Contacts of the strand formed by residues 45 - 52 (chain B) in PDB entry 1F11


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 LEU 45 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  PRO*     3.9    27.4    -      -       +      -
     87A  TYR*     4.1    29.4    -      -       +      -
     98A  PHE*     3.7    58.4    +      -       +      +
     99A  GLY      5.8     0.8    +      -       -      -
     37B  VAL*     3.9    15.9    -      -       +      -
     38B  LYS      3.6     2.2    -      -       -      -
     39B  GLN*     3.7    34.1    -      -       +      +
     44B  SER*     1.3    72.8    +      -       -      +
     46B  GLU*     1.3    66.4    +      -       -      +
     91B  TYR*     4.6     2.5    -      -       +      -
    103B  TRP*     4.3     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  PHE*     4.8     2.0    -      -       -      -
     37B  VAL*     3.0     8.2    -      -       -      +
     38B  LYS*     2.8    63.1    +      -       +      +
     40B  SER*     5.0     3.1    +      -       -      -
     44B  SER*     4.8     8.7    +      -       -      +
     45B  LEU*     1.3    79.9    -      -       -      +
     47B  TRP*     1.3    63.9    +      -       -      +
     48B  ILE*     4.2     0.9    -      -       -      +
     60B  ASN*     4.8     3.1    +      -       -      +
     62B  LYS*     2.9    40.1    +      -       -      -
     63B  PHE*     4.0    12.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ASP*     3.9    16.8    -      -       -      -
     95A  PRO*     3.4    37.0    -      -       +      -
     96A  PHE*     3.5    50.7    +      +       +      +
     98A  PHE*     4.7     4.0    -      -       +      -
     36B  TRP      3.6    11.4    -      -       -      -
     37B  VAL*     4.5     3.6    -      -       -      +
     46B  GLU*     1.3    74.5    -      -       -      +
     48B  ILE*     1.3    63.0    +      -       -      +
     49B  GLY*     3.4    19.8    -      -       -      -
     50B  ASP*     2.5    26.9    +      -       -      -
     58B  GLY      3.8     4.0    -      -       -      -
     59B  TYR      4.0     4.0    -      -       -      -
     60B  ASN*     2.8    58.1    +      -       +      +
     63B  PHE*     3.8     3.8    -      -       -      -
    100B  PHE*     4.1    21.3    +      -       -      -
     28C  ASP*     3.2    26.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  TRP*     2.7    23.6    +      -       +      +
     37B  VAL      4.0     7.4    -      -       -      -
     38B  LYS*     3.8    30.5    -      -       +      +
     46B  GLU      4.2     0.4    -      -       -      +
     47B  TRP*     1.3    75.7    -      -       -      +
     49B  GLY*     1.3    59.7    +      -       -      +
     59B  TYR*     3.6     4.4    -      -       +      +
     60B  ASN*     2.7    30.4    +      -       -      +
     63B  PHE*     3.8    25.6    -      -       +      +
     67B  ALA*     3.6    30.5    -      -       +      -
     69B  LEU*     4.7     3.6    -      -       +      -
     80B  MET*     3.4    35.4    -      -       +      -
     82B  LEU*     5.5     0.9    -      -       +      -
     90B  TYR*     3.8     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  LYS*     3.6     0.2    -      -       -      -
     36B  TRP*     2.9    24.8    +      -       -      +
     47B  TRP*     3.4    11.4    -      -       -      +
     48B  ILE*     1.3    83.7    -      -       -      +
     50B  ASP*     1.3    65.2    +      -       -      +
     58B  GLY      2.8    15.7    -      -       -      -
     59B  TYR*     4.1     1.8    -      -       -      -
     69B  LEU*     3.4    17.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  PHE*     4.1     0.2    -      -       -      -
     33B  TYR*     4.2    11.8    -      -       +      -
     34B  MET      3.2     8.7    -      -       -      +
     35B  LYS*     2.9    37.3    +      -       +      +
     47B  TRP*     2.5    33.8    +      -       -      -
     49B  GLY*     1.3    73.4    -      -       -      +
     51B  ILE*     1.3    61.6    +      -       -      +
     57B  THR*     3.6     1.6    -      -       -      -
     58B  GLY      2.7    29.9    +      -       -      +
     69B  LEU*     3.4     9.3    -      -       -      +
     28C  ASP*     2.5    40.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  TYR*     3.5     5.7    -      -       -      -
     34B  MET*     2.8    49.1    +      -       +      +
     36B  TRP*     5.0     4.5    -      -       -      +
     50B  ASP*     1.3    75.0    -      -       -      +
     52B  ASN*     1.3    65.8    +      -       -      +
     55B  GLY*     4.3     9.2    -      -       -      +
     56B  GLY      3.1    18.6    -      -       -      +
     57B  THR*     3.7    11.0    -      -       -      +
     69B  LEU*     4.1    13.2    -      -       +      +
     70B  THR*     3.6    28.5    -      -       -      +
     71B  VAL*     3.3    37.5    -      -       +      -
     78B  ALA*     5.5     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  THR      4.1     5.0    -      -       -      +
     33B  TYR*     3.4    35.4    +      -       +      +
     51B  ILE*     1.3    72.5    -      -       -      +
     52B  PRO*     1.3    62.1    +      -       -      +
     53B  ASN*     2.9    23.6    +      -       -      +
     54B  ASN*     2.8    26.9    +      -       -      +
     55B  GLY*     2.7    35.1    +      -       -      -
     56B  GLY*     2.7    18.9    +      -       -      +
----------------------------------------------------------
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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