Contacts of the strand formed by residues 27 - 32 (chain A) in PDB entry 1ADN


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 PHE 27 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ARG*     3.1    41.7    -      -       +      -
     15A  SER*     2.9    26.7    -      -       -      -
     16A  VAL*     4.0    18.6    -      -       +      -
     21A  PRO*     5.6     0.2    -      -       +      -
     23A  ALA*     5.3     0.2    -      -       +      -
     24A  ASP*     2.7    60.7    +      -       +      +
     25A  GLY      3.9     0.2    -      -       -      -
     26A  GLU*     1.5    63.3    -      -       -      +
     28A  VAL*     1.5    59.8    +      -       -      +
     29A  PHE*     5.5     0.4    -      -       +      -
     39A  ARG*     4.2     2.1    -      -       -      +
     40A  PRO*     2.8    48.6    -      -       +      +
     54A  PHE*     4.8    15.0    -      +       +      -
     55A  TYR      3.1    18.6    -      -       -      +
     56A  ALA*     3.4     7.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  GLU      3.7     9.6    -      -       -      +
     27A  PHE*     1.5    65.0    -      -       -      +
     29A  PHE*     1.5    59.2    +      -       -      +
     37A  PHE*     4.7     6.3    -      -       +      -
     38A  CYS      3.8     9.0    -      -       -      +
     39A  ARG*     5.1     8.7    -      -       +      +
     40A  PRO*     5.1     0.2    -      -       -      -
     54A  PHE*     3.2     6.1    -      -       -      +
     55A  TYR*     2.8    79.1    +      -       +      +
     57A  ASN      3.4    12.1    -      -       -      +
     58A  ALA*     3.2    38.8    -      -       +      +
     61A  ALA*     4.2     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  TRP*     4.5     9.2    -      +       -      -
     16A  VAL*     4.4    22.9    -      -       +      -
     27A  PHE*     5.5     1.3    -      -       +      -
     28A  VAL*     1.5    58.0    -      -       -      +
     30A  ALA*     1.5    58.4    +      -       -      +
     31A  VAL*     3.2    31.9    -      -       +      -
     36A  ILE*     3.7     8.5    -      -       +      +
     37A  PHE*     3.3     2.2    -      -       -      -
     38A  CYS*     2.9    68.5    +      -       +      -
     39A  ARG      4.7     1.3    -      -       -      -
     40A  PRO*     4.5    10.5    -      -       +      -
     42A  CYS*     4.2    17.0    -      -       +      -
     46A  HIS*     5.0    15.0    -      +       +      -
     47A  ALA      5.5     0.7    -      -       -      -
     52A  VAL*     3.1    26.7    -      -       +      -
     53A  SER      3.3     4.5    -      -       -      -
     54A  PHE*     3.8    20.4    -      -       +      -
     55A  TYR*     4.4     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  PHE*     1.5    55.0    -      -       -      +
     31A  VAL*     1.5    59.8    +      -       -      +
     32A  ARG*     3.7     2.4    +      -       -      +
     36A  ILE      3.6     5.4    -      -       -      -
     37A  PHE*     4.0     0.9    -      -       +      -
     51A  ASN      3.4     4.9    -      -       -      +
     52A  VAL*     3.2     4.4    -      -       -      -
     53A  SER*     2.6    39.9    +      -       -      +
     55A  TYR*     3.0    32.1    -      -       +      +
     66A  PHE*     3.3    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  PHE*     3.2    27.3    -      -       +      -
     30A  ALA*     1.5    54.3    -      -       -      +
     32A  ARG*     1.5    57.0    +      -       -      +
     33A  THR*     3.1    12.7    +      -       +      -
     34A  THR*     4.1     4.7    -      -       -      +
     35A  GLY      3.2    15.4    +      -       -      -
     36A  ILE*     3.2    26.3    +      -       +      +
     46A  HIS*     6.2     0.4    -      -       +      -
     47A  ALA*     2.9    41.7    -      -       +      +
     48A  LEU      4.5     2.5    -      -       -      +
     51A  ASN*     3.0    19.5    -      -       -      +
     52A  VAL*     3.7    16.0    -      -       +      +
     66A  PHE*     4.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ALA      3.7     3.0    +      -       -      +
     31A  VAL*     1.5    51.9    -      -       -      +
     33A  THR*     1.5    54.9    +      -       -      -
     34A  THR      3.8     0.2    -      -       -      -
     35A  GLY*     4.0     6.0    +      -       -      -
     51A  ASN*     2.8    28.9    +      -       -      +
     66A  PHE*     4.0    33.4    -      -       -      -
----------------------------------------------------------
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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