.2    -      -       -      -
    260A  HIS      3.3     1.6    -      -       -      +
    261A  VAL*     3.7    41.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  THR*     4.3    13.2    -      -       -      +
    215A  LEU*     1.3    76.7    +      -       -      +
    217A  TRP*     1.3    78.4    +      -       -      +
    218A  GLN*     4.2     6.5    -      -       +      +
    223A  ASP*     3.3    33.4    +      -       +      +
    224A  GLN      5.0     0.9    -      -       -      +
    225A  THR*     5.6     2.2    -      -       -      +
    228A  THR*     5.9     1.1    -      -       -      -
    258A  THR      3.6     0.5    -      -       -      +
    259A  CYS*     3.2     8.1    -      -       -      -
    260A  HIS*     2.7    49.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  VAL*     4.2    16.4    -      -       +      -
    201A  LEU*     3.7    28.7    +      -       +      -
    202A  ARG      4.2     1.8    -      -       -      -
    203A  CYS*     3.8    27.6    -      -       +      +
    216A  THR*     1.3    83.1    -      -       -      +
    218A  GLN*     1.3    60.7    +      -       -      +
    224A  GLN*     3.0    30.6    +      -       +      -
    228A  THR*     3.9    20.4    +      -       +      +
    245A  ALA*     3.0    44.0    +      -       +      -
    246A  ALA*     3.8    16.2    -      -       -      +
    247A  VAL*     3.9    17.0    -      -       +      -
    257A  TYR*     3.8    29.4    -      -       +      -
    258A  THR      3.1    41.5    -      -       -      -
    259A  CYS*     3.5     9.9    -      -       +      -
    272A  LEU      4.5     1.8    -      -       -      -
    273A  ARG*     5.6     1.8    -      -       -      -
    274A  TRP      5.7     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  THR*     4.2     3.5    -      -       +      +
    217A  TRP*     1.3    78.2    -      -       -      +
    219A  ARG*     1.3    59.8    +      -       -      +
    220A  ASP      3.9     0.6    +      -       -      -
    221A  GLY*     3.5    26.6    +      -       -      -
    222A  GLU      3.3    11.7    -      -       -      +
    223A  ASP*     2.8    30.4    +      -       -      +
    224A  GLN*     4.4     2.0    -      -       -      -
    256A  ARG      3.5     0.9    -      -       -      +
    257A  TYR*     3.0     9.6    -      -       -      -
    258A  THR*     2.6    41.3    +      -       -      +
    260A  HIS*     2.6    45.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  GLN*     1.3    71.2    -      -       -      +
    220A  ASP*     1.3    84.2    +      -       -      +
    222A  GLU*     2.9    24.7    +      -       -      +
    224A  GLN*     3.1    28.6    -      -       +      +
    250A  PRO*     4.7     6.1    -      -       -      +
    253A  GLU*     3.5    19.0    +      -       -      -
    256A  ARG*     3.2    38.3    -      -       +      +
    257A  TYR*     3.4    39.8    +      -       +      -
----------------------------------------------------------
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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