Contacts of the strand formed by residues 109 - 121 (chain A) in PDB entry 1K4R


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 GLY 109 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PRO*     3.7    10.0    -      -       -      +
     98A  ASP*     3.7     3.5    -      -       -      +
     99A  ARG*     2.8    35.2    +      -       -      +
    107A  LEU      3.8     3.0    +      -       -      -
    108A  PHE*     1.3    74.0    -      -       -      +
    110A  LYS*     1.3    64.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PRO*     3.4    21.3    -      -       -      +
     96A  GLN*     3.9    45.2    +      -       +      +
     97A  SER      3.4     8.1    -      -       -      +
     98A  ASP*     2.8    32.0    +      -       -      +
    109A  GLY*     1.3    72.0    -      -       -      -
    111A  GLY*     1.3    60.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ARG      3.3    16.2    -      -       -      -
     74A  CYS      4.3     0.7    -      -       -      -
     75A  PRO*     4.1     6.1    -      -       -      -
     96A  GLN*     3.2     6.8    -      -       -      -
     97A  SER*     2.8    37.4    +      -       -      -
     99A  ARG*     4.0    10.1    -      -       -      +
    109A  GLY      3.7     1.6    +      -       -      -
    110A  LYS*     1.3    75.6    -      -       -      +
    112A  SER*     1.3    65.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  ALA*     3.2     2.9    -      -       -      +
     73A  ARG*     2.8    35.5    +      -       -      +
     74A  CYS      5.0     0.8    +      -       -      -
     78A  GLY      3.7    14.7    +      -       -      -
     79A  PRO*     3.9     4.3    -      -       -      -
     80A  ALA*     2.7    32.9    +      -       -      +
     94A  ARG*     3.5    13.9    +      -       -      -
     95A  ASP      3.9     7.4    +      -       -      -
     96A  GLN*     4.7     3.8    -      -       -      +
     97A  SER*     5.2     0.2    +      -       -      -
    111A  GLY*     1.3    72.7    -      -       -      -
    113A  ILE*     1.3    60.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  VAL*     3.9    14.1    -      -       +      -
     71A  ALA      3.3    11.4    -      -       -      +
     72A  ALA*     4.1     4.0    -      -       +      -
     80A  ALA*     4.2     1.6    -      -       -      -
     93A  LYS      4.1     0.2    -      -       -      +
     94A  ARG*     3.4     3.5    -      -       -      +
     95A  ASP*     2.8    52.0    +      -       +      +
     96A  GLN*     3.7     8.3    -      -       -      +
     97A  SER*     4.0     8.1    -      -       -      +
    112A  SER*     1.3    77.9    +      -       -      +
    114A  VAL*     1.3    64.5    +      -       -      +
    247A  PRO*     4.0    21.1    -      -       +      -
    249A  ALA      3.8    21.1    -      -       -      +
    250A  VAL*     3.8     6.1    -      -       -      -
    251A  LYS      3.8    29.4    -      -       -      +
    252A  MET*     4.3     9.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  VAL*     3.3     4.3    -      -       -      +
     71A  ALA*     2.9    52.9    +      -       +      +
     80A  ALA      3.8    20.9    -      -       -      +
     81A  THR      4.0     1.1    -      -       -      +
     82A  LEU*     3.7    10.2    -      -       +      +
     85A  GLU*     3.7    31.2    -      -       +      +
     92A  CYS*     4.5     2.0    -      -       +      -
     93A  LYS      3.3    13.9    -      -       -      +
     94A  ARG*     3.8    19.7    -      -       +      +
    113A  ILE*     1.3    76.9    -      -       -      +
    115A  ALA*     1.3    66.7    +      -       -      +
    116A  CYS*     4.4     4.9    -      -       -      -
    252A  MET*     4.0     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  THR*     5.5     0.4    -      -       +      -
     69A  LYS      3.2     9.4    -      -       -      +
     70A  VAL*     3.9    16.2    -      -       +      -
     92A  CYS*     3.1     3.8    -      -       -      +
     93A  LYS      2.9    32.5    +      -       -      -
    114A  VAL*     1.3    74.3    -      -       -      +
    116A  CYS*     1.3    61.4    +      -       -      +
    244A  PHE*     3.9    15.5    -      -       +      -
    252A  MET*     3.2    31.1    -      -       +      +
    254A  VAL*     5.0     3.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  ASP      3.8     2.0    -      -       -      +
     68A  THR*     3.4     5.8    -      -       -      +
     69A  LYS*     2.8    33.1    +      -       +      +
     82A  LEU*     3.8    19.5    -      -       +      -
     84A  GLU*     3.8    26.5    -      -       +      -
     85A  GLU*     4.0    11.0    -      -       -      -
     90A  THR*     4.8     0.2    -      -       -      -
     91A  VAL      3.2     6.1    -      -       -      -
     92A  CYS*     2.0    45.5    -      -       -      -
    114A  VAL*     4.4     0.9    -      -       -      -
    115A  ALA*     1.3    74.9    -      -       -      +
    117A  VAL*     1.3    63.0    +      -       -      +
    244A  PHE*     4.9     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  LEU*     4.4    24.2    -      -       +      -
     66A  SER      3.8     7.6    -      -       -      +
     67A  ASP      4.4     1.8    -      -       -      -
     68A  THR*     3.3    35.0    -      -       +      +
     84A  GLU*     6.3     0.2    -      -       -      -
     90A  THR*     3.1     6.0    -      -       -      -
     91A  VAL*     2.8    46.8    +      -       +      +
    116A  CYS*     1.3    76.8    -      -       -      +
    118A  LYS*     1.3    68.0    +      -       -      +
    242A  VAL*     4.5     2.2    -      -       +      -
    244A  PHE*     4.4     4.9    -      -       +      -
    254A  VAL*     3.8    29.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  LYS      3.7     0.9    -      -       -      +
     65A  LEU*     3.3     8.0    -      -       -      +
     66A  SER*     2.9    46.9    +      -       -      +
     67A  ASP*     3.0    38.5    +      -       +      +
     69A  LYS*     6.3     1.1    -      -       -      -
     84A  GLU*     5.5     7.9    -      -       +      +
     87A  GLN*     5.8     2.5    -      -       -      +
     89A  GLY      3.4     7.4    -      -       -      +
     90A  THR*     3.9    19.7    -      -       +      +
    117A  VAL*     1.3    73.5    -      -       -      +
    119A  ALA*     1.3    58.8    +      -       -      +
    120A  ALA*     4.2     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ALA*     5.5     2.7    -      -       +      -
     64A  LYS      3.8     2.7    -      -       -      -
     65A  LEU*     3.9    16.2    -      -       +      -
     89A  GLY*     2.9    25.2    +      -       -      +
     91A  VAL*     3.9    15.5    -      -       +      -
    117A  VAL      3.6     1.0    +      -       -      +
    118A  LYS*     1.3    72.0    -      -       -      +
    120A  ALA*     1.3    62.3    +      -       -      +
    234A  ASN*     5.6     0.9    -      -       -      +
    235A  TRP*     4.2    11.4    +      -       -      +
    238A  ALA*     3.8    27.8    -      -       +      -
    242A  VAL*     5.3     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  CYS*     4.4     1.8    -      -       -      -
     63A  ALA*     3.4     9.9    -      -       -      +
     64A  LYS*     2.9    40.5    +      -       +      +
    118A  LYS      5.7     0.4    -      -       -      -
    119A  ALA*     1.3    74.3    -      -       -      +
    121A  CYS*     1.3    64.7    +      -       -      +
    235A  TRP*     4.1    12.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  CYS*     2.0    52.7    -      -       -      -
     62A  HIS      3.7     1.3    -      -       -      -
     64A  LYS*     4.1     8.9    -      -       -      +
    120A  ALA*     1.3    80.4    -      -       -      +
    122A  GLU*     1.3    71.8    +      -       -      +
    123A  ALA*     3.6     1.6    +      -       -      -
    125A  LYS      3.6    16.6    -      -       -      -
    126A  LYS*     4.5     6.5    -      -       +      -
    235A  TRP*     3.5    26.6    -      -       +      +
----------------------------------------------------------
 Back to top of page


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