Contacts of the strand formed by residues 36 - 45 (chain A) in PDB entry 4CDC


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 36 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  GLN*     3.1    25.1    -      -       +      +
     19A  VAL      3.5    13.9    -      -       -      +
     20A  GLY      3.8    15.5    -      -       -      +
     33A  MET*     3.4    28.9    -      -       +      +
     34A  GLY      4.6     4.2    +      -       -      +
     35A  PRO*     1.3    82.0    -      -       -      +
     37A  GLU*     1.3    60.2    +      -       -      +
     38A  LYS      3.9     0.9    -      -       -      +
    114A  THR*     2.9    26.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  VAL      2.8     8.4    +      -       -      +
     20A  GLY*     3.3     6.3    -      -       -      -
     21A  SER*     3.0    26.3    +      -       -      -
     22A  SER*     3.1    28.6    +      -       -      +
     35A  PRO*     3.9    15.4    -      -       -      +
     36A  GLN*     1.3    73.8    -      -       -      +
     38A  LYS*     1.3    65.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  GLN*     3.6     5.2    -      -       -      +
     19A  VAL*     2.7    46.4    +      -       +      +
     36A  GLN*     3.9     0.7    -      -       -      +
     37A  GLU*     1.3    85.0    -      -       +      +
     39A  LYS*     1.3    80.0    +      -       -      +
     40A  VAL*     4.5     8.1    -      -       +      -
    439F  LEU*     3.1    44.7    +      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
     16A  VAL*     4.1    21.3    -      -       +      +
     17A  PHE      3.2     9.4    -      -       -      +
     18A  GLN*     3.7    18.2    -      -       -      +
     38A  LYS*     1.3    96.2    +      -       -      +
     40A  VAL*     1.3    65.0    +      -       -      +
     41A  VAL*     4.4    19.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  TRP      3.8     0.7    -      -       -      +
     16A  VAL*     3.7     0.9    -      -       -      -
     17A  PHE*     2.7    42.0    +      -       +      +
     19A  VAL*     4.3    10.8    -      -       +      -
     38A  LYS*     4.5     9.6    -      -       +      -
     39A  LYS*     1.3    80.3    -      -       -      +
     41A  VAL*     1.3    67.7    +      -       -      +
     42A  VAL*     3.9    19.8    +      -       +      -
     52A  ASP*     5.7     4.9    -      -       +      -
     72A  LEU*     6.2     0.9    -      -       +      -
     73A  ASN*     6.4     0.2    -      -       -      +
     77A  TRP*     3.8    34.3    -      -       +      -
    439F  LEU*     4.6    17.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  THR*     3.7    28.7    -      -       +      -
     15A  TRP      3.4     4.7    -      -       -      +
     16A  VAL*     4.4    15.3    -      -       +      -
     39A  LYS*     4.4    22.9    -      -       +      +
     40A  VAL*     1.3    77.2    -      -       -      +
     42A  VAL*     1.3    66.5    -      -       -      +
     43A  TYR*     3.8    21.5    -      -       +      +
     52A  ASP*     3.8    16.1    -      -       -      +
     53A  ASP*     3.4    28.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  GLY      4.0     0.2    -      -       -      +
     14A  THR*     3.6     2.9    -      -       -      +
     15A  TRP*     2.8    40.9    +      -       +      +
     17A  PHE*     3.6    34.3    -      -       +      -
     40A  VAL*     4.0    13.5    -      -       +      -
     41A  VAL*     1.3    79.6    -      -       -      +
     43A  TYR*     1.3    65.9    +      -       -      +
     44A  LEU*     3.8    24.0    +      -       +      -
     50A  ALA*     4.4     2.0    -      -       +      -
     51A  TYR      3.5     9.0    -      -       -      +
     70A  ILE*     4.1    12.6    -      -       +      -
     72A  LEU*     4.0    23.8    -      -       +      -
     77A  TRP*     5.1     3.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  GLY      3.6     4.9    -      -       -      +
     14A  THR*     3.3    37.5    -      -       +      -
     41A  VAL*     3.8    13.0    -      -       +      +
     42A  VAL*     1.3    74.0    -      -       -      +
     44A  LEU*     1.3    61.2    +      -       -      +
     45A  GLN*     5.0     3.4    -      -       +      +
     49A  THR      3.7     0.7    -      -       -      +
     50A  ALA*     3.2     6.4    -      -       -      -
     51A  TYR*     2.8    84.1    +      +       +      +
     52A  ASP      4.2     8.3    -      -       -      -
     53A  ASP*     3.8    32.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     3.6    46.2    -      -       +      +
     12A  LEU*     3.6     8.4    -      -       -      +
     13A  GLY*     2.9    29.8    +      -       -      +
     15A  TRP*     3.8    15.9    -      -       +      -
     42A  VAL*     3.8    13.0    -      -       +      -
     43A  TYR*     1.3    83.7    -      -       -      +
     45A  GLN*     1.3    62.9    +      -       -      +
     49A  THR      3.5     1.8    -      -       -      -
     50A  ALA*     3.7    22.9    -      -       +      -
     60A  PHE*     3.7    26.5    -      -       +      -
     68A  PHE*     5.5     0.4    -      -       +      -
     70A  ILE*     3.9    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  LEU*     3.7     5.2    -      -       -      -
     43A  TYR*     5.0     2.5    -      -       +      +
     44A  LEU*     1.3    79.3    -      -       -      +
     46A  LYS*     1.3    66.4    +      -       +      +
     49A  THR*     2.9    44.8    +      -       -      +
     51A  TYR*     3.0    45.3    +      -       +      -
     60A  PHE*     3.3     4.9    -      -       -      -
----------------------------------------------------------
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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