Contacts of the strand formed by residues 111 - 117 (chain A) in PDB entry 4K8T


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 ALA 111 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  ALA      3.4    20.0    +      -       -      +
     11A  ILE*     3.5    14.6    -      -       +      -
     12A  VAL*     3.2    21.0    +      -       -      +
     78A  ASN      5.7     0.4    +      -       -      -
     84A  LEU*     5.0     0.7    -      -       -      +
    109A  PRO      3.4     3.2    +      -       -      -
    110A  THR*     1.3    84.2    -      -       -      +
    112A  ARG*     1.3    61.0    +      -       -      +
    128A  TYR      3.3    13.2    -      -       -      +
    129A  LEU*     3.1    25.2    +      -       -      +
    130A  GLY*     4.5     0.9    -      -       -      +
    131A  ALA*     4.2     2.6    -      -       -      +
    132A  CYS*     3.6     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ILE*     4.0     3.8    -      -       -      -
     12A  VAL*     3.1    14.4    -      -       +      +
     14A  ILE*     3.9    24.0    -      -       +      -
     41A  ALA*     5.3     0.2    -      -       -      -
     84A  LEU*     3.6    26.5    -      -       +      +
    109A  PRO*     3.5    24.4    -      -       -      +
    110A  THR      2.8    30.5    +      -       -      -
    111A  ALA*     1.3    75.5    -      -       -      +
    113A  SER*     1.3    61.8    +      -       -      +
    114A  MSE      5.3     4.7    -      -       +      -
    126A  ASN      3.9     1.0    -      -       -      +
    127A  THR*     3.6     1.2    -      -       -      +
    128A  TYR*     2.9    47.4    +      -       -      +
    402A  E34      3.3    19.9    -      -       -      -
    403A  DMS      3.0    41.4    +      -       -      +
     83B  GLN*     3.9     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ILE*     3.7    17.7    -      -       -      +
     12A  VAL      3.1     7.1    +      -       -      -
     13A  ASP*     3.4    10.5    -      -       -      -
     14A  ILE*     2.9    25.8    +      -       -      -
    112A  ARG*     1.3    75.3    -      -       -      +
    114A  MSE      1.3    62.4    +      -       -      +
    115A  ILE*     3.4     7.3    +      -       -      +
    125A  MSE      3.6    11.1    -      -       -      +
    126A  ASN      3.4    15.1    +      -       -      -
    127A  THR*     2.8    25.2    +      -       -      -
    401A  ADN      3.8     5.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MSE 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ILE*     3.3    21.3    -      -       +      -
     36A  ILE*     3.8    17.0    -      -       +      -
     41A  ALA*     3.1    40.6    -      -       +      +
     44A  LEU*     3.8    13.2    -      -       +      +
     45A  TYR*     3.6    37.9    -      -       -      -
     48A  MSE      3.8    22.9    -      -       +      +
    112A  ARG*     4.2     3.8    -      -       +      -
    113A  SER*     1.3    70.2    -      -       -      +
    115A  ILE*     1.3    60.3    +      -       -      +
    116A  PHE*     4.0     8.1    -      -       +      -
    126A  ASN*     2.9    45.4    +      -       +      +
    403A  DMS      4.2     6.7    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
     13A  ASP*     3.4    38.6    -      -       +      +
     14A  ILE      2.8    11.7    +      -       -      +
     15A  ILE*     3.5    12.9    -      -       +      +
     16A  SER      3.0    27.0    +      -       -      +
     48A  MSE      3.8     1.6    -      -       -      +
    113A  SER*     3.6    19.1    -      -       -      +
    114A  MSE      1.3    71.9    -      -       -      +
    116A  PHE*     1.3    62.7    -      -       -      +
    117A  VAL*     3.9     7.1    +      -       +      -
    123A  ARG*     3.7    31.9    -      -       +      -
    124A  SER      3.5     2.7    -      -       -      +
    125A  MSE      3.9    26.2    -      -       +      -
    272A  THR*     3.7    13.7    -      -       +      +
    401A  ADN      4.0     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  SER*     3.3    10.5    -      -       -      -
     17A  ARG      5.5     0.2    -      -       -      -
     18A  CYS*     3.6    25.7    -      -       +      -
     22A  PHE*     3.4    40.6    -      +       -      -
     23A  LEU*     4.3     7.8    -      -       +      +
     28A  ILE*     4.1    12.3    -      -       +      -
     44A  LEU*     4.4    13.0    -      -       +      -
     48A  MSE      3.6    44.4    -      -       +      -
     49A  GLY      5.2     0.7    -      -       -      -
    114A  MSE      3.9    15.5    -      -       +      -
    115A  ILE*     1.3    72.7    -      -       -      +
    117A  VAL*     1.3    61.2    +      -       -      +
    118A  THR*     4.0     2.3    +      -       -      +
    122A  GLU      3.6     1.4    -      -       -      +
    123A  ARG*     3.5     2.3    -      -       -      -
    124A  SER*     2.9    34.6    +      -       -      +
    126A  ASN*     3.4    28.7    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
     15A  ILE*     4.2    19.7    -      -       +      -
     16A  SER      2.8    12.9    +      -       -      +
     17A  ARG*     3.2    34.1    -      -       -      +
     18A  CYS      3.0    22.2    +      -       -      -
    115A  ILE*     4.4     3.6    -      -       +      -
    116A  PHE*     1.3    76.1    -      -       -      +
    118A  THR*     1.3    71.8    +      -       -      +
    121A  GLY      4.1     8.1    -      -       -      +
    122A  GLU      3.3     7.9    -      -       -      +
    123A  ARG*     4.3     8.3    -      -       +      -
    269A  VAL      3.7    11.7    -      -       -      +
    270A  ASP*     3.4    30.1    -      -       +      +
----------------------------------------------------------
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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