Contacts of the helix formed by residues 192 - 198 (chain B) in PDB entry 3RLQ
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 GLU 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ARG* 3.2 33.5 + - - +
146B GLU* 5.4 0.2 + - - -
191B LYS* 1.3 73.7 - - - +
193B ASP* 1.3 59.1 + - + +
194B GLN 3.4 2.4 + - - -
195B THR* 3.6 19.0 + - + +
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Residues in contact with ASP 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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41B LYS* 5.2 2.8 + - - -
191B LYS* 3.9 10.7 - - - +
192B GLU* 1.3 79.0 - - + +
194B GLN* 1.3 86.5 + - - +
195B THR* 3.7 1.8 - - - -
196B GLU* 4.8 5.5 - - - +
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Residues in contact with GLN 194 (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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41B LYS* 3.5 32.5 - - - +
143B LEU 4.1 9.1 + - - +
144B VAL* 3.7 38.8 - - + +
190B LEU* 3.6 10.8 - - - +
191B LYS* 3.0 17.8 + - + +
193B ASP* 1.3 107.3 + - - +
195B THR* 1.3 59.7 + - - +
196B GLU* 3.2 12.0 + - - +
197B TYR* 3.3 40.5 + - + -
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Residues in contact with THR 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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84B LYS* 5.4 1.0 + - - -
87B ARG* 3.7 35.0 - - + -
190B LEU* 4.3 6.7 - - + -
191B LYS 4.1 3.1 - - - +
192B GLU* 3.6 19.1 + - + +
193B ASP 3.7 1.3 - - - -
194B GLN* 1.3 73.4 - - - +
196B GLU* 1.3 66.5 + - - +
197B TYR 3.0 3.1 - - - -
198B LEU* 2.9 28.7 + - + +
199B GLU* 4.1 4.5 + - - +
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Residues in contact with GLU 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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193B ASP 4.8 7.1 - - - +
194B GLN* 3.2 5.4 - - - +
195B THR* 1.3 78.5 + - - +
197B TYR* 1.3 94.6 + - + +
198B LEU 3.0 0.4 - - - -
199B GLU* 2.9 46.4 + - - +
202B ARG* 2.8 41.5 + - - +
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Residues in contact with TYR 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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41B LYS* 4.0 6.2 + - - +
42B GLU* 3.5 30.7 + - + +
44B PHE* 3.7 28.9 - + + -
45B LEU* 6.2 0.2 - - + -
89B LEU* 3.6 16.5 - - + +
144B VAL* 3.7 15.5 - - + -
190B LEU* 4.4 6.3 - - + -
194B GLN* 3.3 43.7 + - + +
195B THR 3.0 1.6 - - - -
196B GLU* 1.3 103.4 + - + +
198B LEU* 1.3 59.8 + - - +
199B GLU 3.3 0.7 - - - -
202B ARG* 3.9 10.3 + - + -
203B ILE* 3.4 24.4 - - + +
206B ILE* 3.5 35.2 - - + -
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Residues in contact with LEU 198 (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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82B PRO* 3.4 24.4 - - + +
83B ASN 4.1 8.7 - - - +
84B LYS* 3.7 48.4 - - + +
87B ARG* 4.0 16.6 - - + -
88B THR 3.3 31.0 - - - +
89B LEU* 4.2 1.6 - - + +
190B LEU* 3.5 25.1 - - + -
195B THR* 2.9 31.6 + - + +
197B TYR* 1.3 80.4 - - - +
199B GLU* 1.3 61.4 + - - +
200B GLU 3.7 1.7 + - - -
203B ILE* 4.3 0.4 - - - -
222B VAL* 5.5 3.6 - - - +
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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