Contacts of the helix formed by residues 179 - 189 (chain A) in PDB entry 1QVA
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 PHE 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PRO* 3.6 25.1 - - + -
145A THR* 5.6 2.9 - - + -
146A PRO* 3.7 33.4 - - + -
147A GLY* 4.6 9.0 - - - -
148A ARG* 5.9 3.1 - - - -
174A MET* 3.1 41.8 + - + +
175A LEU* 4.0 0.8 + - - -
177A SER* 3.6 23.1 - - - -
178A GLY* 1.3 79.6 - - - +
180A LYS* 1.3 65.4 + - - +
181A GLU 3.2 3.6 - - - -
182A GLN* 3.2 20.9 + - - -
183A ILE* 2.8 26.7 + - + +
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Residues in contact with LYS 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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175A LEU* 3.7 27.3 - - + +
178A GLY 3.4 2.7 - - - -
179A PHE* 1.3 77.2 - - - +
181A GLU* 1.3 57.2 + - - +
183A ILE* 3.6 1.7 - - - +
184A TYR* 2.7 76.3 + - + -
206A ASP* 4.1 25.3 + - - +
209A GLU* 3.3 25.4 + - - -
210A VAL* 5.6 0.9 - - + -
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Residues in contact with GLU 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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178A GLY 4.8 3.5 + - - +
179A PHE 3.2 0.4 - - - -
180A LYS* 1.3 82.7 - - - +
182A GLN* 1.3 65.8 + - - +
184A TYR* 3.3 8.9 + - - +
185A GLN* 2.8 73.3 + - - +
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Residues in contact with GLN 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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146A PRO* 3.7 23.8 - - + +
147A GLY* 4.1 22.4 - - - +
150A PHE* 4.5 16.3 - - + +
178A GLY 3.3 8.8 + - - +
179A PHE* 3.2 32.2 - - - +
181A GLU* 1.3 81.2 + - - +
183A ILE* 1.3 58.4 + - - +
185A GLN* 3.7 9.3 - - - +
186A ILE* 2.8 36.1 + - - +
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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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95A LEU* 4.1 15.7 - - + -
146A PRO* 4.2 7.0 - - + -
166A PHE* 4.5 1.3 - - + -
168A LEU* 4.1 19.3 - - + -
171A ALA* 6.1 0.9 - - + -
174A MET* 3.5 40.4 - - + -
175A LEU* 3.9 20.2 - - + -
179A PHE 2.8 19.5 + - - +
180A LYS* 3.7 4.7 - - - +
182A GLN* 1.3 76.8 - - - +
184A TYR* 1.3 65.7 + - + +
186A ILE* 3.1 9.7 + - - +
187A PHE* 2.9 52.2 + - + -
210A VAL* 5.1 2.9 - - + -
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Residues in contact with TYR 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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180A LYS* 2.7 53.1 + - + +
181A GLU* 3.7 12.1 - - - +
183A ILE* 1.3 77.4 - - + +
185A GLN* 1.3 64.2 + - + +
187A PHE* 3.1 23.0 + - - +
188A THR* 3.5 11.1 + - - +
209A GLU* 2.8 27.9 + - - +
210A VAL* 3.7 23.4 - - + +
213A LYS* 3.3 31.7 - - + +
214A PHE* 3.6 25.6 - + + -
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Residues in contact with GLN 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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150A PHE* 3.7 39.0 - - + -
181A GLU* 2.8 53.1 + - - +
182A GLN* 3.8 7.8 - - - +
184A TYR* 1.3 77.7 - - + +
186A ILE* 1.3 59.4 + - - +
188A THR* 2.7 29.9 + - + +
189A LEU* 3.1 14.0 - - + +
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Residues in contact with ILE 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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93A LEU* 4.1 11.9 - - + -
95A LEU* 3.8 22.4 - - + -
146A PRO* 3.8 24.7 - - + +
149A VAL* 4.0 13.5 - - + -
150A PHE* 4.2 17.0 - - + +
153A ILE* 4.6 6.5 - - + -
166A PHE* 3.4 28.5 - - + -
182A GLN 2.8 29.8 + - - +
183A ILE 3.4 5.4 - - - +
184A TYR 3.1 0.4 - - - -
185A GLN* 1.3 74.9 - - - +
187A PHE* 1.3 64.4 + - - +
189A LEU* 3.0 18.0 + - - +
190A LEU* 3.2 19.2 - - + +
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Residues in contact with PHE 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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166A PHE* 3.6 28.3 - + - -
168A LEU* 4.0 9.0 - - + -
183A ILE* 2.9 52.3 + - + -
184A TYR 3.3 6.7 - - - +
186A ILE* 1.3 76.7 - - - +
188A THR* 1.3 62.1 + - + +
190A LEU* 3.2 28.7 + - + +
194A THR* 6.2 0.2 - - - -
196A VAL* 4.0 17.9 - - + -
210A VAL* 3.9 11.7 - - + -
214A PHE* 3.3 71.1 - + + -
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Residues in contact with THR 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 TYR 3.6 13.9 - - - +
185A GLN* 2.7 23.5 + - + +
187A PHE* 1.3 77.2 - - + +
189A LEU* 1.3 69.4 + - - +
190A LEU 3.2 7.2 + - - +
214A PHE* 6.2 1.3 - - + -
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Residues in contact with LEU 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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150A PHE* 3.9 20.9 - - + -
153A ILE* 3.3 47.8 - - + -
160A THR* 2.5 34.0 + - + -
185A GLN* 3.1 22.0 - - + +
186A ILE* 3.0 5.6 + - - +
188A THR* 1.3 85.9 - - - +
190A LEU* 1.3 56.1 + - - +
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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