Contacts of the helix formed by residues 192 - 197 (chain B) in PDB entry 5UQ3
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.
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 HIS 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 3.2 53.3 - + + -
78B PHE* 4.5 2.7 - - + +
79B ASP* 5.6 4.0 - - - -
189B ALA* 3.0 17.3 + - + +
190B PRO 3.3 2.1 - - - +
191B THR* 1.3 81.5 + - - +
193B TYR* 1.3 88.8 + + - +
194B ILE* 3.3 41.6 + - + +
195B TRP* 3.7 12.7 + + + +
196B GLN* 2.8 26.9 - - - +
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Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PHE* 3.6 36.9 + - + +
79B ASP* 5.9 1.6 - - - -
83B ILE* 5.6 0.2 - - - +
84B GLN* 5.3 4.7 - - - +
87B LEU* 4.6 15.4 - - + +
191B THR 3.6 3.4 + - - -
192B HIS* 1.3 103.1 - + - +
194B ILE* 1.3 78.4 + - + +
196B GLN* 2.9 25.8 + - - +
197B ARG* 3.9 21.7 - - + +
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 5.3 3.4 - - + -
75B PHE* 5.5 2.5 - - + -
78B PHE* 3.5 43.5 - - + -
87B LEU* 6.3 0.4 - - + -
98B LYS* 3.5 7.7 - - - +
101B LEU* 3.6 33.0 - - + -
192B HIS* 3.3 30.9 - - + +
193B TYR* 1.3 95.6 - - + +
195B TRP* 1.3 80.1 + - + +
197B ARG* 3.1 35.0 + - - +
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Residues in contact with TRP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B MET* 3.7 4.9 - - + -
74B PHE* 5.5 6.0 - + - -
75B PHE* 3.4 37.5 - + - -
98B LYS* 3.1 31.3 + - - +
101B LEU 5.4 1.4 + - - -
102B ALA* 5.0 7.5 - - - +
185B VAL* 3.6 13.0 - - + -
186B MET* 3.2 75.7 - - + +
189B ALA 3.0 34.3 - - - -
190B PRO* 3.7 9.6 - - + +
192B HIS* 3.7 10.0 + - + -
193B TYR 3.1 1.4 + - - -
194B ILE* 1.3 99.0 - - + +
196B GLN* 1.3 67.5 + - - +
197B ARG 3.3 0.9 - - - -
198B GLU* 5.0 1.7 - - - +
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Residues in contact with GLN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PRO 3.1 22.7 + - - +
191B THR* 4.0 8.9 + - - +
192B HIS 2.8 21.4 + - - +
193B TYR* 2.9 12.2 + - - +
195B TRP* 1.3 84.5 - - - +
197B ARG* 1.3 60.7 + - - +
198B GLU* 3.6 12.6 + - - +
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Residues in contact with ARG 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 3.0 53.9 + - - +
90B ASP* 3.3 16.8 + - - +
91B CYS 5.2 0.8 + - - -
93B CYS* 3.4 19.7 - - - -
96B ALA 3.1 27.3 + - - -
97B ASP* 3.5 1.3 - - - +
98B LYS* 3.1 31.8 + - + +
101B LEU* 4.9 3.2 - - - +
193B TYR* 3.9 21.2 - - + +
194B ILE* 3.1 29.9 + - - +
195B TRP 3.3 0.6 - - - -
196B GLN* 1.3 78.3 - - - +
198B GLU* 1.3 60.1 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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