Contacts of the helix formed by residues 182 - 194 (chain A) in PDB entry 2HVY
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 TYR 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ASP* 3.9 22.0 + - - -
141A GLN* 4.8 4.2 + - - +
180A GLY 3.6 5.0 + - - +
181A THR* 1.3 73.2 - - - +
183A ILE* 1.3 63.5 + - - +
184A ARG* 3.5 30.9 - - + +
185A SER* 3.2 31.5 + - - -
186A LEU* 3.0 25.1 + - - +
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Residues in contact with ILE 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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113A TYR* 3.6 43.7 - - + -
115A ALA* 4.1 13.5 - - + -
173A PHE* 4.8 0.7 - - + -
175A VAL* 4.0 19.7 - - + -
177A VAL* 4.0 22.2 - - + -
181A THR* 3.5 7.1 + - + +
182A TYR* 1.3 72.0 - - - +
184A ARG* 1.3 66.1 + - - +
186A LEU* 3.2 15.3 + - + +
187A ILE* 3.0 30.1 + - + +
200A MET* 3.9 11.7 - - - -
203A LEU* 3.8 24.2 - - + +
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Residues in contact with ARG 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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87A LYS* 4.8 16.0 - - - +
182A TYR* 3.5 33.3 - - + +
183A ILE* 1.3 79.5 - - - +
185A SER* 1.3 56.2 + - - +
187A ILE* 3.6 2.9 + - - +
188A HIS* 3.1 26.6 + - + +
199A HIS* 4.3 16.2 - - - +
200A MET* 3.0 70.9 + - + +
201A SER 5.7 0.4 - - - -
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Residues in contact with SER 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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141A GLN* 5.5 3.3 + - - +
182A TYR* 3.2 32.2 + - - -
183A ILE 3.2 0.4 - - - -
184A ARG* 1.3 77.9 - - - +
186A LEU* 1.3 65.5 + - - +
188A HIS* 3.2 9.2 + - - +
189A HIS* 3.0 46.1 + - - -
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Residues in contact with LEU 186 (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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135A PHE* 3.7 33.0 - - + -
139A ILE* 4.2 16.4 - - + -
158A VAL* 4.7 9.2 - - + -
161A ILE* 4.8 4.7 - - + -
173A PHE* 4.6 14.4 - - + -
175A VAL* 4.1 25.8 - - + -
177A VAL* 5.0 0.9 - - + -
181A THR* 5.3 5.2 - - + -
182A TYR 3.0 13.6 + - - +
183A ILE* 3.2 22.9 + - + +
185A SER* 1.3 76.3 - - - +
187A ILE* 1.3 56.9 + - + +
189A HIS* 3.4 8.3 + - - +
190A ILE* 3.0 44.4 + - + +
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Residues in contact with ILE 187 (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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115A ALA* 4.1 4.3 - - + -
116A LEU 4.4 0.2 - - - +
117A MET* 3.6 25.1 - - + -
173A PHE* 3.8 37.9 - - + -
183A ILE* 3.0 23.1 + - + +
184A ARG 3.9 4.0 - - - +
186A LEU* 1.3 73.2 - - + +
188A HIS* 1.3 66.3 + - - +
190A ILE* 3.2 9.3 + - + +
191A GLY* 3.0 21.0 + - - -
198A ALA* 3.9 2.1 - - + +
199A HIS* 3.5 32.3 - - - +
200A MET* 3.6 31.9 - - + +
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Residues in contact with HIS 188 (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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184A ARG 3.1 14.8 + - - +
185A SER* 3.2 11.0 + - - +
187A ILE* 1.3 78.2 - - - +
189A HIS* 1.3 74.5 + + - +
191A GLY* 3.4 2.3 + - - -
192A LEU* 3.2 42.4 + - + +
198A ALA 3.9 16.6 + - - +
199A HIS* 5.5 0.9 - - - +
13B GLN* 3.8 33.6 + - - +
15B PHE* 6.2 1.9 - + - -
43B ASP* 5.3 1.9 + - - -
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Residues in contact with HIS 189 (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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135A PHE* 4.0 11.6 - - + -
140A ILE 4.8 8.3 + - - -
141A GLN* 5.4 9.2 - - - -
185A SER* 3.0 39.2 + - - +
186A LEU* 3.7 6.9 + - - +
187A ILE 3.2 0.2 - - - -
188A HIS* 1.3 83.3 - + - +
190A ILE* 1.3 58.2 + - - +
192A LEU* 3.2 10.6 + - + +
193A ALA* 3.0 25.5 + - - +
43B ASP* 2.8 30.6 + - - -
44B VAL 5.5 0.4 - - - -
45B PHE* 3.3 52.5 - + + +
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Residues in contact with ILE 190 (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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117A MET* 3.8 15.7 - - - -
131A VAL* 4.4 5.4 - - + -
132A MET* 4.0 37.9 - - + -
135A PHE* 3.9 32.5 - - + -
161A ILE* 4.9 3.4 - - + -
173A PHE* 5.0 0.9 - - + -
186A LEU* 3.0 42.2 + - + +
187A ILE* 3.2 13.0 + - + +
189A HIS* 1.3 75.6 - - - +
191A GLY* 1.3 58.8 - - - +
193A ALA* 3.2 2.8 + - - +
194A LEU* 2.9 48.0 + - + +
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Residues in contact with GLY 191 (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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119A LEU* 5.0 0.2 - - - -
187A ILE 3.0 10.9 + - - -
188A HIS 3.7 2.9 - - - -
190A ILE* 1.3 77.6 - - - +
192A LEU* 1.3 55.2 + - - +
194A LEU* 3.5 6.6 + - - +
195A GLY 3.0 15.6 + - - -
196A VAL 3.6 0.3 + - - -
197A GLY* 2.9 29.2 + - - -
198A ALA* 3.6 29.4 - - - +
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Residues in contact with LEU 192 (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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188A HIS* 3.2 38.2 + - + +
189A HIS* 3.2 13.4 + - + +
191A GLY* 1.3 74.7 - - - +
193A ALA* 1.3 64.6 + - - +
195A GLY* 3.1 12.4 + - - -
197A GLY* 5.7 0.2 - - - -
9B HIS* 3.5 8.7 + - - -
11B ALA* 4.3 19.3 - - + -
13B GLN* 3.7 22.7 - - + +
15B PHE* 4.4 19.7 - - + -
17B ILE* 3.5 20.0 - - + +
43B ASP* 4.8 4.0 - - + +
45B PHE* 3.6 27.6 - - + -
54B ALA* 4.7 8.5 - - + -
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Residues in contact with ALA 193 (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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127A LYS* 3.4 10.1 + - - -
131A VAL* 3.8 13.5 - - + +
135A PHE* 4.0 5.8 - - + -
189A HIS 3.0 15.9 + - - +
190A ILE 3.2 5.4 + - - +
192A LEU* 1.3 75.7 - - - +
194A LEU* 1.3 57.7 + - - +
8B LEU* 5.1 0.3 - - - +
9B HIS* 3.2 18.5 + - - -
17B ILE* 4.6 0.4 - - - -
45B PHE* 4.1 1.5 - - + -
52B TYR* 3.7 51.6 - - + -
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Residues in contact with LEU 194 (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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117A MET* 4.7 2.7 - - + -
119A LEU* 3.6 33.0 - - + -
123A VAL* 3.9 23.7 - - + +
127A LYS* 3.7 44.4 + - + +
128A ILE* 4.1 13.0 - - + +
131A VAL* 3.8 14.8 - - + -
190A ILE* 2.9 33.9 + - + +
191A GLY* 3.9 5.2 - - - +
193A ALA* 1.3 76.3 - - - +
195A GLY* 1.3 56.4 + - - +
196A VAL* 3.2 17.2 + - + +
9B HIS* 3.6 9.0 + - - -
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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