Contacts of the strand formed by residues 110 - 117 (chain A) in PDB entry 4KHS


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 VAL 110 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  HIS      5.4     1.3    -      -       -      +
    108A  ILE*     3.8    16.8    -      -       +      +
    109A  ARG*     1.3    73.5    -      -       -      +
    111A  ALA*     1.3    61.4    +      -       -      +
    112A  ASN*     4.1    17.0    +      -       -      +
    139A  TYR*     3.7     2.8    -      -       -      +
    140A  ASP*     4.0     0.2    -      -       -      -
    141A  SER*     2.8    45.2    +      -       -      +
    212A  ILE*     3.5    35.2    -      -       +      +
    214A  THR*     4.4     7.4    -      -       +      -
    341A  ILE*     4.6    21.5    -      -       +      -
    345A  LEU*     5.4     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  ARG*     3.9     1.3    +      -       +      -
    110A  VAL*     1.3    73.9    -      -       -      +
    112A  ASN*     1.3    62.0    +      -       -      +
    113A  PHE      4.1     0.2    -      -       -      -
    138A  HIS*     3.5    29.4    -      -       +      +
    139A  TYR      3.3     4.3    -      -       -      +
    140A  ASP*     4.9     4.0    -      -       -      +
    210A  PRO*     3.7    29.4    -      -       +      -
    212A  ILE      2.8     8.9    +      -       -      -
    213A  LEU*     3.7     6.8    -      -       +      +
    214A  THR*     2.8    30.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  VAL*     4.1    10.4    -      -       -      +
    111A  ALA*     1.3    73.5    -      -       -      +
    113A  PHE*     1.3    59.4    +      -       -      +
    138A  HIS*     3.5     0.3    -      -       -      -
    139A  TYR*     2.7    43.1    +      -       +      +
    214A  THR*     3.2    30.6    -      -       -      +
    215A  GLY*     4.4     2.6    -      -       -      +
    273A  TYR*     5.7     0.2    -      -       -      -
    328A  VAL*     3.6    20.7    -      -       +      +
    331A  VAL*     3.5    31.1    -      -       -      +
    332A  LEU*     3.4    31.4    -      -       +      +
    335A  ASP*     6.3     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  ASN*     1.3    75.5    -      -       -      +
    114A  ASP*     1.3    66.0    +      -       -      +
    115A  ILE*     4.0    18.4    -      -       +      -
    136A  ILE*     4.4     3.8    -      -       +      -
    137A  THR      3.2    13.7    -      -       -      +
    138A  HIS*     3.8    17.5    -      -       +      +
    201A  TYR*     3.6    20.9    -      +       -      -
    205A  TRP*     5.2     4.7    -      +       -      -
    213A  LEU*     3.7    36.1    -      -       +      -
    214A  THR      3.3    12.3    +      -       -      -
    215A  GLY*     3.9     7.9    -      -       -      -
    216A  TRP      4.5     0.7    +      -       -      -
    218A  VAL*     3.5    36.4    -      -       +      +
    222A  ALA*     3.8    25.4    -      -       +      -
    223A  ILE*     3.8    17.5    -      -       +      -
    226A  VAL*     4.3    11.7    -      -       +      -
    328A  VAL*     4.1     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PHE*     1.3    80.3    -      -       -      +
    115A  ILE*     1.3    65.2    +      -       -      +
    116A  GLU*     3.0    10.9    -      -       -      +
    136A  ILE*     3.6     2.3    -      -       -      +
    137A  THR      3.1    28.3    +      -       -      +
    216A  TRP*     4.4    17.9    +      -       -      +
    218A  VAL*     5.5     0.4    -      -       -      +
    222A  ALA*     5.2     3.4    -      -       -      -
    290A  LEU*     5.8     1.6    -      -       -      +
    324A  ASN*     3.1    12.7    -      -       -      +
    327A  ALA*     4.3    15.9    -      -       +      +
    328A  VAL*     3.7    19.1    -      -       +      +
   1003A   NA      2.5    28.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  PHE*     4.0    16.4    -      -       +      -
    114A  ASP*     1.3    80.4    +      -       -      +
    116A  GLU*     1.3    60.8    +      -       -      +
    117A  VAL*     3.9    14.8    -      -       +      -
    133A  ILE*     4.4     6.3    -      -       +      -
    135A  ALA      3.2     8.7    -      -       -      +
    136A  ILE*     3.9    16.4    -      -       +      -
    221A  PHE*     3.7    33.5    -      -       +      -
    222A  ALA*     4.1    14.9    -      -       +      +
    225A  TYR*     3.9    25.4    -      -       +      -
    226A  VAL*     3.9    23.1    -      -       +      -
   1003A   NA      2.7    24.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  ASP*     3.0     9.7    -      -       -      +
    115A  ILE*     1.3    71.1    -      -       -      +
    117A  VAL*     1.3    67.6    +      -       -      +
    133A  ILE*     3.7     2.4    -      -       -      +
    134A  ASP*     3.1    29.4    +      -       -      +
    135A  ALA*     2.8    20.2    +      -       +      +
    309A  ILE*     5.4     5.7    -      -       -      +
    320A  TYR*     3.1    37.2    +      -       +      +
    323A  TYR      5.3     0.2    -      -       -      -
    324A  ASN*     3.2    34.5    +      -       +      +
    327A  ALA*     5.4     1.2    -      -       -      +
   1003A   NA      2.5    24.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  ILE*     3.9    20.0    -      -       +      -
    116A  GLU*     1.3    81.0    +      -       -      +
    118A  THR*     1.3    61.3    +      -       -      +
    119A  SER*     3.4     3.5    +      -       -      -
    124A  PRO*     3.9    23.1    -      -       +      +
    131A  HIS*     3.6    13.2    -      -       +      -
    132A  PRO      3.6    15.0    -      -       -      +
    133A  ILE*     4.2     6.5    -      -       +      -
    221A  PHE*     4.2     9.5    -      -       +      -
    225A  TYR*     3.3    46.2    -      -       +      +
    320A  TYR*     3.8     2.7    +      -       -      -
----------------------------------------------------------
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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