Contacts of the strand formed by residues 98 - 103 (chain D) in PDB entry 1U3H


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 ASN 98 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  PRO*     6.2     1.1    -      -       +      -
     96D  GLN      3.9     1.6    +      -       -      -
     97D  PRO*     1.3    75.8    -      -       -      +
     99D  VAL*     1.3    60.9    +      -       -      +
    100D  VAL*     5.4     6.5    -      -       +      +
    118D  SER      3.2     1.9    -      -       -      +
    119D  VAL*     3.2     6.4    -      -       -      -
    120D  THR*     2.8    48.2    +      -       -      +
    121D  ASP*     4.7    13.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 99 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97D  PRO*     4.1    14.8    +      -       +      -
     98D  ASN*     1.3    83.8    +      -       -      +
    100D  VAL*     1.3    67.3    +      -       -      +
    117D  CYS*     3.6    29.6    -      -       -      -
    118D  SER      3.2     3.1    -      -       -      +
    119D  VAL*     4.3     3.4    -      -       +      -
    173D  CYS*     4.1     2.9    -      -       +      +
    175D  VAL*     3.9    26.9    -      -       +      -
    184D  ILE*     4.1    23.1    -      -       +      -
    186D  VAL*     3.5    35.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 100 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  PRO*     3.7    33.9    -      -       +      -
     98D  ASN*     5.4     6.1    -      -       +      +
     99D  VAL*     1.3    84.1    -      -       -      +
    101D  ILE*     1.3    70.2    +      -       -      +
    102D  SER*     4.3     3.8    +      -       -      +
    116D  VAL      3.4     1.7    -      -       -      +
    117D  CYS*     3.4     1.7    -      -       -      -
    118D  SER*     2.8    39.3    +      -       -      +
    186D  VAL*     4.8     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 101 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100D  VAL*     1.3    80.9    -      -       -      +
    102D  SER*     1.3    68.0    +      -       -      +
    115D  LEU*     4.1     9.6    -      -       +      -
    116D  VAL      3.3     6.5    -      -       -      +
    117D  CYS*     4.5     1.6    -      -       -      -
    131D  TRP*     3.6    31.6    -      -       +      -
    171D  TYR      4.7     0.2    -      -       -      +
    173D  CYS*     3.9    17.3    -      -       +      +
    186D  VAL*     3.3    51.5    -      -       +      +
    187D  GLU      4.0    11.0    -      -       -      +
    188D  TRP*     4.0    32.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 102 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100D  VAL*     5.3     4.2    +      -       -      +
    101D  ILE*     1.3    77.4    -      -       -      +
    103D  LEU*     1.3    64.4    +      -       -      +
    114D  THR      3.8     0.3    -      -       -      +
    115D  LEU*     3.6     7.1    -      -       -      -
    116D  VAL*     2.9    45.6    +      -       -      +
    118D  SER*     5.0     4.3    +      -       -      -
    188D  TRP*     5.0     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 103 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102D  SER*     1.3    79.2    +      -       -      +
    104D  SER*     1.3    63.6    +      -       -      +
    105D  ARG      4.2    10.0    -      -       -      +
    106D  THR      3.9    23.3    -      -       -      +
    107D  GLU*     4.1    18.2    -      -       +      +
    113D  ASN*     3.4    35.0    -      -       +      +
    114D  THR      3.7     7.4    -      -       -      +
    115D  LEU*     3.6    22.4    -      -       +      +
    116D  VAL*     5.7     0.4    -      -       -      -
    163D  MET*     4.4     5.6    -      -       +      -
    165D  PRO*     5.6     2.2    -      -       +      -
    188D  TRP*     4.0    30.2    -      -       +      +
----------------------------------------------------------
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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