Contacts of the helix formed by residues 171 - 178 (chain B) in PDB entry 1QHI
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 CYS 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 3.0 21.2 + - - +
167B ALA 4.0 1.1 - - - +
170B LEU* 1.3 84.6 - - - +
172B TYR* 1.3 65.6 + - - +
174B ALA 3.4 0.7 + - - -
175B ALA* 3.0 21.3 + - - +
235B ILE* 3.7 2.8 - - - +
238B VAL* 3.5 25.9 - - + +
239B TYR* 3.6 50.3 - - + +
242B LEU* 3.9 20.4 - - - -
288B LEU* 6.2 0.2 - - - -
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B BPG 3.1 81.8 - + + +
58B HIS* 2.7 44.2 + - - +
125B GLN* 4.0 2.0 - - - +
163B ARG* 3.2 26.0 + - - -
167B ALA 3.0 20.7 + - - +
171B CYS* 1.3 71.1 - - - +
173B PRO* 1.3 76.4 - - + +
175B ALA* 3.2 1.9 + - - +
176B ARG* 2.9 27.9 + - - +
231B MET* 3.7 14.4 - - + -
235B ILE* 3.7 25.8 - - + +
239B TYR* 4.2 3.8 - - - -
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Residues in contact with PRO 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLN* 4.2 13.5 - - + +
167B ALA 3.8 1.8 - - - +
168B ALA 3.3 27.6 - - - +
169B LEU* 4.3 2.5 - - - -
170B LEU* 3.5 19.7 - - - +
172B TYR* 1.3 94.5 - - + +
174B ALA* 1.3 55.6 + - - +
176B ARG* 3.3 2.4 + - - +
177B TYR 2.9 23.4 + - - -
182B MET* 4.0 22.8 - - + +
187B VAL* 3.4 23.0 - - + +
190B PHE* 4.5 17.5 - - + -
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 2.9 26.1 + - + +
171B CYS 3.8 3.8 - - - +
173B PRO* 1.3 75.7 - - - +
175B ALA* 1.3 62.8 + - - +
177B TYR* 3.1 12.0 + - + +
178B LEU* 3.0 25.8 + - - +
187B VAL* 4.2 14.1 - - + +
238B VAL* 4.1 12.6 - - + -
288B LEU* 5.5 0.7 - - + -
291B LEU* 4.1 23.6 - - + -
292B PHE* 5.3 1.8 - - + -
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B CYS 3.0 16.9 + - - +
172B TYR 3.6 4.0 - - - +
174B ALA* 1.3 77.5 - - - +
176B ARG* 1.3 57.1 + - - +
178B LEU* 3.1 6.8 + - - +
179B MET* 2.8 31.1 + - - +
231B MET* 3.8 20.9 - - + -
234B ALA* 4.0 6.6 - - + +
235B ILE* 3.9 28.0 - - + +
238B VAL* 3.8 8.7 - - + +
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Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B BPG 3.2 47.9 + - + +
100B ILE* 3.3 17.8 + - - +
101B TYR* 4.1 13.7 - - - -
104B GLN* 2.9 39.7 + - - +
121B MET* 3.7 9.2 - - + -
172B TYR 2.9 14.5 + - - +
175B ALA* 1.3 73.0 - - - +
177B TYR* 1.3 65.6 + - - +
179B MET* 3.2 4.1 + - - +
180B GLY 3.0 16.3 + - - -
181B SER* 3.0 28.9 + - - +
182B MET* 3.2 33.4 - - + -
228B ASP* 5.1 0.4 + - - -
231B MET* 3.6 34.4 - - + +
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PRO 2.9 14.3 + - - +
174B ALA* 3.1 11.2 + - + +
176B ARG* 1.3 75.8 - - - +
178B LEU* 1.3 83.0 + - + +
180B GLY* 2.7 25.8 + - - -
182B MET* 3.4 17.6 - - - +
184B PRO* 3.3 42.2 - - + -
187B VAL* 3.7 18.2 - - + -
291B LEU* 3.7 27.1 + - + -
292B PHE* 5.5 4.5 - + - -
294B ALA* 3.5 22.7 - - + +
296B GLU* 5.4 2.0 - - - -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ALA 3.0 9.2 + - - +
175B ALA* 3.3 8.1 - - - +
177B TYR* 1.3 102.9 - - + +
179B MET* 1.3 62.6 + - - +
180B GLY* 3.1 1.3 + - - -
234B ALA* 4.3 21.3 - - + +
237B ARG* 4.1 27.1 - - - +
238B VAL* 3.8 27.8 - - + -
291B LEU* 3.8 22.0 - - + -
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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