Contacts of the strand formed by residues 79 - 92 (chain A) in PDB entry 4L8P


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 GLU 79 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  LYS*     2.7    33.5    +      -       -      +
     74A  ALA      3.1    24.5    -      -       -      +
     75A  MSE      3.7    18.9    -      -       -      +
     76A  PRO*     2.9    16.2    +      -       +      +
     77A  LYS      3.2     2.9    -      -       -      -
     78A  GLU*     1.3    77.2    -      -       -      +
     80A  ILE*     1.3    71.9    +      -       -      +
     81A  SER*     4.8     0.9    -      -       -      +
    108A  LEU*     3.5    33.3    -      -       +      +
    109A  ILE      3.4     5.2    -      -       -      +
    110A  PHE*     3.3    38.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  LYS      5.6     0.9    -      -       -      +
     78A  GLU      4.0     0.4    +      -       -      -
     79A  GLU*     1.3    73.4    -      -       -      +
     81A  SER*     1.3    68.5    +      -       -      +
     82A  MSE      5.1    11.4    -      -       +      -
    107A  ASN      4.0     0.7    -      -       -      +
    108A  LEU*     3.3     3.5    -      -       -      -
    109A  ILE*     2.8    61.9    +      -       +      +
    111A  THR*     3.7    24.7    -      -       +      -
    160A  ILE*     4.7    12.1    -      -       +      -
    162A  SER      5.1     1.3    -      -       -      +
    163A  ASN*     3.7    35.7    -      -       +      +
    165A  HIS*     4.2    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LEU      4.3     0.5    +      -       -      -
     35A  ASP*     2.6    46.0    +      -       -      +
     37A  LYS*     4.7     4.0    +      -       -      -
     75A  MSE      3.2    31.6    -      -       -      +
     79A  GLU*     3.7     5.5    +      -       -      -
     80A  ILE*     1.3    77.7    -      -       -      +
     82A  MSE      1.3    70.4    +      -       -      +
     83A  HIS*     3.7     1.3    -      -       -      -
    107A  ASN      3.4     5.2    -      -       -      -
    108A  LEU*     3.6    14.8    -      -       -      -
    165A  HIS*     4.9     4.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with MSE 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ASP*     3.5     5.6    -      -       +      +
     80A  ILE*     5.1    11.0    -      -       +      -
     81A  SER*     1.3    80.2    -      -       -      +
     83A  HIS*     1.3    62.2    +      -       -      +
     84A  MSE      3.7    36.9    -      -       +      +
    105A  GLU      3.6     2.3    -      -       -      +
    106A  ASP*     3.2     4.5    -      -       -      -
    107A  ASN*     2.8    48.0    +      -       +      +
    109A  ILE*     6.5     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PHE*     3.6    36.9    -      -       +      +
     34A  LEU*     3.5    13.8    -      -       +      +
     35A  ASP*     2.8    35.4    +      -       -      +
     75A  MSE      3.5    31.2    -      -       +      +
     81A  SER*     3.7     8.5    -      -       -      -
     82A  MSE      1.3    69.7    -      -       -      +
     84A  MSE      1.3    61.8    +      -       -      +
     85A  GLY      3.9     0.4    +      -       -      -
    104A  LEU*     4.1    10.1    -      -       +      -
    105A  GLU      3.6     3.8    -      -       -      -
    106A  ASP*     4.0    19.8    -      -       +      +
    108A  LEU*     4.1    10.8    -      -       +      +
    204A  1PE      3.9    29.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with MSE 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  MSE      3.7    42.0    -      -       +      +
     83A  HIS*     1.3    74.6    -      -       -      +
     85A  GLY*     1.3    60.7    +      -       -      +
     86A  HIS*     3.1    20.3    +      -       +      +
    104A  LEU*     3.5     3.6    -      -       -      +
    105A  GLU*     2.8    71.7    +      -       -      +
    107A  ASN*     3.7    25.8    -      -       -      +
    201A   NI      4.6    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PHE*     3.9    26.2    -      -       -      -
     83A  HIS      3.9     3.4    +      -       -      -
     84A  MSE      1.3    73.9    -      -       -      +
     86A  HIS*     1.3    65.7    +      -       -      -
    102A  TRP*     4.4    12.4    -      -       -      -
    103A  TYR      3.6     4.5    -      -       -      -
    104A  LEU*     4.4     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  MSE      3.1    23.7    +      -       +      -
     85A  GLY*     1.3    76.4    +      -       -      -
     87A  THR*     1.3    81.9    +      -       +      +
     88A  PRO*     3.3     6.6    -      -       -      -
    102A  TRP*     4.0     4.3    -      -       -      -
    103A  TYR*     2.8    56.6    +      +       +      +
    104A  LEU      4.9     0.2    -      -       -      -
    105A  GLU*     4.0    15.7    +      -       +      -
    201A   NI      2.3    42.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  HIS*     1.3    82.6    +      -       +      +
     88A  PRO*     1.3    74.7    -      -       -      +
     89A  GLU*     3.7    11.1    +      -       -      +
    101A  ARG      4.0     2.6    -      -       -      +
    102A  TRP*     4.7     0.3    -      -       -      -
    103A  TYR*     3.5    23.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  LYS*     4.0    23.1    -      -       +      +
     86A  HIS*     3.3     5.5    -      -       -      +
     87A  THR*     1.3    90.9    -      -       -      +
     89A  GLU*     1.3    62.1    +      -       -      +
     90A  ILE*     3.9    11.5    +      -       +      -
    101A  ARG      3.1    10.8    -      -       -      +
    102A  TRP*     3.6    41.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  THR      4.3     7.2    -      -       -      +
     88A  PRO*     1.3    76.1    -      -       -      +
     90A  ILE*     1.3    61.7    +      -       -      +
     91A  THR*     3.9     4.9    +      -       -      +
     99A  THR*     3.8     1.6    -      -       -      +
    100A  GLY*     3.5     2.1    -      -       -      -
    101A  ARG*     2.9    67.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ARG*     4.9     5.2    +      -       -      -
     20A  ILE*     4.1    33.2    -      -       +      +
     23A  ILE*     3.9    41.7    -      -       +      -
     24A  LYS*     4.2    24.0    -      -       +      -
     88A  PRO*     3.9     8.4    -      -       +      -
     89A  GLU*     1.3    73.8    -      -       -      +
     91A  THR*     1.3    63.1    +      -       -      +
     92A  ILE*     4.0    13.0    +      -       +      -
     99A  THR      3.4     7.2    -      -       -      +
    100A  GLY*     3.6    20.6    -      -       -      -
    102A  TRP*     3.8    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ARG*     6.3     0.4    -      -       -      +
     89A  GLU*     3.9     5.6    +      -       -      +
     90A  ILE*     1.3    73.5    +      -       -      +
     92A  ILE*     1.3    69.2    +      -       -      +
     93A  ASP*     3.5    19.6    +      -       -      +
     98A  ALA*     3.3     3.6    -      -       -      +
     99A  THR*     2.8    46.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ARG*     4.0    31.2    -      -       +      +
     19A  ASP*     3.6    34.5    -      -       +      +
     20A  ILE*     3.8    27.6    -      -       +      +
     23A  ILE*     3.7    25.4    -      -       +      -
     90A  ILE*     4.0     2.7    -      -       +      -
     91A  THR*     1.3    77.6    -      -       -      +
     93A  ASP*     1.3    60.3    +      -       -      +
     94A  SER      3.2    23.1    -      -       -      +
     97A  THR      4.0     4.3    -      -       -      +
     98A  ALA*     4.0     4.5    -      -       +      -
    137A  TRP*     4.6     3.6    -      -       +      -
----------------------------------------------------------
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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