Contacts of the strand formed by residues 133 - 139 (chain B) in PDB entry 4L2A


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 LEU 133 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  VAL*     3.9    10.5    -      -       +      +
     95B  ALA*     3.4    32.5    +      -       +      +
     96B  ILE*     3.5    34.3    -      -       +      +
     99B  LYS*     3.2    28.9    +      -       +      +
    100B  TRP*     3.9    15.5    -      -       +      -
    125B  LEU*     4.2    19.7    -      -       +      -
    126B  VAL      3.3    17.9    -      -       -      +
    127B  LYS*     4.5     0.9    -      -       -      -
    128B  LEU*     4.9     0.2    -      -       -      +
    131B  GLY      4.1     0.2    +      -       -      -
    132B  SER*     1.3    78.6    +      -       -      +
    134B  ASP*     1.3    63.7    +      -       -      +
    153B  ILE*     4.5     5.4    -      -       +      -
    191B  PHE*     3.7    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  LYS*     3.9    19.0    +      -       -      -
    100B  TRP*     3.9     8.5    -      -       -      -
    125B  LEU*     3.5     7.1    -      -       -      +
    126B  VAL*     2.8    34.0    +      -       +      -
    128B  LEU*     3.8    34.8    -      -       +      +
    133B  LEU*     1.3    78.6    -      -       -      +
    135B  ILE*     1.3    83.8    +      -       -      +
    136B  VAL*     4.4     7.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  TRP*     3.5    25.8    -      -       +      +
    106B  PHE*     3.8    21.1    -      -       +      -
    109B  ALA*     3.9    11.9    -      -       +      -
    110B  LEU*     3.6    33.7    -      -       +      +
    113B  LYS*     3.7    31.0    +      -       +      -
    123B  THR*     3.7    24.2    -      -       +      -
    124B  TRP      3.2    11.9    -      -       -      +
    125B  LEU*     4.6     0.9    -      -       +      -
    134B  ASP*     1.3    89.7    +      -       -      +
    136B  VAL*     1.3    73.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  LYS*     4.6     2.9    -      -       -      +
    123B  THR*     3.7     0.5    -      -       -      -
    124B  TRP*     2.8    57.7    +      -       +      -
    126B  VAL*     3.9    25.4    -      -       +      -
    128B  LEU*     5.7     1.8    -      -       +      -
    134B  ASP*     4.4    11.7    -      -       -      +
    135B  ILE*     1.3    82.6    -      -       -      +
    137B  ASN*     1.3    68.2    +      -       -      +
    138B  THR*     5.2     3.1    -      -       +      -
    144B  PRO*     4.8     7.9    -      -       +      -
    150B  VAL*     5.8     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  LYS*     2.9    53.4    +      -       -      +
    116B  ASN      4.8     1.0    +      -       -      -
    117B  ASN*     3.2    30.8    +      -       -      +
    122B  TRP      3.5     3.1    -      -       -      -
    123B  THR*     2.7    30.1    +      -       -      +
    136B  VAL*     1.3    78.2    -      -       -      +
    138B  THR*     1.3    65.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117B  ASN*     3.7     2.4    +      -       -      -
    121B  SER*     2.9    24.5    -      -       -      -
    122B  TRP*     3.0    21.9    +      -       -      +
    124B  TRP*     2.8    30.5    +      -       +      +
    136B  VAL*     5.2     5.2    -      -       +      -
    137B  ASN*     1.3    78.9    -      -       -      +
    139B  SER*     1.3    60.5    +      -       -      +
    142B  ALA*     2.8    41.3    +      -       +      +
    143B  THR*     4.2     7.2    -      -       -      +
    144B  PRO*     4.4     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  ASN*     4.4    11.4    +      -       -      -
    117B  ASN*     5.7     1.1    -      -       -      -
    118B  PHE      5.2     4.8    +      -       -      -
    120B  SER      3.8     6.5    +      -       -      -
    121B  SER*     4.2     2.5    -      -       -      -
    138B  THR*     1.3    74.6    -      -       -      +
    140B  ASN*     1.3    81.6    +      -       -      +
    141B  ALA      3.2     0.7    +      -       -      -
    142B  ALA*     3.2    21.4    +      -       -      +
----------------------------------------------------------
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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