Contacts of the strand formed by residues 25 - 34 (chain A) in PDB entry 1AMN


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 SER 25 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  PRO*     3.6     0.5    -      -       -      +
     22A  VAL      3.0    19.7    +      -       -      -
     23A  LEU      3.9     1.4    -      -       -      +
     24A  SER*     1.3    82.5    +      -       -      +
     26A  HIS*     1.3    84.4    +      -       -      +
    137A  TYR*     3.3    36.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ARG*     3.4    44.4    -      -       +      +
     20A  VAL      3.2     6.3    -      -       -      -
     21A  PRO*     3.2    36.6    -      -       +      +
     22A  VAL*     3.8     3.5    -      -       -      +
     24A  SER      4.5     4.1    +      -       -      -
     25A  SER*     1.3   101.4    +      -       -      +
     27A  ILE*     1.3    78.3    +      -       -      +
    103A  SER*     4.3     9.3    -      -       -      +
    137A  TYR*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ARG*     3.0     9.2    -      -       -      +
     20A  VAL*     2.6    39.5    +      -       +      +
     22A  VAL*     3.9     7.9    -      -       +      -
     26A  HIS*     1.3    89.7    -      -       -      +
     28A  SER*     1.3    72.1    +      -       -      +
    100A  TRP*     4.5    19.7    -      -       +      -
    101A  VAL      3.4    14.4    -      -       -      +
    102A  PRO*     3.7     8.1    -      -       +      -
    103A  SER*     3.7    27.6    -      -       -      +
    133A  LYS*     4.6     9.9    -      -       +      -
    136A  ALA*     5.1     1.3    -      -       +      -
    137A  TYR*     3.8    40.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  GLU*     4.0    21.0    +      -       -      +
      6A  LEU*     3.3    23.9    -      -       -      +
     18A  THR      3.2     8.5    -      -       -      -
     19A  ARG*     4.7     2.1    +      -       -      +
     27A  ILE*     1.3    81.5    -      -       -      +
     29A  ALA*     1.3    60.3    +      -       -      +
     30A  PHE*     4.1    17.5    -      -       -      -
    100A  TRP*     3.5     0.7    -      -       -      -
    101A  VAL*     2.8    41.8    +      -       -      +
    102A  PRO      4.6     2.6    +      -       -      -
    103A  SER*     4.8     1.6    -      -       -      -
    105A  ARG*     5.8     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  GLY*     3.5     1.6    -      -       -      -
     18A  THR*     2.6    45.1    +      -       -      +
     20A  VAL*     3.5    28.9    -      -       +      -
     27A  ILE      4.1     0.6    +      -       -      -
     28A  SER*     1.3    76.3    -      -       -      +
     30A  PHE*     1.3    61.8    +      -       -      +
     31A  LEU*     3.9    15.9    -      -       +      -
     60A  ALA      3.8     1.0    -      -       -      +
     99A  ILE      3.5     4.3    -      -       -      -
    100A  TRP*     3.8    21.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  GLU      3.6    22.7    -      -       -      -
      6A  LEU*     3.1    26.5    -      -       -      -
      8A  VAL*     3.8    18.4    -      -       +      -
     15A  VAL*     3.9    19.1    -      -       +      -
     16A  MET      4.4     0.7    -      -       -      -
     17A  GLY*     3.5    17.3    -      -       -      -
     28A  SER*     4.1    18.2    -      -       -      -
     29A  ALA*     1.3    72.7    -      -       -      +
     31A  LEU*     1.3    61.2    +      -       -      +
     32A  GLY      4.1     0.4    +      -       -      -
     33A  ILE*     4.0    20.3    -      -       +      +
     60A  ALA*     3.4     8.5    -      -       +      -
     97A  LEU      4.5     0.3    -      -       -      +
     98A  ASN*     3.5     2.4    -      -       -      -
     99A  ILE*     2.8    45.7    +      -       +      +
    101A  VAL*     3.8    31.2    -      -       +      -
    105A  ARG*     4.3     2.9    -      -       -      -
    187A  PHE*     3.8    11.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  THR*     5.5     2.0    -      -       +      +
     20A  VAL*     5.1     6.1    -      -       +      -
     29A  ALA*     4.1    23.3    -      -       +      +
     30A  PHE*     1.3    81.0    -      -       -      +
     32A  GLY*     1.3    62.3    +      -       -      +
     33A  ILE      3.7     1.1    -      -       -      -
     59A  ASN      4.7     1.0    -      -       -      +
     60A  ALA*     2.7    30.2    +      -       -      +
     61A  SER*     3.6    22.4    -      -       -      +
     62A  THR*     3.2    29.6    -      -       -      +
     63A  TYR*     4.0    21.5    -      -       +      +
     98A  ASN*     3.1    16.2    -      -       +      +
    100A  TRP*     3.9    30.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LEU*     1.3    75.0    -      -       -      +
     33A  ILE*     1.3    61.7    +      -       -      +
     34A  PRO      3.4     0.9    -      -       -      -
     58A  TRP*     3.4    15.6    +      -       -      -
     62A  THR      4.5     0.9    -      -       -      -
     64A  PRO*     3.6    27.4    -      -       -      -
     96A  TYR*     2.9    22.7    -      -       -      -
     97A  LEU      3.0     7.1    +      -       -      -
     98A  ASN*     2.7    12.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  VAL*     4.0    14.8    -      -       +      -
     30A  PHE*     4.0    14.8    -      -       +      +
     32A  GLY*     1.3    70.3    -      -       -      +
     34A  PRO*     1.3    72.4    -      -       +      +
     54A  TRP*     3.9    19.3    -      -       +      -
     58A  TRP*     4.4     2.5    -      -       -      +
     60A  ALA*     4.3    15.9    -      -       +      -
     97A  LEU*     2.7    48.0    +      -       +      +
     99A  ILE*     3.3    34.5    -      -       +      -
    179A  TRP*     3.8    24.7    -      -       +      -
    187A  PHE*     3.9    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  GLY      3.4     2.9    -      -       -      +
     33A  ILE*     1.3    99.0    -      -       +      +
     35A  PHE*     1.3    60.4    +      -       -      +
     36A  ALA      3.8     3.6    -      -       -      +
     38A  PRO*     6.5     0.7    -      -       +      -
     51A  LYS*     3.6    36.8    -      -       +      +
     54A  TRP*     3.8    19.6    -      -       +      -
     58A  TRP*     3.4    34.5    -      -       +      +
     95A  LEU      3.8     5.2    -      -       -      +
     96A  TYR*     3.6    24.5    -      -       +      +
    179A  TRP*     4.2     5.4    +      -       -      -
----------------------------------------------------------
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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