Contacts of the strand formed by residues 388 - 392 (chain D) in PDB entry 1F9E


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 GLN 388 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    390B  THR*     2.9    34.0    -      -       +      +
    392B  PHE      3.7     8.1    -      -       -      +
    393B  THR*     4.0     8.7    -      -       +      -
    331D  MET*     3.2    37.9    +      -       +      +
    333D  THR      4.6     3.3    -      -       -      +
    334D  VAL*     3.2    39.5    -      -       +      +
    335D  ASN*     4.2     3.5    +      -       -      +
    386D  MET      3.9     0.2    +      -       -      -
    387D  PRO*     1.3    76.0    -      -       -      +
    389D  PRO*     1.3    64.3    -      -       -      +
    390D  THR*     3.8     7.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 389 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    390B  THR*     3.3     2.8    -      -       -      +
    392B  PHE*     3.1    76.9    +      -       +      +
    328D  LEU*     4.7     3.1    -      -       +      -
    329D  LEU      3.3    11.4    -      -       -      +
    330D  GLY*     4.4     4.9    -      -       -      -
    331D  MET      5.1     1.3    -      -       -      +
    349D  TYR*     5.9     0.9    -      -       +      +
    367D  LEU*     5.5     0.4    -      -       +      -
    370D  LEU*     4.0    32.8    -      -       +      -
    374D  ASN*     3.8    13.9    -      -       -      +
    387D  PRO*     4.0     2.2    -      -       +      -
    388D  GLN*     1.3    88.2    -      -       -      +
    390D  THR*     1.3    62.6    +      -       -      +
    392D  PHE*     5.7     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 390 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388B  GLN*     2.9    36.8    -      -       +      +
    389B  PRO      3.4    15.0    -      -       -      +
    390B  THR*     3.3    17.6    -      -       -      +
    328D  LEU*     3.6     1.3    -      -       -      +
    329D  LEU*     2.9    45.2    +      -       -      +
    331D  MET*     5.6     1.0    -      -       -      +
    388D  GLN*     3.9     7.8    +      -       -      -
    389D  PRO*     1.3    77.8    +      -       -      +
    392D  PHE*     1.3    67.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 392 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367B  LEU*     4.0    17.5    -      -       +      -
    370B  LEU*     4.7     2.0    -      -       +      -
    371B  THR*     3.6    22.7    -      -       -      -
    374B  ASN*     3.8     9.4    -      -       -      -
    388B  GLN*     3.8     1.7    -      -       -      -
    389B  PRO*     3.1    60.0    +      -       +      +
    392B  PHE*     3.8    28.5    -      +       -      -
    327D  PHE*     3.4    11.9    -      -       -      +
    328D  LEU*     4.0    11.7    -      -       +      -
    367D  LEU*     3.5    29.8    -      -       +      -
    389D  PRO*     5.7     0.2    -      -       +      -
    390D  THR*     1.3    81.3    -      -       -      +
    393D  THR*     1.3    66.6    +      -       -      +
    394D  LEU*     3.7    22.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 393 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334B  VAL*     4.1     7.0    -      -       +      -
    374B  ASN*     4.0     6.3    -      -       -      +
    386B  MET*     3.6    27.6    -      -       +      +
    387B  PRO      3.8    13.9    -      -       -      +
    388B  GLN*     4.0    14.4    -      -       +      +
    324D  GLU      2.9    24.7    +      -       -      +
    326D  ASP      3.1    12.9    +      -       -      -
    327D  PHE*     2.7    39.0    +      -       +      +
    392D  PHE*     1.3    78.6    -      -       -      +
    394D  LEU*     1.3    67.9    +      -       -      +
    395D  ARG*     3.4     3.1    +      -       -      +
----------------------------------------------------------
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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