Contacts of the strand formed by residues 110 - 118 (chain U) in PDB entry 1IR1


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 U).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155C  ILE*     5.7     0.2    -      -       +      -
    156C  GLN*     3.6    28.7    -      -       +      -
    159C  ARG*     4.3    18.8    -      -       +      +
    160C  ASP*     5.7     3.1    -      -       -      -
    165C  TYR*     4.8     3.1    -      -       +      -
    104U  PHE*     4.9     3.1    -      -       -      -
    105U  ASP*     3.0    27.3    +      -       -      +
    108U  ARG*     3.6    50.5    -      -       +      +
    109U  GLN*     1.3    82.8    -      -       -      +
    111U  GLN*     1.3    78.1    +      -       -      +
    112U  CYS*     3.3     5.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 111 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159C  ARG*     5.0     1.2    -      -       -      -
    160C  ASP*     5.4     1.5    +      -       -      +
    165C  TYR*     3.1    67.7    -      -       +      +
    166C  GLY      4.6     0.2    +      -       -      -
    183D  LYS*     3.7     9.5    -      -       +      +
    187D  ARG*     3.1    33.0    +      -       -      +
     43U  GLU*     5.0     1.9    +      -       -      +
    100U  ARG*     6.4     0.4    -      -       -      -
    102U  ILE*     3.9    31.2    -      -       +      +
    103U  GLY      3.3     9.4    -      -       -      +
    104U  PHE*     3.7    21.8    -      -       +      +
    110U  VAL*     1.3    77.0    -      -       -      +
    112U  CYS*     1.3    59.1    +      -       -      +
    113U  VAL      3.4     5.4    -      -       -      +
    114U  SER*     4.4     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 112 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166C  GLY*     3.3    22.9    -      -       -      +
    396C  ASP*     4.5     7.2    -      -       -      +
     32U  TYR*     5.4     1.2    -      -       -      -
     38U  TRP*     3.7    41.5    -      -       +      -
    103U  GLY      2.9     6.8    +      -       -      +
    105U  ASP*     3.7    31.9    -      -       -      -
    108U  ARG*     4.0    20.0    -      -       -      -
    110U  VAL*     3.3     6.0    +      -       -      -
    111U  GLN*     1.3    74.8    -      -       -      +
    113U  VAL*     1.3    64.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 113 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165C  TYR*     4.8     1.3    -      -       -      -
    166C  GLY*     4.7     2.7    -      -       -      -
    432C  ASN*     6.0     0.4    -      -       -      +
     29U  GLN*     5.4     4.5    -      -       -      +
     32U  TYR*     4.1    15.0    -      -       +      -
     33U  LEU*     4.2    22.0    -      -       +      -
     38U  TRP*     3.6    28.9    -      -       +      -
    101U  ILE      4.3     2.2    -      -       -      +
    102U  ILE*     3.1     5.0    -      -       -      +
    103U  GLY*     2.9    31.6    +      -       -      +
    111U  GLN*     3.4     4.2    -      -       -      +
    112U  CYS*     1.3    86.3    -      -       -      +
    114U  SER*     1.3    70.0    +      -       -      +
    115U  PHE*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 114 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165C  TYR*     4.0    35.7    +      -       -      +
    166C  GLY*     5.1     1.0    -      -       -      -
     13U  GLU*     5.4     2.9    -      -       -      +
     14U  THR*     3.7    22.4    +      -       -      +
    100U  ARG*     4.2    12.3    +      -       -      -
    101U  ILE      3.3     7.9    -      -       -      -
    102U  ILE*     3.7    16.3    -      -       -      +
    111U  GLN*     4.4     1.1    +      -       -      -
    113U  VAL*     1.3    80.0    -      -       -      +
    115U  PHE*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 115 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12U  TYR      5.2     2.9    -      -       -      -
     14U  THR*     3.6    19.7    -      -       +      +
     15U  LEU*     4.0    16.4    -      -       +      -
     21U  LEU*     4.2    15.9    -      -       +      -
     26U  LEU*     3.5    29.6    -      -       +      -
     29U  GLN*     3.8    28.3    -      -       +      -
     30U  VAL*     4.8     4.9    -      -       +      -
     33U  LEU*     5.7     0.9    -      -       +      -
    100U  ARG*     3.3     5.7    -      -       -      +
    101U  ILE*     3.0    58.8    +      -       +      -
    113U  VAL*     3.7    28.9    -      -       +      -
    114U  SER*     1.3    75.7    +      -       -      +
    116U  ILE*     1.3    73.6    +      -       -      +
    117U  ALA*     4.4     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 116 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12U  TYR*     3.6    48.8    +      -       +      +
     14U  THR      5.0     1.0    +      -       -      -
     21U  LEU*     5.2     4.0    -      -       -      +
     67U  TRP*     4.1    24.0    -      -       +      -
     98U  PHE*     4.9     3.4    -      -       +      -
     99U  ILE      3.7     9.2    -      -       -      +
    100U  ARG*     4.0    13.7    -      -       +      +
    115U  PHE*     1.3    81.4    -      -       -      +
    117U  ALA*     1.3    60.5    +      -       -      +
    118U  TYR      3.9     9.4    -      -       -      +
    119U  LYS*     3.5    36.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 117 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21U  LEU*     6.3     0.2    -      -       -      -
     26U  LEU*     4.4    12.2    -      -       +      +
     87U  LEU*     4.2    22.6    -      -       +      +
     91U  LYS*     5.8     0.5    +      -       -      +
     99U  ILE      2.8    10.9    +      -       -      +
    101U  ILE*     3.9    34.5    -      -       +      -
    115U  PHE*     3.4     9.3    +      -       +      +
    116U  ILE*     1.3    75.3    -      -       -      +
    118U  TYR*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 118 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87U  LEU*     4.7     1.8    -      -       +      -
     91U  LYS*     3.7    39.7    -      -       +      -
     94U  TYR      4.2     4.5    -      -       -      -
     95U  PRO*     2.7    38.4    +      -       +      +
     97U  ALA      3.2    27.4    -      -       -      -
     98U  PHE*     3.6     2.6    -      -       -      +
     99U  ILE*     3.0    50.5    +      -       +      +
    116U  ILE*     3.6     3.1    -      -       -      +
    117U  ALA*     1.3    82.0    -      -       -      +
    119U  LYS*     1.3    88.5    +      -       -      +
    120U  PRO*     4.2     2.4    -      -       -      +
    121U  ALA      4.9     1.6    +      -       -      -
----------------------------------------------------------
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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