Contacts of the strand formed by residues 103 - 112 (chain A) in PDB entry 4FQX


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 ASN 103 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  THR*     3.7     6.5    -      -       -      -
     94A  ASN*     3.5     7.0    +      -       -      +
     95A  SER*     3.1    55.5    +      -       -      +
     96A  PRO      3.4    12.7    +      -       -      -
     97A  VAL*     3.8    11.4    -      -       -      +
     98A  GLU      4.8     0.4    -      -       -      +
    101A  GLU*     3.8     9.1    +      -       -      +
    102A  PRO*     1.3    75.4    +      -       -      +
    104A  VAL*     1.3    81.6    +      -       -      +
    152A  PRO*     3.3     1.9    -      -       -      +
    153A  PHE*     2.7    48.1    +      -       +      +
    155A  PRO*     4.3     2.5    -      -       +      -
    190C  TYR*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  THR*     3.3     3.3    -      -       -      -
     94A  ASN*     2.8    55.4    +      -       +      +
    103A  ASN*     1.3    91.5    +      -       -      +
    105A  LEU*     1.3    75.2    +      -       -      +
    106A  ILE*     3.6     3.2    +      -       +      +
    150A  TYR*     4.1    18.6    -      -       +      -
    151A  LEU      3.6    16.4    -      -       -      +
    152A  PRO*     4.1    13.9    -      -       +      -
    153A  PHE*     3.8     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  VAL*     4.2    11.4    -      -       +      -
     92A  LEU      3.7     2.0    -      -       -      +
     93A  THR*     3.8    22.7    -      -       +      -
    104A  VAL*     1.3    73.1    -      -       -      +
    106A  ILE*     1.3    58.8    +      -       -      +
    121A  TRP*     3.4    23.7    -      -       +      -
    149A  HIS      3.6     0.3    -      -       -      +
    150A  TYR*     3.2     7.3    -      -       -      -
    151A  LEU*     2.9    38.7    +      -       +      +
    153A  PHE*     3.6    15.8    -      -       +      -
    161A  TYR*     3.4    51.4    -      -       +      -
    178A  TRP*     3.8    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  THR      3.7     0.9    -      -       -      +
     91A  VAL*     3.4     4.7    -      -       -      +
     92A  LEU*     2.7    40.0    +      -       +      +
     94A  ASN*     4.2    22.4    -      -       -      +
    104A  VAL*     4.1     9.0    -      -       +      +
    105A  LEU*     1.3    77.0    -      -       -      +
    107A  CYS*     1.3    62.3    +      -       -      +
    108A  PHE*     3.5    24.0    -      -       +      -
    121A  TRP*     4.1     2.7    -      -       -      -
    148A  PHE*     4.2     8.5    -      -       +      -
    149A  HIS      3.4     4.7    -      -       -      +
    150A  TYR*     3.8    30.7    -      -       +      -
    150B  ASN*     3.3    42.8    -      -       +      +
    152B  ASP*     6.0     0.4    -      -       -      +
    156B  GLN*     4.2     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  VAL*     3.8    19.1    -      -       -      -
     90A  THR      3.5     2.9    -      -       -      -
     91A  VAL*     4.2     2.7    -      -       +      -
    106A  ILE*     1.3    73.5    -      -       -      +
    108A  PHE*     1.3    60.8    +      -       -      +
    109A  ILE*     3.4    16.0    -      -       -      +
    121A  TRP*     3.7    16.7    -      -       +      -
    148A  PHE*     3.4     7.3    -      -       -      +
    149A  HIS*     2.8    37.3    +      -       +      +
    163A  CYS*     2.0    48.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  GLU      3.5     1.6    -      -       -      +
     89A  VAL*     3.2     7.3    -      -       -      +
     90A  THR*     2.7    53.8    +      -       -      +
     92A  LEU*     3.3    42.2    -      -       +      -
    106A  ILE*     3.5    20.6    -      -       +      -
    107A  CYS*     1.3    74.2    -      -       -      +
    109A  ILE*     1.3    61.5    +      -       -      +
    110A  ASP*     4.0     6.0    -      -       +      +
    147A  LYS      3.7     4.5    -      -       -      +
    148A  PHE*     3.4    24.5    -      +       +      -
    148B  ILE*     3.7    18.8    -      -       +      -
    149B  GLN      3.2    25.4    -      -       -      -
    150B  ASN*     4.2     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  PRO*     3.6    29.2    -      -       +      -
     88A  GLU      3.6     2.2    -      -       -      -
     89A  VAL*     4.4     2.7    -      -       +      -
    107A  CYS*     3.4    33.9    -      -       -      +
    108A  PHE*     1.3    73.6    -      -       -      +
    110A  ASP*     1.3    60.6    +      -       -      +
    112A  PHE*     3.4    15.9    -      -       +      -
    117A  VAL*     4.4     6.5    -      -       +      -
    119A  VAL*     4.1    10.5    -      -       +      -
    146A  ARG*     3.2     4.9    -      -       -      +
    147A  LYS*     2.8    52.1    +      -       +      +
    149A  HIS*     3.8    24.0    -      -       -      +
    165A  VAL*     4.2    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  PRO*     3.1     4.0    -      -       -      +
     88A  GLU*     2.7    47.6    +      -       +      +
    108A  PHE*     5.1     6.7    -      -       +      +
    109A  ILE*     1.3    76.6    -      -       -      +
    111A  LYS*     1.3    91.7    +      -       +      +
    112A  PHE*     3.4     3.4    -      -       -      -
    140A  ARG*     3.0    27.6    +      -       -      -
    145A  PHE      3.7     1.6    -      -       -      -
    146A  ARG*     3.0    23.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  VAL*     3.6    11.6    -      -       -      +
     86A  PRO      3.5    13.9    -      -       -      +
     88A  GLU*     2.8    41.2    +      -       -      +
    110A  ASP*     1.3   100.2    +      -       +      +
    112A  PHE*     1.3    57.7    +      -       -      +
    140A  ARG*     3.5    32.1    -      -       -      +
    142A  ASP*     5.4     1.1    -      -       -      +
    144A  LEU*     3.6    22.9    -      -       +      -
    145A  PHE      3.1     6.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  VAL*     3.2    15.3    -      -       -      +
     87A  PRO*     3.6    31.9    -      -       +      -
    109A  ILE*     3.4    31.0    -      -       +      -
    110A  ASP      3.8     5.2    -      -       -      -
    111A  LYS*     1.3    79.4    -      -       -      +
    113A  THR*     1.3    62.5    +      -       -      +
    114A  PRO      3.7    16.6    -      -       -      -
    115A  PRO*     4.1     2.9    -      -       +      -
    117A  VAL*     3.9    16.2    -      -       +      -
    137A  PHE*     3.9    34.3    -      +       -      -
    144A  LEU*     3.8     4.8    -      -       -      +
    145A  PHE*     2.9    45.7    +      -       +      -
    146A  ARG*     3.9     1.8    -      -       -      -
    147A  LYS*     4.4     7.6    -      -       +      -
    167A  HIS*     3.8    11.2    -      +       -      +
----------------------------------------------------------
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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