Contacts of the helix formed by residues 191 - 205 (chain S) in PDB entry 5A0Q
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 LEU 191 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42S THR* 3.9 12.2 - - - +
44S GLU* 3.2 33.5 + - + +
45S GLY* 3.9 19.3 - - - +
46S VAL 5.0 2.7 - - - +
47S CYS* 6.5 0.4 - - + -
190S THR* 1.3 78.5 - - - +
192S LYS* 1.3 68.7 + - + +
194S ALA* 3.3 3.6 + - - +
195S ILE* 3.2 45.3 + - + +
219S THR* 5.7 2.2 - - - +
220S VAL 4.5 1.3 - - - +
221S GLN* 3.2 60.8 - - + +
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Residues in contact with LYS 192 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190S THR* 3.5 6.3 - - + +
191S LEU* 1.3 84.2 - - + +
193S GLU* 1.3 63.6 + - + +
195S ILE* 3.3 15.7 + - + +
196S LYS* 3.1 25.3 + - - +
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Residues in contact with GLU 193 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189S MET* 5.6 4.6 - - + +
190S THR* 3.2 37.1 + - + +
191S LEU 3.3 0.8 - - - -
192S LYS* 1.3 82.8 - - + +
194S ALA* 1.3 57.5 + - - +
196S LYS* 3.4 9.2 + - - +
197S SER* 3.2 22.9 + - - -
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Residues in contact with ALA 194 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40S ILE* 3.5 25.1 - - + +
42S THR* 2.1 46.4 - - + -
47S CYS* 5.3 0.4 - - + -
189S MET* 3.9 14.1 - - - -
190S THR 3.1 6.5 + - - +
191S LEU 3.4 2.9 - - - +
193S GLU* 1.3 73.6 - - - +
195S ILE* 1.4 62.9 + - + +
197S SER* 3.3 18.5 - - - -
198S SER 3.5 4.3 + - - -
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Residues in contact with ILE 195 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47S CYS* 3.4 28.0 - - + -
191S LEU* 3.2 43.0 + - + +
192S LYS* 3.4 12.8 - - + +
194S ALA* 1.4 73.6 - - - +
196S LYS* 1.3 63.8 + - - +
198S SER* 2.7 20.6 + - - -
199S LEU* 3.1 20.8 + - + +
217S LEU* 3.8 23.1 - - + -
219S THR* 4.0 17.9 - - + +
229S PHE* 5.2 11.9 - - + -
234S LEU* 5.8 0.4 - - + -
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Residues in contact with LYS 196 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192S LYS 3.1 13.4 + - - +
193S GLU* 3.4 13.0 + - - +
195S ILE* 1.3 75.0 - - - +
197S SER* 1.4 62.0 + - - +
199S LEU* 3.2 15.8 + - + +
200S ILE* 3.1 46.5 + - + +
236S GLU 6.2 5.2 - - - -
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Residues in contact with SER 197 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S ILE* 4.2 11.3 - - - +
181S LEU* 4.4 1.6 - - - +
184S VAL* 4.1 19.5 - - - +
189S MET* 5.5 8.2 - - - +
193S GLU 3.2 12.0 + - - -
194S ALA* 3.3 14.6 - - - -
195S ILE 3.1 0.6 - - - -
196S LYS* 1.4 74.9 - - - +
198S SER* 1.4 56.3 + - - +
200S ILE* 3.4 7.2 + - - +
201S ILE* 3.0 47.9 + - - +
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Residues in contact with SER 198 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S ILE* 3.6 16.6 - - - +
40S ILE* 3.9 14.3 - - - +
47S CYS* 3.5 19.6 - - - -
49S ALA* 3.8 24.2 - - - -
194S ALA 3.5 1.4 + - - -
195S ILE* 2.7 19.3 + - - -
197S SER* 1.4 77.8 - - - +
199S LEU* 1.3 55.8 + - - +
202S LEU* 3.0 36.8 + - - +
217S LEU* 3.8 7.5 - - - +
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Residues in contact with LEU 199 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195S ILE* 3.1 31.3 + - + +
196S LYS* 3.2 18.1 + - + +
198S SER* 1.3 77.1 - - - +
200S ILE* 1.4 60.4 + - + +
202S LEU* 5.0 0.2 - - - -
203S LYS* 3.8 21.1 + - - +
210S LEU* 3.9 16.8 - - + +
215S ILE* 3.7 27.8 - - + -
217S LEU* 4.7 7.0 - - + -
233S GLU 5.0 1.8 - - - +
234S LEU* 3.8 44.6 - - + +
236S GLU 4.6 14.6 - - - -
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Residues in contact with ILE 200 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196S LYS* 3.1 45.7 + - + +
197S SER* 3.9 5.2 - - - +
199S LEU* 1.4 76.3 - - + +
201S ILE* 1.3 68.5 + - + +
202S LEU 3.2 0.2 - - - -
203S LYS* 3.2 25.7 + - + +
204S GLN* 3.7 18.1 + - + +
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Residues in contact with ILE 201 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S ILE* 3.6 19.7 - - + -
177S ALA* 4.0 8.3 - - + +
180S SER* 3.7 20.0 - - - +
181S LEU* 3.8 24.0 - - + -
184S VAL* 4.4 10.8 - - + -
197S SER* 3.0 35.6 + - - +
200S ILE* 1.3 78.6 - - + +
202S LEU* 1.4 56.7 + - - +
204S GLN* 3.0 42.6 + - - +
205S VAL* 3.2 24.4 + - + +
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Residues in contact with LEU 202 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S THR* 4.2 11.2 - - + +
38S ILE* 3.9 17.0 - - + +
49S ALA* 3.9 19.3 - - + -
50S VAL* 4.3 4.5 - - - +
51S GLU* 4.0 22.7 - - + +
198S SER 3.0 21.2 + - - +
200S ILE 3.2 0.6 - - - -
201S ILE* 1.4 77.2 - - - +
203S LYS* 1.4 55.8 + - - +
205S VAL* 3.5 18.4 - - + +
206S MET* 3.1 29.8 + - - +
210S LEU* 3.9 21.9 - - + +
215S ILE* 3.4 37.5 - - + -
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Residues in contact with LYS 203 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199S LEU 3.8 14.1 + - - +
200S ILE* 3.2 15.0 + - + +
202S LEU* 1.4 75.2 - - - +
204S GLN* 1.4 62.2 + - + +
206S MET* 3.5 13.1 - - - +
208S GLU 4.2 6.4 - - - +
209S LYS* 3.8 36.5 - - + +
210S LEU* 3.1 46.6 + - + +
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Residues in contact with GLN 204 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176S GLY 4.9 1.7 - - - +
180S SER* 3.6 29.4 + - - -
200S ILE* 3.7 21.4 - - + +
201S ILE* 3.0 22.9 + - - +
203S LYS* 1.4 75.4 - - + +
205S VAL* 1.3 67.7 + - + +
206S MET 3.3 7.4 - - - +
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Residues in contact with VAL 205 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36S THR* 3.5 29.8 - - + +
38S ILE* 5.8 0.7 - - + -
173S ALA* 3.3 38.4 - - + +
176S GLY 5.0 0.9 - - - -
177S ALA* 3.7 33.9 - - + +
201S ILE* 3.4 19.1 - - + +
202S LEU* 3.5 22.4 - - + +
204S GLN* 1.3 77.9 - - + +
206S MET* 1.3 64.8 + - - +
207S GLU 4.0 0.3 + - - -
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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