Contacts of the helix formed by residues 174 - 184 (chain A) in PDB entry 4COO
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 SER 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A MET* 4.6 0.2 - - - +
172A LYS 3.6 0.6 + - - -
173A MET* 1.3 76.8 - - - +
175A SER* 1.3 64.6 + - - +
176A GLU* 3.3 8.5 - - - -
177A LYS* 3.2 36.3 + - - +
178A VAL* 3.5 8.0 + - - +
304A GLU* 3.0 13.0 + - - -
380A ASN 2.7 29.6 + - - -
384A LYS* 3.7 24.9 - - - +
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A MET 3.8 0.8 + - - -
174A SER* 1.3 72.1 - - - +
176A GLU* 1.3 68.6 + - - +
178A VAL* 3.2 11.1 + - - +
179A ASP* 2.9 38.9 + - - +
383A THR* 4.6 5.2 + - - -
384A LYS* 5.5 0.2 - - - +
505B MET* 4.3 23.3 - - - +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A SER* 3.1 16.5 - - - -
175A SER* 1.3 83.8 + - - +
177A LYS* 1.3 60.5 + - - +
179A ASP* 3.3 5.4 + - - +
180A VAL* 3.2 28.9 + - - +
379A ARG 3.3 26.7 - - - +
380A ASN* 3.5 12.2 - - - +
381A TYR* 4.6 1.0 - - - -
382A MET* 3.6 17.8 + - + +
383A THR* 2.6 46.6 + - - +
384A LYS* 4.8 2.3 - - - +
382B MET* 3.7 23.5 - - + +
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Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A SER 2.8 29.6 + - - +
148A GLY* 4.1 9.4 - - - -
149A ASN* 4.5 8.2 - - - +
152A ILE* 4.1 17.4 - - + +
169A MET* 4.2 11.0 - - + -
173A MET* 4.1 3.6 - - + -
174A SER* 3.2 22.5 + - - +
175A SER 3.2 0.2 - - - -
176A GLU* 1.3 75.7 - - - +
178A VAL* 1.3 61.0 + - - +
180A VAL* 3.4 2.9 + - - +
181A LEU* 2.9 36.2 + - + +
304A GLU* 2.8 40.2 + - - +
305A GLY* 5.6 0.8 - - - -
380A ASN* 3.5 36.1 - - - +
381A TYR* 4.0 6.9 + - - -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A MET* 3.7 14.1 - - + +
174A SER 3.5 7.8 + - - +
175A SER* 3.2 11.1 + - - +
177A LYS* 1.3 77.7 - - - +
179A ASP* 1.3 57.7 + - - +
181A LEU* 3.3 8.7 + - - +
182A ARG* 2.9 63.2 + - - +
188A ILE* 3.8 14.5 - - + +
190A ARG* 3.3 29.8 - - - +
504B GLU* 4.0 9.4 - - + +
505B MET* 4.1 10.1 - - - -
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Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A SER* 2.9 28.2 + - - +
176A GLU* 3.8 8.8 - - - +
177A LYS 3.2 0.4 - - - -
178A VAL* 1.3 77.4 - - - +
180A VAL* 1.3 56.5 + - - +
182A ARG* 3.2 32.1 + - - +
183A ALA* 3.0 28.1 + - - +
382B MET* 4.2 15.2 - - + +
383B THR* 5.8 2.4 - - - +
386B LEU* 3.9 32.3 - - + +
387B SER* 5.6 5.8 - - - -
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ILE* 4.2 22.0 - - + -
176A GLU 3.2 17.2 + - - +
177A LYS 3.9 3.1 - - - +
179A ASP* 1.3 73.0 - - - +
181A LEU* 1.3 67.4 + - - +
183A ALA* 3.2 6.9 + - - +
184A LEU* 2.9 41.3 + - + +
379A ARG* 3.7 29.6 - - - +
345B LEU* 4.2 17.3 - - + -
378B VAL* 5.0 5.6 - - + -
382B MET* 3.9 12.8 - - + -
386B LEU* 4.4 7.2 - - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLY 5.0 2.0 - - - +
151A GLY 3.6 33.9 - - - +
152A ILE* 3.7 15.9 - - + +
155A ALA* 4.1 7.4 - - + -
167A ILE* 3.8 28.9 - - + -
169A MET* 3.9 29.2 - - + -
177A LYS* 2.9 23.8 + - + +
178A VAL* 3.7 4.9 - - - +
180A VAL* 1.3 78.7 - - - +
182A ARG* 1.3 62.0 + - - +
184A LEU* 3.2 10.2 + - - -
185A GLY 3.2 0.2 + - - -
186A ALA* 3.0 27.3 + - + +
188A ILE* 3.8 16.6 - - + -
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Residues in contact with ARG 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A VAL* 2.9 34.8 + - - +
179A ASP* 3.2 29.7 + - - +
181A LEU* 1.3 76.0 - - - +
183A ALA* 1.3 63.5 + - - +
185A GLY* 3.0 14.7 + - - -
186A ALA 4.3 7.6 - - - +
188A ILE* 3.6 15.5 - - + +
388B ASP* 5.4 9.9 - - - -
501B HIS* 4.7 10.5 + - - +
504B GLU* 2.5 43.6 + - - +
505B MET* 5.2 9.1 - - - +
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP 3.0 8.7 + - - +
180A VAL* 3.2 6.0 + - - +
182A ARG* 1.3 79.0 - - - +
184A LEU* 1.3 58.2 + - - +
185A GLY 3.2 1.1 + - - -
336B ARG* 4.6 5.7 - - + +
339B ILE* 3.6 19.5 - - + +
340B ALA* 3.5 24.1 - - - +
345B LEU* 6.0 0.2 - - + -
386B LEU* 3.4 34.8 - - + +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 3.8 28.5 - - + +
155A ALA* 4.0 18.3 - - + +
156A LEU* 3.9 25.8 - - + +
159A ALA* 3.6 23.2 - - + +
180A VAL* 2.9 37.0 + - + +
181A LEU* 3.7 5.6 - - - +
182A ARG 3.2 0.4 - - - -
183A ALA* 1.3 75.0 - - - +
185A GLY* 1.3 60.5 + - - +
186A ALA 3.4 0.6 + - - -
339B ILE* 3.5 33.2 - - + +
340B ALA* 4.4 7.6 - - - +
343B GLY* 4.3 10.1 - - - -
345B LEU* 4.5 5.6 - - + -
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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