Contacts of the strand formed by residues 26 - 33 (chain D) in PDB entry 2UZC


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 MET 26 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ASP*     5.8     2.5    -      -       -      +
     20D  GLY*     4.2     7.4    -      -       -      -
     21D  GLY*     3.0    28.3    +      -       -      +
     22D  LYS*     3.9     1.0    +      -       -      -
     24D  PHE*     3.1    21.7    -      -       +      +
     25D  ASN*     1.3    83.3    -      -       -      +
     27D  PRO*     1.3    88.8    -      -       +      +
     28D  LEU      3.6     0.2    +      -       -      -
     59D  GLN      5.4     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 27 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  GLN      3.6     0.9    -      -       -      +
     20D  GLY*     3.5     8.0    -      -       -      -
     21D  GLY      3.3     7.3    +      -       -      -
     25D  ASN      4.9     0.4    -      -       -      +
     26D  MET*     1.3   104.8    -      -       +      +
     28D  LEU*     1.3    62.0    +      -       -      +
     29D  THR*     3.6    10.1    +      -       +      +
     49D  VAL*     3.9    35.2    -      -       +      -
     59D  GLN*     5.8     9.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 28 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  LEU*     4.5    12.6    -      -       +      -
     19D  GLN      3.4     5.4    -      -       -      +
     20D  GLY      3.7     9.2    -      -       -      +
     21D  GLY*     3.6    24.9    -      -       -      -
     26D  MET      3.6     0.4    +      -       -      -
     27D  PRO*     1.3    72.5    -      -       -      +
     29D  THR*     1.3    59.4    +      -       -      +
     49D  VAL*     3.4     7.8    -      -       -      +
     50D  VAL*     2.8    44.9    +      -       +      +
     53D  ILE*     4.8     2.9    -      -       +      -
     58D  ALA*     3.8    36.1    -      -       +      +
     59D  GLN*     6.2     1.8    -      -       -      +
     61D  MET*     4.4     6.1    -      -       +      +
     63D  HIS*     4.2    17.7    -      -       -      +
     66D  ALA*     3.6    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 29 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  LEU*     3.3    10.2    -      -       -      -
     19D  GLN*     2.9    62.7    +      -       -      +
     27D  PRO*     4.2    14.9    +      -       +      +
     28D  LEU*     1.3    79.4    -      -       -      +
     30D  ILE*     1.3    64.8    +      -       -      +
     31D  SER      3.2     0.3    +      -       -      -
     47D  GLY*     3.8    20.4    -      -       -      +
     48D  ASP      3.2     5.6    -      -       -      -
     49D  VAL*     3.8    17.5    -      -       +      -
     50D  VAL      4.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 30 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16D  PHE*     3.6    29.4    -      -       +      -
     17D  ARG      3.5     3.1    -      -       -      +
     18D  LEU*     3.9    10.1    -      -       +      -
     19D  GLN*     5.0     1.2    +      -       -      -
     29D  THR*     1.3    71.0    +      -       -      +
     31D  SER*     1.3    60.5    +      -       -      +
     32D  SER      3.6    20.0    -      -       -      +
     33D  LEU*     4.0    17.0    -      -       +      -
     44D  VAL*     3.6    23.1    -      -       +      -
     45D  ARG      3.7    11.9    -      -       -      +
     46D  ILE*     3.6    14.6    -      -       -      +
     47D  GLY*     2.8    28.6    +      -       -      -
     48D  ASP      2.9    18.5    +      -       -      +
     50D  VAL*     4.1    10.5    -      -       +      -
     79D  MET*     5.0     3.4    -      -       +      -
     81D  LEU*     3.9    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 31 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  ARG*     2.8    28.2    +      -       -      +
     18D  LEU      3.3    13.3    +      -       -      -
     19D  GLN*     3.9    35.2    -      -       -      +
     29D  THR      3.2     0.6    +      -       -      -
     30D  ILE*     1.3    74.0    -      -       -      +
     32D  SER*     1.3    61.0    +      -       -      +
     46D  ILE*     4.1    15.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 32 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16D  PHE*     3.3     8.0    -      -       -      +
     17D  ARG*     3.1    62.7    +      -       -      -
     30D  ILE*     3.6     6.4    -      -       -      +
     31D  SER*     1.3    80.0    +      -       -      +
     33D  LEU*     1.3    66.9    +      -       -      +
     46D  ILE*     4.0     7.4    -      -       -      -
   1090D  EDO      3.3    19.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  GLY      3.4    13.5    -      -       -      +
     16D  PHE*     3.9     6.1    -      -       +      -
     30D  ILE*     4.0     9.9    -      -       +      -
     32D  SER*     1.3    83.8    +      -       -      +
     34D  LYS*     1.3    67.0    +      -       -      +
     35D  ASP*     3.5     2.3    +      -       -      -
     39D  ALA*     3.8    21.8    -      -       +      -
     40D  ALA*     4.1    15.5    -      -       +      +
     44D  VAL*     3.3    29.6    -      -       +      +
     45D  ARG*     4.1     0.7    -      -       -      -
     46D  ILE*     3.9    35.0    -      -       +      +
   1090D  EDO      3.7     8.1    -      -       -      -
----------------------------------------------------------
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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