Contacts of the strand formed by residues 62 - 68 (chain A) in PDB entry 1LWW


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 62 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  VAL*     3.2     5.5    -      -       -      +
     59A  LEU      2.7    35.0    +      -       -      +
     60A  ALA*     3.9     8.8    -      -       -      +
     61A  ASP*     1.3    84.5    -      -       +      +
     63A  VAL*     1.3    63.6    +      -       -      +
     64A  TRP*     3.5    13.4    +      -       -      +
     77A  VAL*     3.7    14.6    -      -       +      +
     78A  TYR      4.5     3.4    -      -       -      +
     79A  ARG*     3.8    28.0    -      -       -      +
     92A  GLU*     3.4    30.4    +      -       -      +
    170A  LEU*     5.0     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  SER*     5.2     0.7    -      -       -      -
     57A  GLY      3.5     8.3    -      -       -      +
     58A  VAL*     4.3     5.4    -      -       +      -
     62A  GLN*     1.3    77.4    -      -       -      +
     64A  TRP*     1.3    66.8    +      -       -      +
     77A  VAL*     3.5     6.8    -      -       -      +
     78A  TYR*     2.9    48.2    +      -       +      -
    170A  LEU*     4.4     7.6    -      -       +      -
    171A  ILE*     3.6    24.7    -      -       +      -
    173A  LEU*     4.2     5.8    -      -       +      -
    178A  TYR*     3.5    56.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  TRP*     4.0     8.4    -      -       +      -
     55A  TRP      3.7     0.8    -      -       -      +
     56A  SER*     3.1     5.0    -      -       -      -
     57A  GLY      2.9    32.9    +      -       -      +
     59A  LEU*     3.2    39.5    +      -       +      +
     60A  ALA*     5.3     0.6    -      -       +      +
     62A  GLN*     3.5    19.1    +      -       -      +
     63A  VAL*     1.3    80.8    -      -       -      +
     65A  THR*     1.3    64.6    +      -       -      +
     66A  LEU*     4.3    11.0    -      -       +      -
     75A  CYS*     3.8    23.6    -      -       +      -
     76A  THR      3.3    20.2    -      -       -      -
     77A  VAL*     3.8    15.3    -      -       +      -
     78A  TYR*     4.0     3.1    -      -       -      -
     88A  PRO*     3.9    19.1    -      -       +      -
     92A  GLU*     3.4    47.8    -      -       +      -
     93A  LEU*     4.2     1.6    -      -       +      -
     95A  ALA*     5.1     4.5    -      -       +      -
     96A  VAL*     3.7    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  HIS*     4.7     1.3    -      -       +      -
     14A  ARG      3.8    14.1    +      -       -      +
     23A  TRP*     3.5    19.8    -      -       +      -
     54A  HIS*     4.0    18.2    -      -       +      -
     55A  TRP      3.1     6.5    -      -       -      +
     56A  SER*     2.7    22.8    +      -       -      +
     64A  TRP*     1.3    72.0    -      -       -      +
     66A  LEU*     1.3    67.3    +      -       -      +
     76A  THR*     3.1    42.6    +      -       -      +
     78A  TYR*     2.6    26.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  TRP*     4.2     1.1    -      -       -      -
     35A  LEU*     4.0    18.6    -      -       +      +
     39A  LEU*     5.0     0.9    -      -       +      -
     47A  TRP*     3.7    33.2    -      -       +      -
     53A  ALA      3.8     0.7    -      -       -      +
     54A  HIS*     3.4     1.4    -      -       -      -
     55A  TRP*     2.7    42.4    +      -       +      +
     59A  LEU*     4.7     2.0    -      -       +      -
     64A  TRP*     4.3    15.0    -      -       +      -
     65A  THR*     1.3    84.4    -      -       -      +
     67A  THR*     1.3    63.9    +      -       -      +
     73A  LEU*     4.4     4.9    -      -       +      -
     74A  HIS      3.4     4.5    -      -       -      +
     75A  CYS*     3.7    32.5    -      -       +      -
     96A  VAL*     4.8     4.7    -      -       +      -
    100A  PHE*     3.7    33.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  LEU*     4.0    15.0    -      -       +      -
     23A  TRP*     3.8     9.2    -      -       +      -
     35A  LEU*     3.9     6.7    -      -       -      -
     53A  ALA*     2.6    27.7    +      -       -      +
     54A  HIS*     3.5    33.3    -      -       +      +
     66A  LEU*     1.3    76.2    -      -       -      +
     68A  GLN*     1.3    62.8    +      -       -      +
     73A  LEU*     3.6     2.3    -      -       -      +
     74A  HIS*     2.6    50.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  CYS*     4.9     6.9    +      -       -      -
     30A  ARG*     3.9    22.3    -      -       +      +
     33A  LEU*     3.0    31.6    +      -       -      +
     34A  ARG*     3.4     6.1    -      -       -      -
     35A  LEU*     2.8    41.5    +      -       +      +
     36A  ASP*     4.3     4.3    -      -       -      +
     53A  ALA*     4.5     2.7    +      -       -      +
     67A  THR*     1.3    83.8    +      -       -      +
     69A  THR*     1.3    69.6    +      -       -      +
     72A  GLN      3.1    13.8    +      -       -      +
     73A  LEU*     4.2     8.2    -      -       +      +
     74A  HIS*     4.2     1.6    -      -       -      -
----------------------------------------------------------
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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