Contacts of the strand formed by residues 23 - 32 (chain U) in PDB entry 2FD6


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 23 (chain U).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1U  LEU*     3.3     8.1    -      -       -      +
      3U  CYS*     3.8     0.9    -      -       -      -
     21U  GLN      3.3     0.4    -      -       -      -
     22U  ASP*     1.3    90.2    -      -       -      +
     24U  CYS*     1.3    57.1    +      -       -      +
     45U  CYS*     3.4     4.7    -      -       -      +
     46U  THR*     2.5    44.1    +      -       +      +
     47U  HIS      3.4    10.5    -      -       -      +
     48U  SER*     3.1    30.1    -      -       -      +
     50U  LYS*     3.7    13.7    -      -       +      +
     70U  VAL*     3.2    31.0    -      -       +      -
     71U  CYS*     3.4    17.7    -      -       -      +
     72U  GLY*     3.8     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 24 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1U  LEU*     3.9     6.5    -      -       -      -
      2U  ARG      3.5    11.7    -      -       -      -
      3U  CYS*     2.0    47.6    -      -       -      -
     23U  LEU*     1.3    73.5    -      -       -      +
     25U  ARG*     1.3    58.9    +      -       -      +
     44U  SER      3.6     1.1    -      -       -      -
     46U  THR*     4.0     0.4    -      -       -      -
     70U  VAL*     3.2     9.9    -      -       -      +
     71U  CYS*     2.7    34.9    +      -       -      +
     73U  LEU      3.8     4.3    -      -       -      -
     75U  LEU      4.6     0.7    -      -       -      -
     76U  CYS*     3.6    25.6    -      -       -      -
     77U  ASN*     3.2    16.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 25 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  SER*     3.2    24.9    +      -       -      +
     24U  CYS*     1.3    77.1    -      -       -      +
     26U  THR*     1.3    61.0    +      -       -      +
     27U  THR*     2.5    43.6    +      -       -      +
     42U  GLU*     3.0    42.5    +      -       -      +
     43U  LYS*     3.1    20.4    +      -       -      -
     44U  SER*     2.8    45.2    +      -       -      +
     46U  THR*     3.6    27.4    -      -       +      +
     68U  GLU*     4.4     8.1    -      -       -      -
     69U  VAL      3.4     8.5    -      -       -      +
     70U  VAL*     4.1     6.7    -      -       +      -
     77U  ASN*     3.2     6.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 26 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25U  ARG*     1.3    70.8    -      -       -      +
     27U  THR*     1.3    62.1    +      -       -      +
     28U  ILE*     3.9    25.5    +      -       +      +
     41U  VAL*     4.1     5.6    -      -       +      -
     42U  GLU      3.3     3.4    -      -       -      -
     43U  LYS*     3.7    21.8    -      -       +      +
     67U  THR      3.6     1.7    -      -       -      +
     68U  GLU*     3.5     3.5    -      -       -      -
     69U  VAL*     3.1    45.5    +      -       +      +
     77U  ASN*     3.2    30.8    +      -       -      -
     79U  GLY      4.9     3.5    +      -       -      +
     80U  ASN      5.8     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 27 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  PHE*     3.5    33.9    -      -       +      +
     26A  SER*     3.4     0.2    +      -       -      -
     28A  ILE*     3.7    22.6    -      -       +      +
     25U  ARG*     2.5    32.9    +      -       -      -
     26U  THR*     1.3    71.9    -      -       -      +
     28U  ILE*     1.3    63.2    +      -       -      +
     29U  VAL*     4.8     2.2    -      -       +      -
     40U  LEU      3.8     0.7    -      -       -      +
     41U  VAL*     3.4     3.3    -      -       -      -
     42U  GLU*     2.7    37.8    +      -       -      +
     67U  THR      3.6     6.7    -      -       -      +
     68U  GLU*     2.9    19.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 28 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26U  THR*     3.9    22.9    -      -       +      +
     27U  THR*     1.3    77.7    -      -       -      +
     29U  VAL*     1.3    66.3    +      -       -      +
     30U  ARG*     3.7    33.7    -      -       +      +
     39U  GLU*     3.6    26.7    -      -       +      +
     40U  LEU      3.3     9.2    -      -       -      +
     41U  VAL*     4.3     8.1    -      -       +      -
     65U  SER      3.4     4.1    -      -       -      +
     66U  LEU*     3.4     1.7    -      -       -      -
     67U  THR*     2.8    53.7    +      -       +      +
     69U  VAL*     5.9     4.7    -      -       +      -
     80U  ASN      5.3     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 29 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  ILE*     3.4    39.0    -      -       +      -
     30A  TRP*     4.3    17.0    -      -       +      -
     27U  THR*     4.8     1.8    -      -       +      -
     28U  ILE*     1.3    76.3    -      -       -      +
     30U  ARG*     1.3    62.7    +      -       -      +
     31U  LEU*     3.3    23.3    -      -       +      -
     38U  LEU      3.7     0.7    -      -       -      +
     39U  GLU*     3.3     2.6    -      -       -      -
     40U  LEU*     2.7    48.4    +      -       +      +
     64U  THR*     4.3     4.5    -      -       +      -
     65U  SER      3.4     2.5    -      -       -      -
     66U  LEU*     3.4    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 30 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28U  ILE*     3.7    20.4    -      -       +      +
     29U  VAL*     1.3    78.0    -      -       -      +
     31U  LEU*     1.3    62.5    +      -       -      +
     32U  TRP      4.1     0.4    -      -       -      -
     37U  GLU*     3.9    28.8    +      -       -      +
     38U  LEU      3.1     5.8    -      -       -      +
     39U  GLU*     3.6    36.2    +      -       +      -
     63U  ILE      3.3     4.9    -      -       -      +
     64U  THR*     3.4     2.1    -      -       -      -
     65U  SER*     2.9    46.4    +      -       -      +
     67U  THR*     3.7    26.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 31 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  TRP*     3.6    30.5    -      -       +      +
     31A  CYS      4.7     7.0    -      -       -      +
     40A  GLN*     6.2     0.9    -      -       -      -
     29U  VAL*     3.3    29.8    -      -       +      +
     30U  ARG*     1.3    81.1    -      -       -      +
     32U  TRP*     1.3    61.2    +      -       -      +
     33U  GLU*     5.6     0.2    -      -       -      -
     37U  GLU*     3.4     2.9    -      -       -      -
     38U  LEU*     2.7    60.1    +      -       +      +
     40U  LEU*     4.4     9.2    -      -       +      -
     62U  LYS*     4.5    18.4    -      -       +      +
     63U  ILE      3.6     4.3    -      -       -      -
     64U  THR*     4.6     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 32 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30U  ARG      4.1     0.6    -      -       -      -
     31U  LEU*     1.3    73.0    -      -       -      +
     33U  GLU*     1.3    98.1    +      -       -      +
     37U  GLU*     4.2    33.7    -      -       +      +
     58U  ARG*     5.8     1.3    -      -       -      -
     61U  LEU*     3.0    24.7    -      -       +      -
     62U  LYS*     3.2    19.1    -      -       -      +
     63U  ILE*     3.1    45.0    +      -       +      +
----------------------------------------------------------
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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