Contacts of the strand formed by residues 35 - 39 (chain A) in PDB entry 1FD4


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 THR 35 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  HIS      3.7     7.0    -      -       -      -
     17A  PRO*     4.2    10.1    -      -       +      -
     29A  THR*     3.3    21.3    -      -       -      +
     30A  CYS*     3.2    34.1    +      -       -      -
     31A  GLY      3.5     0.2    +      -       -      -
     32A  LEU*     2.6    41.0    +      -       +      +
     33A  PRO      3.9     4.5    -      -       -      +
     34A  GLY*     1.3    78.0    -      -       -      +
     36A  LYS*     1.3    64.3    +      -       -      +
      9B  LEU*     4.3    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ILE      3.5     0.5    -      -       -      +
     15A  CYS*     3.5     4.2    -      -       -      -
     16A  HIS      2.8    39.0    +      -       -      +
     18A  VAL      3.5    15.5    -      -       -      -
     19A  PHE*     3.9    18.8    -      -       -      +
     20A  CYS*     3.8     6.5    -      -       -      +
     26A  GLN*     4.0    27.8    +      -       -      +
     28A  GLY      3.9     4.3    -      -       -      +
     29A  THR*     5.5     2.8    -      -       +      +
     30A  CYS*     4.2     3.6    -      -       -      -
     34A  GLY*     3.3    25.3    +      -       -      +
     35A  THR*     1.3    78.7    +      -       -      +
     37A  CYS*     1.3    60.2    +      -       -      +
     38A  CYS*     3.5    19.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     3.9     6.3    -      -       +      -
      8A  CYS*     2.1    51.1    -      -       -      -
     13A  ALA*     3.4    15.3    -      -       -      -
     14A  ILE      3.4     3.1    -      -       -      -
     26A  GLN*     3.4     5.5    -      -       -      +
     27A  ILE*     2.8    42.7    +      -       -      -
     28A  GLY*     2.9    29.2    +      -       -      +
     29A  THR*     3.7    11.9    -      -       -      +
     30A  CYS*     4.0     0.7    -      -       -      -
     36A  LYS*     1.3    70.4    -      -       -      +
     38A  CYS*     1.3    55.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ALA*     3.3     3.0    -      -       -      +
     14A  ILE*     2.9    47.2    +      -       +      +
     16A  HIS*     4.2     7.4    -      -       -      -
     19A  PHE      4.1     3.4    -      -       -      -
     20A  CYS*     2.0    57.2    -      -       +      -
     24A  TYR*     3.7    11.2    -      -       +      -
     25A  LYS      3.3     4.7    -      -       -      +
     27A  ILE*     4.7     0.4    -      -       -      +
     36A  LYS*     3.5    20.6    -      -       -      -
     37A  CYS*     1.3    73.3    -      -       -      +
     39A  LYS*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  SER      3.3    23.1    -      -       -      +
     12A  GLY*     4.0    11.7    -      -       -      +
     13A  ALA*     4.0    11.0    -      -       +      -
     24A  TYR*     3.7     6.2    -      -       -      -
     25A  LYS*     2.9    32.1    +      -       -      +
     27A  ILE*     4.0    27.4    -      -       +      +
     38A  CYS*     1.3    77.1    -      -       -      +
     40A  LYS*     1.3    78.2    +      -       -      +
     41A  PRO*     3.4     2.9    -      -       -      +
     11G  SER      3.1    32.3    +      -       -      +
     12G  GLY*     4.4     7.7    +      -       -      -
----------------------------------------------------------
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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