Contacts of the strand formed by residues 105 - 116 (chain T) in PDB entry 5IYB


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 SER 105 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7T  LEU*     3.8     6.1    -      -       -      -
      8T  ASP*     3.3    26.4    +      -       -      +
     96T  PHE*     3.1     1.9    -      -       -      -
     97T  THR*     2.6    49.8    +      -       -      -
    103T  LYS*     3.6     8.3    +      -       -      +
    104T  LEU*     1.3    79.2    +      -       -      +
    106T  LEU*     1.3    61.5    +      -       -      +
    107T  GLU*     3.6     9.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 106 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29S  MET*     3.9    10.8    -      -       +      -
     39S  PHE*     6.0     0.9    -      -       +      -
     42S  TRP*     4.4    18.6    -      -       +      -
      7T  LEU*     3.8     7.9    -      -       +      +
      8T  ASP*     2.8    22.4    +      -       -      +
      9T  LEU*     3.7    18.8    -      -       +      -
     10T  THR*     4.9     1.0    +      -       -      -
     11T  GLY*     3.3    21.3    +      -       -      -
     12T  ALA*     3.6    27.1    -      -       +      -
     94T  THR*     3.8    25.1    -      -       +      +
     95T  VAL      3.3    23.6    -      -       -      +
     96T  PHE*     3.8    11.0    -      -       +      -
    105T  SER*     1.3    72.1    -      -       -      +
    107T  GLU*     1.3    64.3    +      -       -      +
    108T  GLY      4.7     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 107 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24S  LYS*     2.7    31.9    +      -       -      -
     26S  TYR*     5.0     4.3    -      -       +      -
     11T  GLY*     3.5    10.6    -      -       -      -
     16T  THR*     3.4    20.3    +      -       -      +
     18T  VAL*     6.1     3.1    -      -       +      -
     95T  VAL*     2.6    25.2    +      -       +      +
     97T  THR*     3.3    33.6    +      -       +      +
    105T  SER*     4.3     9.1    -      -       -      +
    106T  LEU*     1.3    73.3    -      -       -      +
    108T  GLY*     1.3    55.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 108 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11T  GLY      4.3     7.9    -      -       -      -
     12T  ALA*     4.7     1.5    -      -       -      +
     16T  THR*     3.3    17.5    -      -       -      -
     18T  VAL*     5.0     8.3    -      -       -      -
     94T  THR*     3.1     6.9    -      -       -      -
     95T  VAL*     2.8    25.6    +      -       -      +
    106T  LEU*     3.5     4.3    -      -       -      +
    107T  GLU*     1.3    82.0    -      -       -      +
    109T  ILE*     1.3    64.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 109 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39S  PHE*     3.8    25.6    -      -       +      -
     12T  ALA*     4.0    19.5    -      -       +      +
     15T  ASN*     3.9    32.8    -      -       -      +
     16T  THR      2.5    23.9    +      -       -      +
     17T  GLY*     3.2     8.0    -      -       -      -
     18T  VAL*     3.0    24.6    +      -       -      -
     92T  THR*     4.8     6.3    -      -       +      -
     93T  LEU      3.2    10.8    -      -       -      +
     94T  THR*     3.6    19.5    -      -       +      -
    108T  GLY*     1.3    75.3    -      -       -      -
    110T  VAL*     1.3    74.0    +      -       -      +
    111T  VAL*     3.3     7.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 110 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28S  ILE*     4.6     4.5    -      -       +      -
    126S  ILE*     5.2     1.6    -      -       +      -
     18T  VAL*     3.6    22.0    -      -       +      +
     20T  LEU*     4.0    17.0    -      -       +      -
     88T  VAL*     5.0     9.2    -      -       +      +
     92T  THR*     5.9     0.2    -      -       -      +
     93T  LEU*     2.5    57.3    +      -       +      +
     94T  THR*     4.1     9.9    -      -       -      +
     95T  VAL*     4.5     7.4    -      -       +      -
    109T  ILE*     1.3    76.0    -      -       -      +
    111T  VAL*     1.3    61.4    +      -       -      +
    112T  GLN      3.5    24.7    -      -       -      +
    113T  ARG*     4.8     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15T  ASN*     5.7     2.2    -      -       -      +
     17T  GLY*     3.7    15.3    -      -       -      -
     18T  VAL      3.0    19.6    +      -       -      +
     19T  TRP*     3.8    18.6    -      -       +      +
     88T  VAL*     3.8    19.1    -      -       -      +
    109T  ILE*     3.7    19.3    -      -       +      +
    110T  VAL*     1.3    74.7    -      -       -      +
    112T  GLN*     1.3    67.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 112 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18T  VAL      3.6     0.8    +      -       -      -
     19T  TRP*     3.5    40.3    -      -       +      +
     20T  LEU      2.7    31.2    +      -       -      -
     85T  LEU*     4.0    33.5    -      -       +      +
     86T  GLN      3.3    14.2    +      -       -      +
     88T  VAL*     3.9     9.1    -      -       -      +
    110T  VAL*     3.5     7.9    -      -       -      +
    111T  VAL*     1.3    85.7    +      -       -      +
    113T  ARG*     1.3    82.9    +      -       -      +
    114T  ALA*     5.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 113 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551B  GLU*     4.7    12.5    +      -       -      +
    555B  GLU*     3.2    41.4    +      -       -      +
    556B  ILE*     5.6     0.6    -      -       -      +
    143S  TRP*     5.0     9.1    -      -       -      -
     20T  LEU*     3.3    28.7    -      -       +      +
     22T  LYS*     6.1     0.4    -      -       -      +
     85T  LEU*     3.3     2.8    -      -       -      -
     86T  GLN*     2.8    51.4    +      -       +      +
     87T  SER      3.8    17.3    +      -       -      -
     88T  VAL*     3.5    15.0    -      -       +      +
     91T  GLN*     4.3    16.2    +      -       -      +
     93T  LEU*     5.4     8.6    -      -       +      +
    110T  VAL*     4.8     3.8    -      -       +      -
    112T  GLN*     1.3    87.6    +      -       -      +
    114T  ALA*     1.3    66.6    +      -       -      +
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Residues in contact with ALA 114 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19T  TRP*     6.2     3.6    -      -       +      -
     20T  LEU      2.7    13.0    +      -       -      +
     21T  VAL*     3.2    20.5    -      -       +      -
     22T  LYS*     2.8    24.7    +      -       -      +
     83T  PHE*     4.3    12.1    -      -       +      -
     84T  VAL      3.1    13.7    -      -       -      +
     85T  LEU*     3.8    17.0    -      -       +      -
     86T  GLN*     4.3     4.9    -      -       -      +
    112T  GLN*     5.4     1.1    -      -       +      -
    113T  ARG*     1.3    77.7    -      -       -      +
    115T  GLU*     1.3    61.7    +      -       -      +
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Residues in contact with GLU 115 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    546B  GLU      4.7     4.2    -      -       -      +
    547B  GLU      4.1    16.1    -      -       -      +
    548B  TRP      4.2     6.6    -      -       -      +
    549B  SER*     4.4    17.0    -      -       -      +
    551B  GLU*     6.0     1.4    -      -       -      +
     21T  VAL*     4.5     1.1    -      -       -      -
     22T  LYS*     3.5    36.0    +      -       +      +
     82T  PRO      3.7     0.2    -      -       -      +
     83T  PHE*     3.6     2.5    -      -       -      -
     84T  VAL*     2.8    54.8    +      -       +      +
     86T  GLN*     4.4    12.8    +      -       +      +
    114T  ALA*     1.3    74.8    -      -       -      +
    116T  CYS*     1.3    72.5    +      -       -      +
    117T  ARG*     3.5    13.0    +      -       +      +
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Residues in contact with CYS 116 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21T  VAL*     4.1     2.5    -      -       +      +
     22T  LYS      2.5    19.1    +      -       -      +
     23T  VAL*     3.7    14.6    -      -       +      -
     24T  PRO*     3.1    29.0    -      -       +      +
     27T  LEU*     4.2    10.8    -      -       -      -
     81T  HIS*     3.3    46.4    -      -       -      -
     82T  PRO      3.7     4.3    -      -       -      -
     83T  PHE*     3.9    18.8    -      -       +      -
    115T  GLU*     1.3    76.4    -      -       -      +
    117T  ARG*     1.3    59.2    +      -       -      +
    118T  PRO*     4.5     0.2    -      -       -      +
----------------------------------------------------------
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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