Contacts of the strand formed by residues 52 - 66 (chain A) in PDB entry 1NH0


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 GLY 52 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  GLY*     3.2     1.7    -      -       -      -
     49A  GLY      3.0    32.0    +      -       -      +
     50A  ILE      3.3     1.2    +      -       -      -
     51A  GLY*     1.3    80.6    -      -       -      +
     53A  PHE*     1.3    77.7    +      -       -      -
     51B  GLY*     3.7    11.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  MET*     3.9    22.1    -      -       +      +
     47A  ILE      3.1    18.8    -      -       -      +
     48A  GLY*     3.8    12.6    -      -       -      -
     49A  GLY      5.4     0.9    -      -       -      -
     52A  GLY*     1.3    84.5    -      -       -      -
     54A  ILE*     1.3    70.7    +      -       -      +
     51B  GLY*     4.3     4.1    +      -       -      +
      4I  GLU*     6.0     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  VAL*     4.6     3.1    -      -       +      -
     46A  MET*     3.5     9.2    -      -       -      -
     47A  ILE*     2.9    50.9    +      -       +      +
     53A  PHE*     1.3    79.7    -      -       -      +
     55A  LYS*     1.3    60.9    +      -       -      +
     56A  VAL*     4.1    16.2    -      -       +      -
     79A  PRO*     4.1    43.3    -      -       +      +
     80A  THR*     4.2     2.7    -      -       -      +
     50B  ILE*     3.7    42.6    -      -       +      +
     51B  GLY*     4.3     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  LYS      3.7     6.1    -      -       -      +
     46A  MET*     3.5    24.7    -      -       +      -
     54A  ILE*     1.3    73.5    -      -       -      +
     56A  VAL*     1.3    60.4    +      -       -      +
     78A  GLY*     3.9     0.7    -      -       -      -
     79A  PRO*     3.3    26.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  VAL*     4.5     2.0    -      -       +      -
     44A  PRO*     3.4     6.2    -      -       -      +
     45A  LYS*     2.9    56.3    +      -       +      +
     47A  ILE*     3.7    32.8    -      -       +      -
     54A  ILE*     4.1     6.7    -      -       +      -
     55A  LYS*     1.3    80.4    -      -       -      +
     57A  ARG*     1.3    65.1    +      -       -      +
     76A  LEU*     4.0    32.8    -      -       +      -
     77A  VAL      3.2    14.8    -      -       -      +
     78A  GLY*     4.0     9.2    -      -       -      -
   6001A  SO4      5.0     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  GLU*     5.6     6.5    +      -       -      -
     42A  TRP*     3.3    56.0    -      -       +      +
     43A  LYS      3.8     3.4    -      -       -      -
     56A  VAL*     1.3    75.1    -      -       -      +
     58A  GLN*     1.3    59.1    +      -       -      +
     59A  TYR*     3.5    25.4    +      -       +      -
     76A  LEU*     3.4     3.5    -      -       -      -
     77A  VAL*     2.8    37.2    +      -       +      +
   6001A  SO4      2.8    39.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  TRP*     3.1     7.1    -      -       -      -
     43A  LYS*     2.8    73.7    +      -       +      +
     45A  LYS*     3.2    24.7    +      -       +      -
     56A  VAL*     4.1     0.8    -      -       -      +
     57A  ARG*     1.3    69.7    -      -       -      +
     59A  TYR*     1.3    62.9    +      -       -      +
     60A  ASP*     3.0    28.8    +      -       -      +
     74A  THR*     3.5    22.8    +      -       +      +
     76A  LEU*     3.6    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  GLU*     5.1     8.7    +      -       -      -
     38A  LEU*     3.5    42.4    +      -       +      -
     39A  PRO      4.0     5.6    -      -       -      -
     40A  GLY      3.5    15.9    -      -       -      -
     41A  ARG      3.6    16.6    -      -       -      -
     42A  TRP*     3.6    23.1    -      -       +      -
     57A  ARG*     3.5    37.2    +      -       +      -
     58A  GLN*     1.3    73.8    -      -       -      +
     60A  ASP*     1.3    63.1    +      -       -      +
     62A  ILE*     3.9    21.7    -      -       +      +
     74A  THR*     3.3     3.5    -      -       -      +
     75A  VAL      2.9    36.6    +      -       -      +
     77A  VAL*     3.9    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  ARG      5.3     1.8    +      -       -      -
     58A  GLN*     3.0    28.9    +      -       -      +
     59A  TYR*     1.3    74.4    -      -       -      +
     61A  GLN*     1.3    83.7    +      -       +      +
     62A  ILE*     3.3    11.4    +      -       -      +
     74A  THR*     2.8    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  ASP*     1.3    85.6    -      -       +      +
     62A  ILE*     1.3    62.7    +      -       -      +
     63A  LEU*     3.8     7.6    +      -       -      +
     72A  ILE*     3.8    20.9    -      -       +      +
     73A  GLY*     3.5    10.2    +      -       -      -
     74A  THR*     4.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ILE*     4.0    24.9    -      -       +      -
     38A  LEU*     4.0    21.5    -      -       +      -
     39A  PRO*     5.7     4.7    -      -       +      +
     59A  TYR*     3.9    33.9    -      -       +      +
     60A  ASP      3.6    15.3    -      -       -      +
     61A  GLN*     1.3    76.7    -      -       -      +
     63A  LEU*     1.3    73.8    +      -       -      +
     64A  ILE*     3.6     6.2    +      -       +      +
     72A  ILE*     3.2     5.2    -      -       -      -
     73A  GLY      2.9    31.4    +      -       -      +
     75A  VAL*     3.9    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LYS      4.1     0.2    -      -       -      +
     15A  ILE*     3.8    16.8    -      -       -      +
     16A  GLY      4.7     1.7    +      -       -      -
     61A  GLN      4.3     6.1    -      -       -      +
     62A  ILE*     1.3    78.8    -      -       -      +
     64A  ILE*     1.3    59.9    +      -       -      +
     70A  LYS*     4.5    15.0    +      -       -      +
     71A  ALA      3.6     5.6    -      -       -      +
     72A  ILE*     3.3    44.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ILE*     4.2    12.6    -      -       +      -
     14A  LYS      3.4     5.6    -      -       -      +
     15A  ILE*     3.8    29.6    -      -       +      -
     31A  THR*     5.3     0.2    -      -       +      -
     33A  LEU*     4.8     4.3    -      -       +      -
     62A  ILE*     4.2     9.9    -      -       +      +
     63A  LEU*     1.3    75.3    -      -       -      +
     65A  GLU*     1.3    65.0    +      -       -      +
     66A  ILE*     3.9    21.7    +      -       +      -
     69A  HIS      3.8     0.5    -      -       -      +
     70A  LYS*     3.7     6.7    +      -       -      +
     71A  ALA*     2.9    45.9    +      -       +      +
     75A  VAL*     5.2     2.5    -      -       +      -
     85A  ILE*     4.2    18.8    -      -       +      -
     89A  LEU*     3.9    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  THR      3.9     0.3    -      -       -      +
     13A  ILE*     3.1     8.1    -      -       -      +
     14A  LYS*     2.9    55.8    +      -       +      +
     64A  ILE*     1.3    73.5    -      -       -      +
     66A  ILE*     1.3    60.0    -      -       -      +
     68A  GLY*     3.0    46.0    -      -       -      +
     69A  HIS      3.4     6.7    -      -       -      +
     70A  LYS*     4.1    27.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  VAL*     3.9    22.4    -      -       +      -
     12A  THR      3.7     2.5    -      -       -      -
     13A  ILE*     4.1     7.6    -      -       +      -
     24A  LEU*     4.1    10.8    -      -       +      -
     64A  ILE*     3.9    27.4    -      -       +      -
     65A  GLU*     1.3    76.7    -      -       -      +
     67A  CYS*     1.3    72.3    +      -       +      +
     69A  HIS*     2.9    31.6    +      -       -      +
     71A  ALA*     4.7     2.0    -      -       +      -
     85A  ILE*     3.9    22.9    -      -       +      -
     89A  LEU*     3.9    20.9    -      -       +      +
     93A  ILE*     4.0    33.4    -      -       +      -
     99B  PHE*     4.4     1.8    -      -       +      -
----------------------------------------------------------
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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