Contacts of the strand formed by residues 112 - 124 (chain E) in PDB entry 4IHB


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 PRO 112 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104E  PRO*     5.3     2.9    -      -       +      -
    105E  LEU      3.4     9.6    -      -       -      +
    106E  LEU*     3.7    11.9    -      -       +      -
    107E  ASP*     4.8     1.0    -      -       -      +
    110E  LYS      4.1     1.1    -      -       -      +
    111E  GLN*     1.3    86.2    +      -       -      +
    113E  THR*     1.3    63.6    +      -       -      +
    114E  GLY      4.4     4.0    -      -       -      +
      0F  PHE*     6.1     1.6    -      -       -      -
     59F  LEU*     4.1     8.3    -      -       +      -
     92F  LEU*     4.3     7.0    -      -       +      -
     97F  LEU*     3.8    34.1    -      -       +      -
    123F  TYR*     3.6    50.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 113 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81E  LEU      3.5    22.3    +      -       -      +
     82E  GLY*     4.4     0.9    -      -       -      -
    105E  LEU*     2.9    25.4    +      -       -      +
    106E  LEU      3.8     2.2    -      -       -      +
    107E  ASP*     3.6    30.7    -      -       +      +
    112E  PRO*     1.3    73.0    -      -       -      +
    114E  GLY*     1.3    55.7    +      -       -      +
    115E  ALA*     3.0    25.3    +      -       -      +
    205E  FMT      3.5    27.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 114 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11E  ASN*     3.7    23.0    +      -       -      +
    105E  LEU      4.5     0.2    +      -       -      -
    112E  PRO*     3.2     8.2    -      -       -      +
    113E  THR*     1.3    78.8    -      -       -      +
    115E  ALA*     1.3    61.3    +      -       -      +
    116E  SER*     5.4     0.3    -      -       -      -
    205E  FMT      4.7     0.2    -      -       -      -
     95F  PRO*     6.1     1.0    -      -       -      +
     97F  LEU*     5.7     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 115 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E  GLU      3.2    10.3    -      -       -      +
     11E  ASN      3.2    20.4    +      -       -      +
     12E  VAL*     4.1     5.4    -      -       +      -
    104E  PRO*     3.6     4.2    -      -       -      +
    105E  LEU*     2.9    39.6    +      -       +      +
    113E  THR*     3.0    16.1    +      -       -      +
    114E  GLY*     1.3    82.0    +      -       -      +
    116E  SER*     1.3    62.9    +      -       -      +
    205E  FMT      3.7    11.7    -      -       -      +
     95F  PRO*     5.8     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 116 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  ALA*     3.1     7.3    -      -       -      +
     10E  GLU*     2.9    48.0    +      -       -      +
     11E  ASN*     5.5     1.4    +      -       -      -
    102E  ASN*     3.6    10.2    +      -       -      -
    103E  ALA      3.2    12.3    -      -       -      -
    104E  PRO*     4.2     0.4    -      -       -      -
    105E  LEU*     4.1     4.7    -      -       -      +
    114E  GLY      4.2     1.0    +      -       -      -
    115E  ALA*     1.3    76.9    -      -       -      +
    117E  LEU*     1.3    62.1    +      -       -      +
    118E  VAL*     5.4     1.5    -      -       -      +
     95F  PRO*     3.5    32.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 117 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  ILE*     4.1    13.5    -      -       +      -
      8E  TYR      3.4    15.9    -      -       -      +
      9E  ALA*     4.2     3.8    -      -       +      -
     24E  CYS*     4.2     5.2    -      -       -      -
     46E  TRP*     3.6    24.9    -      -       +      -
     67E  VAL*     3.3    35.2    -      -       +      -
     69E  VAL*     4.6     3.8    -      -       +      -
     84E  ALA*     5.0     4.0    -      -       +      -
    101E  PHE      3.3     2.9    -      -       -      +
    103E  ALA*     2.7    39.6    +      -       +      +
    105E  LEU*     3.8    23.1    -      -       +      -
    116E  SER*     1.3    74.7    -      -       -      +
    118E  VAL*     1.3    64.6    +      -       -      +
    119E  LEU*     3.7    25.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 118 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  ILE*     4.2     0.3    -      -       -      -
      7E  LEU*     3.1    38.3    +      -       +      -
      8E  TYR*     2.8    63.4    +      -       +      +
     10E  GLU*     5.7     0.4    -      -       +      +
    100E  SER*     6.2     2.0    -      -       -      -
    101E  PHE      3.3     7.4    -      -       -      +
    102E  ASN*     3.3    33.7    -      -       +      +
    116E  SER*     5.4     1.8    -      -       -      +
    117E  LEU*     1.3    73.3    -      -       -      +
    119E  LEU*     1.3    67.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  VAL*     4.3     5.4    -      -       +      -
      5E  PHE      3.2    16.2    -      -       -      +
      6E  ILE*     4.3     8.5    -      -       +      -
      7E  LEU*     4.5     2.9    -      -       -      +
     65E  LEU*     4.1    18.2    -      -       +      -
     67E  VAL*     4.6    11.0    -      -       +      -
     86E  VAL*     4.4    15.5    -      -       +      -
    100E  SER*     3.4     3.4    -      -       -      -
    101E  PHE*     2.7    57.3    +      -       +      +
    103E  ALA*     4.8     4.5    -      -       +      -
    117E  LEU*     3.7    35.7    -      -       +      +
    118E  VAL*     1.3    79.0    -      -       -      +
    120E  GLN*     1.3    57.7    +      -       -      +
    121E  VAL*     4.0    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 120 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3E  ARG*     4.3     2.3    +      -       -      +
      4E  VAL*     3.4     3.6    -      -       -      +
      5E  PHE*     2.8    68.3    +      -       +      +
      7E  LEU*     5.0     8.9    -      -       +      +
     98E  SER*     4.3    12.1    -      -       -      -
     99E  ALA      3.5    14.2    +      -       -      +
    100E  SER*     4.3    10.2    -      -       -      -
    119E  LEU*     1.3    74.6    -      -       -      +
    121E  VAL*     1.3    74.8    +      -       -      +
    122E  SER*     3.8    18.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 121 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2E  LEU*     3.6    27.4    -      -       +      -
      3E  ARG      3.3     3.6    -      -       -      -
      4E  VAL*     4.0    17.9    -      -       +      -
     65E  LEU*     4.2     5.8    -      -       +      -
     86E  VAL*     4.8     3.1    -      -       +      -
     88E  LEU*     4.6     7.4    -      -       +      -
     91E  VAL*     3.9    21.5    -      -       +      +
     98E  SER*     3.2     3.8    -      -       -      -
     99E  ALA      2.9    34.3    +      -       -      +
    101E  PHE*     4.1    13.9    -      -       +      -
    119E  LEU*     4.0    23.1    -      -       +      -
    120E  GLN*     1.3    84.0    +      -       -      +
    122E  SER*     1.3    65.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 122 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1E  MET      3.3     1.2    -      -       -      +
      2E  LEU*     3.4     7.2    -      -       -      +
      3E  ARG*     2.8    66.5    +      -       -      +
     91E  VAL*     4.1     2.0    -      -       -      -
     97E  LEU      3.2    14.1    -      -       -      -
     98E  SER*     3.5     4.9    -      -       -      -
    120E  GLN*     3.8     7.6    +      -       -      -
    121E  VAL*     1.3    78.3    -      -       -      +
    123E  TYR*     1.3    66.2    +      -       -      +
    201E  FMT      3.4    19.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 123 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112D  PRO*     3.9    23.1    -      -       +      -
      0E  PHE*     4.1    11.8    -      -       +      -
      1E  MET      3.1     5.8    -      -       -      +
      2E  LEU*     4.0    20.4    -      -       +      -
     28E  PHE*     5.9     0.4    -      +       -      -
     54E  LEU*     3.7    31.0    -      -       +      -
     59E  LEU*     3.5    25.6    -      -       +      +
     88E  LEU*     3.3    32.4    +      -       +      +
     91E  VAL*     3.5    28.5    -      -       +      -
     92E  LEU*     3.5    29.5    -      -       +      +
     97E  LEU*     2.9    29.3    +      -       +      +
    122E  SER*     1.3    73.4    -      -       -      +
    124E  THR*     1.3    59.6    +      -       -      +
    201E  FMT      3.8    13.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 124 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      0E  PHE*     3.4    10.2    -      -       -      -
      1E  MET*     2.7    51.9    +      -       +      +
      3E  ARG*     3.4    49.5    +      -       +      +
     51E  GLU*     4.0    10.5    -      -       -      +
    122E  SER*     4.5     0.2    -      -       -      -
    123E  TYR*     1.3    75.4    -      -       -      +
    125E  ALA*     1.3    72.2    +      -       -      +
    201E  FMT      4.6     3.9    +      -       -      -
----------------------------------------------------------
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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