Contacts of the strand formed by residues 199 - 207 (chain B) in PDB entry 1A1A


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 GLY 199 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194B  PHE*     3.5    18.6    -      -       -      -
    195B  ASP      2.6    39.6    +      -       -      -
    196B  ASN      4.1     2.7    +      -       -      -
    197B  ALA      3.4     2.6    +      -       -      -
    198B  LYS*     1.3    76.3    -      -       -      +
    200B  LEU*     1.3    61.1    +      -       -      -
    201B  ASN*     3.2     6.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  LEU*     4.1    24.8    -      -       +      +
    170B  ASN      5.0    14.1    -      -       -      +
    172B  ARG*     4.8    10.5    -      -       +      +
    192B  SER*     5.5     4.7    -      -       -      -
    193B  ASP      3.2    20.0    -      -       -      +
    194B  PHE*     3.8    21.9    -      -       +      -
    198B  LYS      3.6     5.7    -      -       -      +
    199B  GLY*     1.3    73.9    -      -       -      -
    201B  ASN*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  LEU*     4.0     8.6    -      -       -      +
    192B  SER*     3.4     3.1    -      -       -      -
    193B  ASP*     2.8    46.2    +      -       -      +
    194B  PHE      4.2     0.2    -      -       -      +
    195B  ASP*     3.2    23.2    +      -       -      -
    198B  LYS*     3.9    19.8    -      -       +      +
    199B  GLY      3.2    17.3    +      -       -      +
    200B  LEU*     1.3    75.5    -      -       -      +
    202B  VAL*     1.3    66.0    +      -       -      +
    203B  LYS*     2.6    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162B  GLU*     3.9    28.8    +      -       +      +
    165B  LEU*     3.8    28.3    -      -       +      -
    166B  LEU*     3.5    37.2    -      -       +      +
    191B  VAL      3.4     8.7    -      -       -      +
    192B  SER*     4.7     1.6    -      -       -      -
    201B  ASN*     1.3    78.4    -      -       -      +
    203B  LYS*     1.3    71.4    +      -       -      +
    204B  HIS*     3.5    35.9    -      -       +      +
    102D  GLU*     5.2     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  LEU      3.6     1.0    -      -       -      +
    190B  SER*     3.3     4.7    -      -       -      -
    191B  VAL      2.9    31.3    +      -       -      -
    193B  ASP*     2.7    20.3    +      -       +      -
    195B  ASP*     4.3     5.1    +      -       -      -
    198B  LYS*     4.8     9.9    -      -       -      +
    201B  ASN*     2.6    31.0    +      -       -      +
    202B  VAL*     1.3    79.5    -      -       -      +
    204B  HIS*     1.3    63.5    +      -       -      +
    205B  TYR*     3.7    28.9    -      -       +      +
    241B  CYS*     3.9    21.3    -      -       +      -
    102D  GLU*     3.7    35.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  ARG*     3.3    39.5    +      -       +      +
    161B  SER*     3.6    18.8    -      -       -      -
    162B  GLU*     2.7    31.4    +      -       +      -
    178B  ARG*     3.1     6.9    +      -       -      -
    189B  LEU      3.3     3.8    -      -       -      -
    190B  SER*     3.0    19.6    +      -       -      -
    202B  VAL*     3.5    27.9    +      -       +      +
    203B  LYS*     1.3    78.0    -      -       -      +
    205B  TYR*     1.3    60.2    +      -       -      +
    100D  ACE      4.0     3.5    +      -       -      +
    101D  PTH      3.2    25.0    -      -       -      +
    102D  GLU*     3.0    30.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  LEU*     2.8    50.1    +      -       +      +
    191B  VAL*     4.2    17.3    -      -       +      -
    203B  LYS*     3.7    27.5    -      -       +      +
    204B  HIS*     1.3    74.1    -      -       -      +
    206B  LYS*     1.3    64.6    +      -       -      +
    207B  ILE*     4.0     0.2    -      -       -      +
    217B  ILE*     4.0    24.7    -      -       +      -
    239B  GLY      4.5     1.4    +      -       -      -
    240B  LEU*     3.5    34.7    -      -       +      -
    241B  CYS*     2.9    33.2    +      -       -      +
    101D  PTH      3.1     5.3    +      -       -      +
    102D  GLU*     3.5    30.1    -      -       +      +
    103D  DIP      3.8    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180B  SER*     4.0     4.0    +      -       -      +
    182B  THR*     3.3    14.5    +      -       -      -
    183B  THR*     2.8    25.8    +      -       -      +
    186B  ALA*     4.3     6.3    -      -       +      -
    187B  TYR      3.7     9.2    -      -       -      +
    205B  TYR*     1.3    74.1    -      -       -      +
    207B  ILE*     1.3    73.0    +      -       -      +
    208B  ARG*     3.0    54.0    +      -       +      +
    216B  TYR      3.8     0.5    -      -       -      +
    217B  ILE*     3.4    25.1    -      -       -      +
    101D  PTH      3.6    35.2    +      -       +      +
    102D  GLU      5.3     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177B  VAL*     4.2    10.5    -      -       +      -
    186B  ALA*     3.2     8.3    -      -       -      +
    187B  TYR*     2.9    46.7    +      -       +      +
    189B  LEU*     3.9    22.2    -      -       +      +
    205B  TYR      4.0     6.1    -      -       -      +
    206B  LYS*     1.3    77.3    -      -       -      +
    208B  ARG*     1.3    59.3    +      -       -      +
    215B  PHE*     3.8    22.4    -      -       +      -
    216B  TYR      3.4     4.3    -      -       -      +
    217B  ILE*     3.9    14.8    -      -       +      -
    226B  LEU*     3.9    24.0    -      -       +      -
    229B  LEU*     3.7    32.5    -      -       +      -
----------------------------------------------------------
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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