Contacts of the helix formed by residues 176 - 185 (chain A) in PDB entry 2HQQ
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 ARG 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A TYR* 3.6 31.7 + - - -
141A ARG* 4.4 24.6 + - - +
174A LYS* 2.8 50.5 + - + +
175A PRO* 1.3 77.7 - - + +
177A GLU* 1.3 67.1 + - - +
178A GLU* 3.2 19.5 + - + +
179A LEU* 2.9 32.7 + - + +
180A PHE* 3.6 8.5 - - - -
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Residues in contact with GLU 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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175A PRO 4.2 0.8 + - - -
176A ARG* 1.3 71.6 - - - +
178A GLU* 1.3 66.1 + - - +
180A PHE* 3.0 44.0 + - + +
181A GLN 4.4 1.2 + - - -
198A HIS* 6.0 0.4 + - - -
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Residues in contact with GLU 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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141A ARG 3.4 22.0 - - - +
142A ASN* 4.0 3.8 - - - -
143A ALA* 3.1 20.9 + - + +
144A SER 5.0 1.4 + - - +
176A ARG* 3.1 21.0 + - + +
177A GLU* 1.3 82.4 - - - +
179A LEU* 1.3 71.6 - - + +
181A GLN* 2.8 37.1 + - - +
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Residues in contact with LEU 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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140A GLY* 3.7 17.3 - - - +
141A ARG* 3.4 42.4 - - - +
143A ALA* 4.1 9.2 - - + -
172A VAL* 3.9 24.0 - - + +
173A GLU 4.6 3.1 - - - +
174A LYS* 3.4 42.0 - - + +
176A ARG* 2.9 21.0 + - + +
178A GLU* 1.3 83.8 - - + +
180A PHE* 1.3 59.0 + - - +
181A GLN 3.2 3.1 - - - -
182A LEU* 2.9 30.8 + - + +
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Residues in contact with PHE 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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172A VAL* 4.3 6.3 - - + -
174A LYS 4.5 0.4 - - - -
175A PRO 4.3 0.4 - - - -
176A ARG 3.6 27.1 - - - -
177A GLU* 3.0 40.4 + - + +
179A LEU* 1.3 78.4 - - - +
181A GLN* 1.3 62.9 + - - +
183A PHE* 3.0 53.3 + + + +
195A VAL* 3.9 22.2 - - + -
198A HIS* 4.3 14.1 - + - -
199A LEU* 3.9 30.7 - - + -
214A ARG* 4.0 22.3 + - - +
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Residues in contact with GLN 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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143A ALA* 3.7 15.3 - - + +
144A SER* 4.3 12.0 - - - +
147A VAL* 3.6 28.6 - - + +
177A GLU 4.4 1.6 + - - -
178A GLU* 2.8 32.0 + - - +
180A PHE* 1.3 77.0 - - - +
182A LEU* 1.3 64.0 + - - +
183A PHE 3.2 0.9 + - - -
184A GLY* 3.3 10.0 + - - -
185A TYR* 3.5 17.4 - - + -
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Residues in contact with LEU 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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138A ILE* 5.7 2.0 - - + -
140A GLY* 3.6 31.0 - - - -
143A ALA* 4.2 14.1 - - + +
146A GLN* 3.8 14.1 - - + +
147A VAL* 3.9 19.5 - - + -
150A LEU* 3.8 27.1 - - + -
170A VAL* 3.8 17.3 - - + +
171A GLU 4.7 1.1 - - - +
172A VAL* 4.0 14.6 - - + -
179A LEU* 2.9 26.9 + - + +
181A GLN* 1.3 73.1 - - - +
183A PHE* 1.3 64.3 + - - +
184A GLY 3.0 3.1 - - - -
185A TYR* 3.0 25.5 + - - +
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Residues in contact with PHE 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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172A VAL* 3.7 29.8 - - + -
180A PHE* 3.0 49.3 + + + +
182A LEU* 1.3 79.1 - - - +
184A GLY* 1.3 56.9 + - - +
185A TYR 3.3 9.1 + - - +
189A VAL* 3.7 21.3 - - + +
191A VAL* 4.0 26.7 - - + -
195A VAL* 4.2 5.4 - - + -
199A LEU* 4.7 2.5 - - + -
211A LEU* 4.3 22.9 - - + -
214A ARG* 3.6 42.2 - - + +
215A VAL* 3.3 27.0 - - + +
216A ARG 4.1 0.3 + - - -
221A LEU* 5.1 3.8 - - + -
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Residues in contact with GLY 184 (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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181A GLN 3.3 8.5 + - - -
182A LEU 3.0 1.4 + - - -
183A PHE* 1.3 78.1 - - - +
185A TYR* 1.3 70.1 + - - +
214A ARG 3.4 14.5 + - - -
215A VAL 4.4 0.2 - - - -
216A ARG* 3.5 29.5 + - - +
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Residues in contact with TYR 185 (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 VAL* 3.3 27.5 - - + +
150A LEU* 3.7 39.7 - - + -
151A GLN* 3.3 35.0 + - + -
154A ASP* 3.9 20.6 - - - -
170A VAL* 3.9 4.9 - - + +
181A GLN* 3.5 23.3 - - + -
182A LEU* 3.0 19.2 + - - +
183A PHE 3.6 0.5 - - - +
184A GLY* 1.3 86.5 - - - +
186A GLY* 1.3 65.9 + - - +
189A VAL* 3.3 15.6 - - - +
216A ARG* 4.5 7.4 - - - +
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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