Contacts of the strand formed by residues 252 - 261 (chain B) in PDB entry 2WLM


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 GLN 252 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  TYR*     4.7     7.6    +      -       -      -
    136B  THR*     4.2    13.2    +      -       -      +
    138B  PRO*     2.9    34.8    -      -       +      +
    246B  HIS*     3.4    12.2    -      -       -      -
    247B  HIS*     2.9    27.1    +      -       -      +
    250B  PHE*     3.1    15.6    -      -       +      +
    251B  ALA*     1.3    80.1    -      -       -      +
    253B  ASN*     1.3    70.4    +      -       -      +
    254B  VAL*     3.8     1.3    +      -       -      +
    251C  ALA*     5.5     5.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 253 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138B  PRO*     4.4     6.9    -      -       -      +
    173B  GLU*     5.2     5.9    +      -       -      +
    244B  THR*     5.5     2.8    +      -       -      -
    245B  GLY*     3.5    20.5    +      -       -      +
    246B  HIS*     3.4    23.9    +      -       -      +
    252B  GLN*     1.3    88.0    +      -       -      +
    254B  VAL*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 254 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138B  PRO*     3.6    28.7    -      -       +      -
    139B  THR*     4.4     0.4    -      -       -      +
    140B  ALA*     3.7    33.2    -      -       +      +
    171B  ILE*     4.4     7.4    -      -       +      -
    243B  PHE*     4.7     0.9    -      -       +      -
    244B  THR*     3.4     2.8    -      -       -      -
    245B  GLY      2.8    45.8    +      -       -      +
    247B  HIS*     3.7    32.3    -      -       +      -
    250B  PHE*     4.1     2.0    -      -       +      -
    252B  GLN      4.2     0.4    -      -       -      +
    253B  ASN*     1.3    81.2    -      -       -      +
    255B  HIS*     1.3    68.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 255 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139B  THR*     5.3     1.6    -      -       -      +
    140B  ALA*     3.9    15.8    +      -       -      +
    242B  LEU*     4.3     3.8    -      -       +      -
    243B  PHE*     3.0    17.3    -      -       -      +
    244B  THR*     3.4    13.6    -      -       +      +
    254B  VAL*     1.3    80.5    -      -       -      +
    256B  ALA*     1.3    70.1    +      -       -      +
    257B  ARG*     5.5     3.8    -      -       +      -
    172C  ILE*     3.2    36.8    -      -       +      +
    246C  HIS*     3.7    22.2    -      +       -      -
    248C  GLU*     4.1    25.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 256 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140B  ALA*     4.3    14.1    -      -       +      +
    142B  VAL*     4.4    11.7    -      -       +      +
    144B  PHE*     3.7    24.6    -      -       +      -
    242B  LEU*     3.5     3.6    -      -       -      +
    243B  PHE*     2.7    36.3    +      -       +      +
    255B  HIS*     1.3    80.9    -      -       -      +
    257B  ARG*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 257 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  ASP*     3.4    25.8    +      -       -      +
     19B  GLY*     3.2     7.0    -      -       -      -
     20B  SER*     3.2    29.5    -      -       -      +
    144B  PHE*     3.9     7.2    -      -       -      -
    241B  VAL      3.1    11.4    -      -       -      +
    242B  LEU*     4.6     4.9    -      -       +      -
    255B  HIS*     5.5     4.2    -      -       +      -
    256B  ALA*     1.3    78.5    -      -       -      +
    258B  HIS*     1.3    66.3    +      -       -      +
    170C  GLN*     2.6    35.3    +      -       -      +
    172C  ILE*     5.4     2.5    -      -       +      -
    207C  ILE*     4.2    26.2    -      -       +      -
    248C  GLU*     2.3    44.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 258 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  SER*     3.2    33.1    +      -       -      -
     18B  ASP*     5.2     0.8    -      -       -      -
     19B  GLY*     4.5     2.0    -      -       -      +
    144B  PHE*     3.4    42.5    -      +       +      +
    145B  SER      4.2     3.2    +      -       -      -
    146B  SER*     4.7     5.6    +      -       -      -
    240B  LEU*     2.9     7.5    -      -       -      +
    241B  VAL*     2.7    35.3    +      -       +      +
    257B  ARG*     1.3    77.6    +      -       -      +
    259B  ALA*     1.3    73.5    +      -       -      +
    260B  TYR*     3.2    47.2    +      +       -      -
----------------------------------------------------------
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Residues in contact with ALA 259 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ARG*     3.7    12.8    +      -       -      +
     15B  LEU*     4.2    17.9    -      -       +      +
     16B  ASN      3.2    24.0    -      -       -      +
     17B  SER*     3.1    12.4    +      -       -      -
     19B  GLY*     4.2     2.2    -      -       -      -
    238B  GLU*     5.4     1.1    -      -       +      +
    239B  PHE      3.2     7.4    -      -       -      +
    240B  LEU*     3.8    14.1    -      -       +      -
    258B  HIS*     1.3    90.0    +      -       -      +
    260B  TYR*     1.3    66.1    +      -       -      +
    264B  GLU*     4.5     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 260 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ARG*     4.4     2.9    -      -       -      -
    144B  PHE*     3.8     1.7    -      -       -      +
    145B  SER*     2.3    41.4    +      -       -      -
    146B  SER      3.4    18.8    -      -       -      -
    147B  ARG      3.9     4.5    -      -       -      -
    148B  MET*     3.3    44.0    -      -       +      -
    161B  MET*     3.5    25.6    -      -       +      +
    238B  GLU*     3.3     7.7    -      -       -      +
    239B  PHE*     2.6    47.7    +      -       +      +
    241B  VAL*     4.0    13.9    -      -       +      -
    258B  HIS*     3.2    28.8    -      +       -      -
    259B  ALA*     1.3    79.2    -      -       -      +
    261B  SER*     1.3    65.9    +      -       -      +
    264B  GLU*     4.2    13.7    -      -       +      -
    265B  ILE*     5.7     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 261 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ARG*     4.0    23.4    +      -       -      +
    237B  SER      4.3     0.2    -      -       -      -
    238B  GLU*     4.5    13.0    -      -       -      +
    239B  PHE*     5.0     1.3    -      -       -      -
    260B  TYR*     1.3    75.6    -      -       -      +
    262B  CYS*     1.3    73.1    +      -       -      +
    263B  ASP*     2.7    24.8    +      -       -      -
    264B  GLU*     2.8    40.5    +      -       -      +
    265B  ILE*     3.9     6.7    +      -       -      +
----------------------------------------------------------
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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