Contacts of the strand formed by residues 24 - 31 (chain A) in PDB entry 4ICK


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 ILE 24 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.9    25.1    -      -       +      -
     12A  ARG      3.5     3.6    -      -       -      -
     13A  ARG*     4.3    13.7    -      -       +      +
     22A  ASN*     3.5    16.8    -      -       -      +
     23A  ALA*     1.3    84.6    -      -       +      +
     25A  GLU*     1.3    63.4    +      -       -      +
     26A  PHE*     3.9    29.2    -      -       +      -
    118A  GLY*     3.8     6.8    -      -       -      -
    119A  LEU      4.5     2.9    +      -       -      -
    139A  HIS*     3.5    27.1    -      -       +      +
    142A  LEU*     4.0    22.4    -      -       +      -
    143A  CYS*     4.6     5.6    -      -       -      -
    146A  GLU*     4.0    18.4    -      -       -      +
    201A  GOL      3.3    11.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  PHE*     3.0     6.3    -      -       -      +
     12A  ARG*     2.9    77.0    +      -       +      +
     14A  CYS*     3.4    21.0    -      -       -      +
     20A  ASP*     5.8     0.3    -      -       -      +
     22A  ASN*     4.4    14.5    +      -       +      +
     24A  ILE*     1.3    77.1    -      -       -      +
     26A  PHE*     1.3    62.6    +      -       -      +
    101A  TYR*     4.5     2.4    +      -       -      -
    116A  TRP*     3.7    15.4    -      -       +      +
    117A  LEU*     3.3    21.3    -      -       -      +
    118A  GLY      4.0     3.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  ILE*     3.6    32.1    -      -       +      -
     10A  ILE      3.4     7.4    -      -       -      +
     11A  PHE*     4.1    13.2    -      -       +      -
     24A  ILE*     3.9    20.2    -      -       +      -
     25A  GLU*     1.3    73.7    -      -       -      +
     27A  LEU*     1.3    63.2    -      -       -      +
     28A  LEU*     3.7     4.2    +      -       +      +
     95A  LEU*     4.7     7.4    -      -       +      -
    115A  ARG      3.4     2.6    -      -       -      +
    116A  TRP*     3.3     5.9    -      -       -      -
    117A  LEU*     2.7    40.6    +      -       -      +
    119A  LEU*     3.9    38.4    -      -       +      -
    122A  ALA*     4.3    13.7    -      -       +      -
    135A  LEU*     3.9    30.5    -      -       +      -
    138A  GLY*     5.2     0.4    -      -       -      -
    139A  HIS*     3.9    17.3    -      +       +      -
    142A  LEU*     4.9     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  ILE*     2.9    29.0    +      -       +      +
     26A  PHE*     1.3    71.3    -      -       -      +
     28A  LEU*     1.3    69.2    +      -       -      +
     29A  LEU*     4.0    16.4    -      -       +      -
     40A  PRO*     3.7    18.2    -      -       -      +
     41A  PRO*     4.3     6.1    -      -       +      +
     63A  ALA*     4.2     6.5    -      -       +      -
     65A  ILE*     3.9    28.5    -      -       +      -
    105A  ILE*     3.9    10.8    -      -       +      -
    114A  TYR*     3.7    38.6    -      -       +      -
    115A  ARG      3.4     7.2    -      -       -      +
    116A  TRP*     3.6    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  PHE*     4.7     5.4    -      -       +      +
     27A  LEU*     1.3    79.9    -      -       -      +
     29A  LEU*     1.3    64.6    +      -       -      +
     38A  TRP*     3.8    20.5    -      -       +      +
     39A  THR*     3.6    25.8    -      -       -      +
     40A  PRO*     3.6    14.6    -      -       +      -
    114A  TYR*     3.2     5.5    -      -       -      +
    115A  ARG*     2.8    35.3    +      -       +      +
    117A  LEU*     5.0     3.6    -      -       +      -
    122A  ALA*     3.5    39.9    -      -       +      +
    125A  LEU*     4.2    14.6    -      -       +      -
    126A  ALA*     4.1    12.6    -      -       +      +
    135A  LEU*     4.7    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  LEU*     4.0    20.9    -      -       +      -
     28A  LEU*     1.3    75.5    -      -       -      +
     30A  GLN*     1.3    60.3    +      -       -      +
     31A  ALA      3.8     0.7    +      -       -      -
     37A  HIS      3.5     1.7    -      -       -      +
     38A  TRP*     3.3     4.9    -      -       -      -
     39A  THR*     2.8    37.4    +      -       -      +
     40A  PRO      5.2     0.4    -      -       -      +
     41A  PRO*     4.2    21.5    -      -       +      -
     62A  GLU*     3.7    40.2    -      -       +      +
     63A  ALA*     4.4     3.4    -      -       +      -
    105A  ILE*     4.7     1.1    -      -       +      -
    107A  LEU*     3.9    11.7    -      -       +      -
    111A  HIS*     3.6    28.2    -      -       +      +
    113A  ALA      3.5     4.7    -      -       -      +
    114A  TYR*     3.8    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  LEU*     1.3    71.8    -      -       -      +
     31A  ALA*     1.3    64.8    +      -       -      +
     36A  HIS*     3.7    31.6    +      -       +      +
     37A  HIS      3.3     3.4    -      -       -      -
     38A  TRP*     3.4    50.4    -      -       +      +
    111A  HIS*     3.2     5.5    -      -       -      -
    112A  GLN*     2.8    56.6    +      -       -      +
    113A  ALA*     2.9    23.9    +      -       -      +
    115A  ARG*     5.6     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  GLN*     1.3    76.5    -      -       -      +
     32A  SER*     1.3    58.5    +      -       -      +
     33A  ASP*     3.4    17.5    -      -       -      +
     36A  HIS*     3.1    27.2    +      -       -      +
     37A  HIS*     2.8    31.9    +      -       +      +
    110A  GLU      3.6     9.2    -      -       -      +
    111A  HIS*     3.6    11.1    -      -       +      +
    112A  GLN*     3.8     2.6    -      -       -      +
----------------------------------------------------------
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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