Contacts of the helix formed by residues 164 - 178 (chain B) in PDB entry 2QNU
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 THR 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B VAL* 1.3 92.6 - - + +
165B PRO* 1.3 69.7 - - + +
166B ALA* 3.7 8.9 + - - +
167B GLN* 3.2 29.8 + - - +
168B ARG* 2.9 32.8 + - - +
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Residues in contact with PRO 165 (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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106A GLY* 3.4 21.5 - - - +
107A GLY 3.2 30.3 - - - +
108A ASP* 4.7 3.6 - - - -
109A ASP* 3.8 19.7 - - - +
163B VAL 4.9 0.2 - - - +
164B THR* 1.3 87.7 - - + +
166B ALA* 1.3 57.0 + - - +
168B ARG* 3.7 20.3 - - - +
169B LEU* 2.9 24.3 + - - +
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Residues in contact with ALA 166 (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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164B THR* 3.2 8.2 - - - +
165B PRO* 1.3 78.7 - - - +
167B GLN* 1.3 60.3 + - + +
169B LEU* 3.4 7.4 + - - +
170B ALA* 3.0 28.1 + - - +
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Residues in contact with GLN 167 (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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148B ILE* 3.8 26.2 - - + +
161B GLU 3.5 16.4 + - - +
162B ALA* 3.6 13.5 - - + +
163B VAL* 2.9 31.9 + - - +
164B THR* 3.2 25.6 + - - +
166B ALA* 1.3 75.8 - - + +
168B ARG* 1.3 61.7 + - - +
170B ALA* 3.4 2.6 + - - +
171B ALA* 2.9 29.3 + - - +
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Residues in contact with ARG 168 (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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59A ARG* 5.5 0.4 - - - +
104A LEU 5.3 0.4 + - - -
105A VAL* 2.8 40.9 + - + +
106A GLY* 4.7 1.3 - - - -
107A GLY 3.9 3.8 + - - -
109A ASP* 3.0 27.3 + - - -
112A PHE* 6.3 0.4 - - - -
184A TRP* 3.4 49.4 - - - +
195A LEU* 4.0 15.9 - - + -
162B ALA* 3.9 22.6 + - + +
163B VAL* 4.0 13.1 + - - +
164B THR 2.9 24.4 + - - +
165B PRO* 3.7 20.5 - - - +
167B GLN* 1.3 78.9 - - - +
169B LEU* 1.3 61.4 + - - +
171B ALA* 3.6 2.4 - - - +
172B LEU* 3.0 32.0 + - - +
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Residues in contact with LEU 169 (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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102A GLY 3.6 25.6 - - - +
103A GLY* 4.7 4.3 - - - -
106A GLY* 4.1 15.4 - - - +
169A LEU* 4.0 29.4 - - + +
170A ALA* 5.6 4.7 - - - +
173A ALA* 3.9 19.5 - - + +
165B PRO 2.9 16.9 + - - +
166B ALA* 3.7 7.6 - - - +
167B GLN 3.3 0.2 - - - -
168B ARG* 1.3 75.1 - - - +
170B ALA* 1.3 66.6 + - - +
172B LEU* 3.3 5.0 + - - +
173B ALA* 3.1 23.4 + - - +
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Residues in contact with ALA 170 (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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169A LEU* 5.6 4.7 - - - -
100B ASP* 4.5 7.7 - - - +
148B ILE* 4.3 15.0 - - + -
166B ALA 3.0 17.7 + - - +
167B GLN* 3.9 4.5 - - - +
169B LEU* 1.3 77.1 - - - +
171B ALA* 1.3 53.5 + - - +
173B ALA* 3.5 5.8 + - - +
174B GLN* 2.7 41.2 + - - +
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Residues in contact with ALA 171 (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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195A LEU* 4.3 4.3 - - + -
227A ACT 3.5 14.0 - - + +
148B ILE* 4.1 8.7 - - + +
150B GLN* 4.3 2.5 + - - +
160B SER* 4.0 30.7 - - - +
162B ALA* 4.4 1.3 - - + -
167B GLN 2.9 18.3 + - - +
168B ARG* 3.6 8.3 - - - +
169B LEU 3.2 0.2 - - - -
170B ALA* 1.3 74.6 - - - +
172B LEU* 1.3 65.0 + - - +
174B GLN* 3.4 13.5 + - - +
175B HIS 3.1 18.2 + - - -
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Residues in contact with LEU 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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102A GLY* 4.3 9.6 - - - +
105A VAL* 4.0 22.7 - - + -
106A GLY 5.3 0.4 - - - +
173A ALA* 3.7 17.0 - - + +
176A ALA* 3.1 24.9 - - + +
177A CYS* 3.5 29.8 - - - -
182A HIS* 3.7 9.4 - - + +
195A LEU* 3.7 22.2 - - + -
227A ACT 3.6 22.7 - - - +
168B ARG 3.0 26.9 + - - +
169B LEU* 3.8 4.3 - - - +
171B ALA* 1.3 77.2 - - - +
173B ALA* 1.3 62.5 + - - +
175B HIS* 3.3 2.1 + - - +
176B ALA* 3.2 9.2 + - - +
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Residues in contact with ALA 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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169A LEU* 3.6 36.6 - - + +
172A LEU* 3.8 22.0 - - + +
173A ALA* 4.0 4.1 - - + +
102B GLY* 4.0 9.9 - - - -
169B LEU 3.1 15.2 + - - +
170B ALA* 3.9 4.5 - - - +
172B LEU* 1.3 76.7 - - - +
174B GLN* 1.3 62.2 + - - +
176B ALA* 3.2 12.1 + - - +
177B CYS* 3.6 15.2 + - - -
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Residues in contact with GLN 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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100B ASP* 3.5 20.6 - - - +
101B LEU* 5.5 0.9 - - - +
102B GLY* 4.1 12.4 - - - +
146B PRO 4.6 0.2 - - - +
147B ARG* 3.0 49.3 - - + +
148B ILE* 2.7 48.6 + - - +
150B GLN* 3.8 13.3 - - - +
170B ALA* 2.7 28.1 + - - +
171B ALA* 3.6 5.3 - - - +
172B LEU 3.4 0.2 - - - -
173B ALA* 1.3 73.2 - - - +
175B HIS* 1.3 63.1 + - - +
177B CYS* 3.0 18.1 + - - +
178B ASP* 3.5 10.7 - - - +
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Residues in contact with HIS 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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176A ALA* 4.1 9.2 - - + +
197A ARG* 3.2 45.2 + - - -
227A ACT 3.8 17.5 - - + +
147B ARG* 4.2 1.5 - - - +
150B GLN* 5.0 0.9 - - - +
158B LEU* 3.5 26.2 - - + +
171B ALA 3.1 12.1 + - - +
172B LEU 3.3 8.5 + - - +
174B GLN* 1.3 79.5 - - - +
176B ALA* 1.3 62.7 + - - +
177B CYS 3.1 1.0 + - - -
178B ASP* 3.2 34.7 + - + +
197B ARG* 5.1 0.9 + - - -
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Residues in contact with ALA 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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172A LEU* 3.1 41.7 - - + +
175A HIS* 4.0 20.4 - - + -
176A ALA* 4.3 2.7 - - - +
172B LEU 3.2 8.2 + - - +
173B ALA 3.2 8.9 + - - +
175B HIS* 1.3 79.6 + - - +
177B CYS* 1.3 56.1 + - - +
178B ASP 3.5 0.2 - - - -
180B ALA* 3.9 0.2 - - - +
182B HIS* 3.5 5.8 - - - -
197B ARG* 3.0 34.3 + - - +
227B ACT 4.1 1.8 - - - +
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Residues in contact with CYS 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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172A LEU* 3.6 29.2 - - - -
61B ALA* 5.9 0.4 - - - -
63B ALA* 3.5 11.4 - - - +
101B LEU* 3.9 44.9 - - + -
105B VAL* 4.3 3.1 - - - -
173B ALA 3.7 6.3 - - - -
174B GLN* 3.0 10.4 + - - +
176B ALA* 1.3 78.6 - - - +
178B ASP* 1.3 65.4 + - - +
179B GLY 3.4 0.2 + - - -
180B ALA* 3.1 18.3 + - - +
182B HIS* 4.0 18.4 - - + +
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Residues in contact with ASP 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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63B ALA* 4.4 2.7 - - - -
64B PRO* 5.7 3.7 - - - +
147B ARG* 2.9 44.3 + - - -
158B LEU* 5.8 0.3 - - - +
174B GLN 3.5 7.0 - - - +
175B HIS* 3.2 28.7 + - + +
177B CYS* 1.3 78.2 - - - +
179B GLY* 1.3 64.0 + - - +
180B ALA* 3.2 4.9 + - - +
197B ARG* 3.9 9.4 + - - -
199B GLN* 4.5 4.2 + - - -
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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