Contacts of the helix formed by residues 174 - 188 (chain C) in PDB entry 3H0Z
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 VAL 174 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C LEU* 3.2 20.4 - - + +
172C ALA* 3.3 16.8 - - + +
173C GLY* 1.3 73.7 - - - +
175C GLU* 1.3 62.6 + - - +
176C HIS* 3.6 2.9 - - - -
177C GLN* 3.6 34.8 - - + +
178C LEU* 3.9 12.1 + - + +
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Residues in contact with GLU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LYS* 5.1 12.2 - - + -
169C LEU* 3.7 25.6 - - + +
170C GLU* 3.5 37.3 - - + +
173C GLY 3.0 8.6 + - - +
174C VAL* 1.3 78.8 - - - +
176C HIS* 1.3 66.6 + - - +
178C LEU* 3.8 8.3 + - - +
179C ARG* 3.3 31.8 + - - +
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Residues in contact with HIS 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C GLY 5.2 4.9 - - - -
174C VAL* 5.5 0.7 - - - -
175C GLU* 1.3 83.8 - - + +
177C GLN* 1.3 90.6 + - + +
178C LEU 3.2 0.2 - - - -
179C ARG* 3.2 26.2 + - - +
180C ARG* 3.2 36.2 + - - +
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Residues in contact with GLN 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C VAL* 3.6 35.3 + - + +
175C GLU 3.3 1.0 - - - -
176C HIS* 1.3 98.6 + - + +
178C LEU* 1.3 59.1 + - - +
180C ARG* 3.6 12.2 - - + +
181C GLU* 2.8 56.2 + - + +
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C LEU* 4.1 22.0 - - + -
169C LEU* 3.9 26.7 - - + -
174C VAL* 3.9 9.3 + - + +
175C GLU 3.8 11.1 + - - +
176C HIS 3.2 0.6 - - - -
177C GLN* 1.3 75.3 - - - +
179C ARG* 1.3 63.7 + - - +
181C GLU* 4.6 9.0 - - + +
182C VAL* 2.9 52.8 + - + +
206C VAL* 4.3 17.0 - - + -
208C LEU* 4.4 17.9 - - + -
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Residues in contact with ARG 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LYS* 5.8 5.1 - - - +
175C GLU* 3.3 34.8 + - - +
176C HIS* 3.2 27.6 + - - +
178C LEU* 1.3 82.3 - - - +
180C ARG* 1.3 61.5 + - - +
182C VAL* 4.0 5.4 - - - +
183C GLU* 3.3 30.2 + - - +
199C TYR* 3.3 42.9 + - + +
201C HIS* 6.0 3.8 - - - -
206C VAL* 6.4 1.8 - - - -
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Residues in contact with ARG 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C HIS* 3.2 30.5 + - - +
177C GLN* 3.6 18.4 - - - +
178C LEU 3.2 0.2 - - - -
179C ARG* 1.3 77.0 - - - +
181C GLU* 1.3 63.6 + - - +
183C GLU* 3.5 29.4 - - - +
184C ILE* 3.6 20.6 + - - +
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Residues in contact with GLU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C GLN* 2.8 49.8 + - + +
178C LEU* 4.1 9.3 - - + +
180C ARG* 1.3 74.1 - - + +
182C VAL* 1.3 55.1 + - + +
184C ILE* 3.1 10.6 + - - +
185C GLN* 2.7 44.0 + - + +
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C LEU* 2.9 43.5 + - + +
179C ARG* 4.0 4.3 - - - +
180C ARG 3.4 0.2 - - - -
181C GLU* 1.3 73.8 - - + +
183C GLU* 1.3 64.9 + - - +
185C GLN* 3.9 7.1 - - + +
186C SER* 3.0 25.2 + - - -
196C LEU* 3.8 34.3 - - + -
198C GLY* 5.0 2.7 - - - -
199C TYR* 3.5 33.0 - - + -
208C LEU* 4.1 13.9 - - + -
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Residues in contact with GLU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ARG* 3.3 16.0 + - - +
180C ARG* 3.5 26.2 - - - +
181C GLU 3.3 0.2 - - - -
182C VAL* 1.3 77.6 - - + +
184C ILE* 1.3 60.3 + - + +
186C SER* 2.7 21.0 + - - -
187C HIS* 3.4 17.3 + - + -
199C TYR* 6.1 2.7 - - + -
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Residues in contact with ILE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C ARG* 3.6 21.3 + - - +
181C GLU* 3.1 10.8 + - - +
183C GLU* 1.3 79.1 - - + +
185C GLN* 1.3 66.0 + - + +
187C HIS* 3.1 24.6 + - + +
188C LEU* 3.2 17.8 + - + +
250C LYS* 5.0 9.4 - - + +
251C ARG 6.1 0.7 - - - +
252C VAL* 3.5 33.0 - - + -
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Residues in contact with GLN 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C GLU* 2.7 30.7 + - + +
182C VAL* 3.9 2.2 - - + +
183C GLU 3.5 0.2 - - - -
184C ILE* 1.3 74.1 - - + +
186C SER* 1.3 60.8 + - - +
188C LEU* 3.5 34.1 + - + +
193C ILE* 5.1 6.1 - - - +
194C LEU* 4.2 18.8 + - - +
196C LEU* 3.8 40.5 + - + +
210C LEU* 5.7 2.0 - - - +
254C HIS* 3.8 21.8 + - - -
272C ILE 6.0 0.2 + - - -
273C ALA* 6.0 4.9 - - - +
274C ASP 4.5 13.5 + - - +
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Residues in contact with SER 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C VAL* 3.0 16.3 + - - -
183C GLU* 2.7 24.3 + - - -
185C GLN* 1.3 73.7 - - - +
187C HIS* 1.3 69.7 + - - +
188C LEU 3.4 5.2 + - - +
189C ARG* 4.3 13.7 + - - +
195C ARG* 5.7 3.6 + - - -
196C LEU* 3.6 21.6 + - - +
197C TYR 4.9 6.1 - - - -
198C GLY* 6.0 1.3 - - - -
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Residues in contact with HIS 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C GLU* 3.4 17.9 + - + +
184C ILE* 3.1 22.2 + - + +
186C SER* 1.3 86.0 + - - +
188C LEU* 1.3 63.6 + - + +
189C ARG* 3.4 22.2 + - - +
246C TYR* 4.2 4.0 + - - -
250C LYS* 5.7 5.2 + - + -
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ILE* 3.2 17.0 + - + +
185C GLN* 3.6 31.0 - - - +
186C SER 3.3 3.6 - - - +
187C HIS* 1.3 78.4 - - + +
189C ARG* 1.3 64.1 + - - +
190C HIS 4.3 0.4 - - - -
193C ILE* 4.6 21.4 - - + +
194C LEU 5.6 0.5 - - - +
195C ARG* 5.0 11.6 - - - +
246C TYR* 3.6 25.8 - - + -
247C CYS* 4.4 18.2 - - - -
250C LYS* 3.8 26.9 - - + -
252C VAL* 4.1 26.2 - - + -
254C HIS* 5.8 2.2 - - + +
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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
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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