Contacts of the helix formed by residues 164 - 178 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A VAL* 1.3 87.7 - - + +
165A PRO* 1.3 76.4 - - + +
166A ALA* 3.6 7.3 + - - +
167A GLN* 3.2 36.2 + - - +
168A ARG* 3.1 28.1 + - - +
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Residues in contact with PRO 165 (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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164A THR* 1.3 88.9 - - - +
166A ALA* 1.3 56.5 + - - +
168A ARG* 3.4 13.9 + - - +
169A LEU* 3.0 23.9 + - - +
106B GLY* 3.4 17.8 - - - +
107B GLY* 3.3 35.2 - - - +
108B ASP* 4.5 2.0 - - - -
109B ASP* 3.5 29.2 - - - +
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Residues in contact with ALA 166 (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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164A THR* 3.4 8.0 + - - +
165A PRO* 1.3 76.3 - - - +
167A GLN* 1.3 59.9 + - + +
169A LEU* 3.4 8.1 + - - +
170A ALA* 3.0 29.8 + - - +
106B GLY 5.2 0.4 - - - -
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Residues in contact with GLN 167 (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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148A ILE* 3.8 17.8 - - + +
161A GLU 3.8 6.1 - - - +
162A ALA* 3.6 16.5 - - + +
163A VAL* 2.9 30.7 + - - +
164A THR* 3.2 30.3 + - - +
166A ALA* 1.3 79.2 - - + +
168A ARG* 1.3 57.9 + - - +
170A ALA* 3.4 6.9 + - - +
171A ALA* 2.8 29.8 + - - +
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Residues in contact with ARG 168 (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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162A ALA* 3.8 22.4 + - + +
163A VAL* 3.8 15.8 + - - +
164A THR 3.1 21.4 + - - +
165A PRO* 3.5 27.9 - - - +
167A GLN* 1.3 74.7 - - - +
169A LEU* 1.3 65.0 + - - +
171A ALA* 3.2 1.2 + - - +
172A LEU* 3.0 30.7 + - - +
59B ARG* 5.2 1.4 - - - +
104B LEU 5.2 0.2 + - - -
105B VAL* 2.8 35.0 + - + +
106B GLY* 4.4 1.3 - - - -
107B GLY 3.7 4.6 + - - -
109B ASP* 2.9 27.3 + - - -
184B TRP* 3.5 49.0 - - - +
195B LEU* 3.9 20.2 - - + -
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Residues in contact with LEU 169 (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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165A PRO 3.0 16.7 + - - +
166A ALA* 3.7 8.3 - - - +
168A ARG* 1.3 74.6 - - - +
170A ALA* 1.3 63.5 + - - +
172A LEU* 3.2 5.8 + - - +
173A ALA* 3.0 23.8 + - - +
102B GLY 3.6 25.8 - - - +
103B GLY* 4.6 4.5 - - - -
106B GLY* 3.9 17.1 - - - +
169B LEU* 4.0 29.4 - - + +
170B ALA* 5.6 3.8 - - - +
173B ALA* 3.6 22.3 - - + +
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Residues in contact with ALA 170 (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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100A ASP* 5.8 0.7 - - - +
148A ILE* 4.4 7.0 - - + -
166A ALA 3.0 18.0 + - - +
167A GLN* 3.6 8.3 - - - +
169A LEU* 1.3 77.1 - - - +
171A ALA* 1.3 61.9 + - - +
173A ALA* 3.9 4.9 - - - +
174A GLN* 2.9 46.3 + - - +
169B LEU* 5.6 5.4 - - - -
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Residues in contact with ALA 171 (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 ARG* 5.3 0.5 + - - -
148A ILE* 4.1 16.4 - - + -
150A GLN* 4.9 2.6 - - - +
160A SER* 4.2 14.8 - - - +
162A ALA* 4.5 0.9 - - + -
167A GLN 2.8 17.7 + - - +
168A ARG* 3.2 5.3 + - - +
170A ALA* 1.3 77.3 - - - +
172A LEU* 1.3 64.1 + - - +
174A GLN* 3.5 12.3 + - - +
175A HIS 3.1 16.3 + - - -
195B LEU* 4.4 6.1 - - + -
227B ACT 3.4 22.4 - - + +
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Residues in contact with LEU 172 (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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168A ARG 3.0 18.4 + - - +
169A LEU* 3.2 6.7 + - - +
171A ALA* 1.3 73.7 - - - +
173A ALA* 1.3 60.1 + - - +
175A HIS* 3.0 3.1 + - - +
176A ALA* 2.9 23.6 + - - +
102B GLY* 4.2 10.5 - - - +
105B VAL* 3.9 22.9 - - + -
106B GLY 5.1 0.4 - - - +
173B ALA* 3.8 14.1 - - + +
176B ALA* 3.1 21.0 - - + +
177B CYS* 3.6 28.7 - - - -
182B HIS* 3.6 11.2 - - + +
195B LEU* 3.7 13.9 - - + -
227B ACT 3.3 31.4 - - - +
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Residues in contact with ALA 173 (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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102A GLY* 4.1 9.0 - - - -
169A LEU 3.0 16.3 + - - +
170A ALA* 3.9 3.8 - - - +
172A LEU* 1.3 76.6 - - - +
174A GLN* 1.3 62.5 + - - +
176A ALA* 3.3 10.9 + - - +
177A CYS* 3.5 17.3 + - - -
169B LEU* 3.9 29.2 - - + +
172B LEU* 3.7 23.3 - - + +
173B ALA* 4.0 8.2 - - - +
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Residues in contact with GLN 174 (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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99A ALA 5.8 0.2 - - - +
100A ASP* 2.8 40.8 + - - +
101A LEU 5.5 0.9 - - - +
102A GLY* 4.3 10.3 - - - +
146A PRO 4.7 1.2 + - - -
147A ARG* 3.5 46.1 + - + +
148A ILE* 3.1 30.8 + - - +
170A ALA* 2.9 39.4 + - - +
171A ALA* 3.6 7.1 - - - +
173A ALA* 1.3 75.8 - - - +
175A HIS* 1.3 62.5 + - - +
177A CYS* 3.2 17.0 + - - +
178A ASP* 3.6 5.0 + - - +
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Residues in contact with HIS 175 (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 ARG* 3.9 3.3 - - - +
150A GLN* 5.1 2.3 + - - +
158A LEU* 3.5 32.1 - - + +
171A ALA 3.1 12.9 + - - +
172A LEU 3.0 8.9 + - - +
174A GLN* 1.3 74.8 - - - +
176A ALA* 1.3 65.6 + - - +
178A ASP* 3.1 37.2 + - + +
197A ARG* 5.1 0.9 + - - -
176B ALA* 4.0 13.7 - - + -
197B ARG* 3.4 38.5 + - - -
199B GLN* 5.2 1.0 + - - -
227B ACT 3.8 15.9 - - + +
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Residues in contact with ALA 176 (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 LEU 2.9 8.2 + - - +
173A ALA 3.6 8.7 - - - +
174A GLN 3.2 0.6 - - - -
175A HIS* 1.3 78.7 - - - +
177A CYS* 1.3 57.2 + - - +
182A HIS* 3.6 3.9 - - - -
197A ARG* 3.1 32.4 + - - +
227A ACT 4.4 1.6 - - - +
172B LEU* 3.1 39.5 - - + +
175B HIS* 4.1 19.3 - - + +
176B ALA* 4.2 4.3 - - - +
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Residues in contact with CYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ALA* 5.7 0.9 - - + +
63A ALA* 3.2 18.0 + - - +
101A LEU* 3.8 29.8 - - + -
102A GLY 3.7 14.6 - - - -
105A VAL* 4.3 4.0 - - - -
173A ALA 3.5 6.3 + - - -
174A GLN 3.2 9.1 + - - +
175A HIS 3.1 1.2 - - - -
176A ALA* 1.3 76.6 - - - +
178A ASP* 1.3 63.8 + - - +
180A ALA* 3.3 12.9 + - - +
182A HIS* 3.8 18.3 + - + +
172B LEU* 3.5 30.5 - - - -
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Residues in contact with ASP 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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63A ALA* 4.1 3.4 - - - -
64A PRO* 5.3 6.6 - - - +
147A ARG* 2.8 46.9 + - - -
150A GLN* 4.9 1.7 + - - -
174A GLN 3.9 1.2 - - - +
175A HIS* 3.1 33.8 + - + +
177A CYS* 1.3 78.1 - - - +
179A GLY* 1.3 63.7 + - - +
180A ALA 3.2 1.3 + - - -
197A ARG* 4.0 12.5 + - - -
221B PHE* 4.5 8.0 - - - -
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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