Contacts of the strand formed by residues 34 - 43 (chain A) in PDB entry 1LHR


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 GLU 34 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  GLU*     5.9     5.7    -      -       +      +
      5A  CYS      2.9    16.3    +      -       -      +
      6A  ARG*     3.3    47.1    +      -       +      +
      7A  VAL*     2.6    34.3    +      -       -      +
     32A  GLY      4.1     0.8    +      -       -      -
     33A  PHE*     1.3    70.1    -      -       -      +
     35A  VAL*     1.3    55.6    +      -       -      +
     36A  ASP*     4.5     0.7    -      -       -      +
     17B  GLY      5.5     0.5    +      -       -      -
     18B  TYR*     2.4    43.4    +      -       -      -
     22B  ARG*     4.6     2.9    +      -       -      -
    291B  LEU      5.4     0.9    -      -       -      +
    292B  ARG*     5.3     3.3    -      -       -      -
    293B  MET      5.8     0.3    +      -       -      -
    294B  VAL*     4.8     7.5    +      -       -      +
    295B  GLN*     3.9    24.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  VAL*     3.4     8.3    -      -       +      +
      9A  SER*     4.4    14.1    -      -       -      -
     24A  ALA      5.9     0.2    -      -       -      -
     25A  THR*     4.0    32.1    -      -       +      +
     28A  LEU*     3.5    38.8    -      -       +      -
     29A  GLN*     4.3    11.6    +      -       +      +
     33A  PHE*     3.5    11.3    +      -       +      +
     34A  GLU*     1.3    79.3    +      -       -      +
     36A  ASP*     1.3    73.4    +      -       -      +
     37A  ALA*     4.4     2.7    -      -       +      +
     18B  TYR*     4.7     3.1    +      -       -      -
     22B  ARG*     2.8    33.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ARG*     2.8    30.6    +      -       -      +
      7A  VAL      2.7     8.5    +      -       -      +
      8A  LEU*     3.5     4.6    -      -       +      +
      9A  SER      2.8    26.0    +      -       -      +
     34A  GLU*     4.1     1.6    +      -       -      +
     35A  VAL*     1.3    76.5    -      -       -      +
     37A  ALA*     1.3    60.3    +      -       -      +
     77A  TYR*     2.6    45.9    +      -       +      +
     15B  VAL*     3.0    23.9    -      -       +      +
     16B  ARG*     3.5    18.6    +      -       -      +
     17B  GLY      4.7     0.2    +      -       -      -
     22B  ARG*     4.2     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  SER      3.4     3.6    -      -       -      +
     21A  ASN*     3.6    23.1    -      -       +      +
     25A  THR*     4.3    12.8    -      -       +      +
     35A  VAL*     3.7     5.1    +      -       +      -
     36A  ASP*     1.3    73.0    -      -       -      +
     38A  VAL*     1.3    62.3    +      -       -      +
     39A  ASN*     4.4     5.4    -      -       -      +
     13B  HIS*     3.0    32.0    +      -       +      -
     15B  VAL*     3.2    16.8    +      -       -      +
     22B  ARG*     4.0    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  LEU*     4.0    16.8    -      -       +      -
      9A  SER      2.9     6.1    +      -       -      -
     10A  ILE*     3.4    28.6    -      -       +      -
     11A  GLN      3.1    15.6    +      -       -      +
     21A  ASN*     3.0    12.3    -      -       -      +
     37A  ALA*     1.3    73.8    -      -       -      +
     39A  ASN*     1.3    67.7    +      -       -      +
     40A  SER      3.5     0.2    +      -       -      -
     57A  LEU*     4.4     4.7    -      -       +      -
     62A  LEU*     4.0    19.1    -      -       +      -
     65A  LEU*     4.1    22.7    -      -       +      -
     66A  TYR*     6.2     0.7    -      -       -      +
     69A  LEU*     5.5     2.5    -      -       +      -
     15B  VAL*     3.4    28.5    -      -       +      -
     42B  GLN*     3.7     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLN      3.2     4.3    -      -       -      -
     13A  HIS*     3.4    32.7    +      -       +      +
     21A  ASN*     3.3    21.7    -      -       -      +
     37A  ALA*     4.4     5.0    -      -       -      +
     38A  VAL*     1.3    70.4    -      -       -      +
     40A  SER*     1.3    65.7    +      -       -      +
     41A  VAL*     3.1     8.3    +      -       -      +
     42A  GLN*     5.6     2.0    -      -       +      -
     57A  LEU*     3.5     9.6    -      -       -      +
     13B  HIS*     3.5    24.8    +      -       -      -
     39B  ASN*     3.3    28.5    -      -       -      +
     42B  GLN*     2.7    30.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  ILE*     4.8     0.7    -      -       -      -
     11A  GLN*     2.9    30.2    +      -       -      -
     12A  SER*     3.1     2.1    +      -       -      -
     38A  VAL*     3.5     3.8    +      -       -      +
     39A  ASN*     1.3    71.4    -      -       -      +
     41A  VAL*     1.3    67.5    +      -       -      +
     56A  VAL*     4.2     0.2    -      -       -      +
     57A  LEU*     3.0    28.9    +      -       -      +
     84A  TYR      5.0     0.4    +      -       -      -
     90A  PHE*     3.6    35.9    -      -       -      -
    123A  GLU*     3.0    25.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  SER*     3.3    29.8    -      -       -      -
     13A  HIS*     3.0    25.8    +      -       -      +
     39A  ASN*     3.1     8.2    -      -       -      +
     40A  SER*     1.3    87.4    +      -       -      +
     42A  GLN*     1.3    63.6    +      -       -      +
     43A  PHE*     3.9     7.0    -      -       +      -
     55A  GLN      3.5    11.2    -      -       -      +
     56A  VAL*     3.6    30.5    -      -       +      +
     57A  LEU*     4.4     1.6    -      -       -      +
    122A  GLY      3.3    17.7    -      -       -      +
    123A  GLU*     3.8    24.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  HIS*     3.2    26.9    -      -       +      -
     15A  VAL*     4.6     2.1    -      -       +      +
     39A  ASN*     5.6     1.8    -      -       +      -
     41A  VAL*     1.3    76.7    -      -       -      +
     43A  PHE*     1.3    63.0    +      -       -      +
     54A  GLY*     3.1     4.5    -      -       -      -
     55A  GLN*     3.0    31.6    +      -       +      +
     37B  ALA      3.9     0.6    +      -       -      -
     38B  VAL*     3.7     6.5    -      -       -      +
     39B  ASN*     2.7    56.2    -      -       -      +
     57B  LEU*     3.7    16.6    -      -       -      +
     65B  LEU*     3.7    25.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  HIS      2.9     6.3    +      -       -      -
     14A  VAL*     3.0     5.5    -      -       +      -
     15A  VAL*     2.8    27.0    +      -       -      +
     41A  VAL*     3.9    17.0    -      -       +      -
     42A  GLN*     1.3    80.0    -      -       -      +
     44A  SER*     1.3    59.5    +      -       -      +
     45A  ASN      3.8    12.8    -      -       -      +
     52A  TRP*     3.7    22.0    -      +       +      -
     53A  LYS*     3.3    22.4    -      -       -      -
     54A  GLY      3.7    20.0    -      -       -      -
     55A  GLN      4.0     5.2    -      -       -      -
     56A  VAL*     3.9    17.7    -      -       +      -
    122A  GLY      3.4    23.3    -      -       -      +
    123A  GLU      3.6    15.3    -      -       -      -
    124A  GLY*     3.6    23.3    -      -       -      -
     65B  LEU*     3.7     4.9    -      -       -      -
----------------------------------------------------------
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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