Contacts of the helix formed by residues 161 - 172 (chain A) in PDB entry 2Q7V
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 GLY 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A GLY 3.8 0.8 - - - -
160A GLY* 1.3 79.6 - - - +
162A ASP* 1.3 66.7 + - - -
163A ALA* 3.2 4.1 + - - -
164A ALA* 3.3 4.3 + - - +
165A VAL* 3.2 21.5 + - - +
188A ARG* 4.0 12.2 - - - +
189A ALA* 3.7 10.1 - - - -
244A PHE 5.1 2.5 + - - -
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Residues in contact with ASP 162 (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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161A GLY* 1.3 68.9 - - - -
163A ALA* 1.3 58.4 + - - +
165A VAL* 3.3 0.7 + - - +
166A GLU* 2.8 54.2 + - - +
188A ARG 5.0 0.6 - - - -
189A ALA* 3.2 8.0 - - - +
190A ASN* 2.7 50.1 + - - +
193A ALA* 5.5 0.4 - - - -
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Residues in contact with ALA 163 (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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161A GLY* 3.2 1.2 - - - -
162A ASP* 1.3 77.3 - - - +
164A ALA* 1.3 56.2 + - - +
166A GLU* 4.4 5.4 + - - -
167A GLU* 2.9 41.2 + - + +
244A PHE* 4.0 26.9 - - + +
291A ARG* 6.0 4.3 - - - +
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Residues in contact with ALA 164 (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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157A VAL* 3.6 23.7 - - + +
159A GLY* 3.6 34.1 - - - +
160A GLY* 3.9 2.0 - - - +
161A GLY 3.3 7.8 + - - +
163A ALA* 1.3 78.2 - - - +
165A VAL* 1.3 60.2 + - + +
168A GLY* 2.9 25.5 + - - -
180A VAL* 4.6 4.4 - - + +
244A PHE* 3.6 21.6 + - + +
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Residues in contact with VAL 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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160A GLY* 4.3 3.6 - - - +
161A GLY 3.2 9.4 + - - +
162A ASP 4.1 0.7 - - - +
164A ALA* 1.3 76.4 - - + +
166A GLU* 1.3 59.7 + - - +
168A GLY* 3.3 0.7 + - - -
169A MET* 2.9 34.1 + - + +
180A VAL* 5.3 3.4 - - + -
187A LEU* 4.2 22.9 - - + -
189A ALA* 3.5 27.1 - - + -
193A ALA* 3.4 34.3 - - + +
194A GLN* 4.4 2.5 - - + +
197A ALA* 3.5 19.5 - - + -
203A MET* 4.1 6.9 - - + +
205A PHE* 5.0 6.7 - - + -
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Residues in contact with GLU 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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162A ASP* 2.8 42.3 + - - +
163A ALA* 4.3 3.8 + - - +
165A VAL* 1.3 72.1 - - - +
167A GLU* 1.3 59.4 + - + +
169A MET* 3.3 14.5 + - + +
170A PHE* 2.9 25.6 + - - +
190A ASN* 4.4 9.7 + - - -
193A ALA* 4.4 16.1 - - + +
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Residues in contact with GLU 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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141A THR 4.7 0.2 - - - +
142A CYS* 4.3 2.9 - - - -
143A ALA* 3.3 34.2 + - + +
144A THR* 4.5 5.1 + - - -
163A ALA* 2.9 27.6 + - + +
166A GLU* 1.3 74.5 - - + +
168A GLY* 1.3 60.9 + - - +
170A PHE* 3.1 12.9 + - - +
171A LEU* 2.7 34.4 + - - +
244A PHE* 3.5 37.0 - - + -
309B ARG* 4.9 14.6 + - - -
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Residues in contact with GLY 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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157A VAL* 4.1 20.8 - - - +
164A ALA 2.9 20.5 + - - -
165A VAL 3.7 1.1 - - - -
166A GLU 3.3 0.2 - - - -
167A GLU* 1.3 77.8 - - - +
169A MET* 1.3 61.7 + - - +
171A LEU* 3.2 12.9 + - - +
172A THR* 3.3 16.8 + - - +
178A VAL* 3.8 5.1 - - - +
203A MET* 3.8 14.8 - - - -
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Residues in contact with MET 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 VAL* 2.9 24.8 + - + +
166A GLU* 3.4 18.2 - - + +
168A GLY* 1.3 76.6 - - - +
170A PHE* 1.3 62.0 + - - +
172A THR* 2.7 24.6 + - - -
173A LYS* 3.9 3.1 + - - +
193A ALA* 3.9 21.1 - - + +
196A ARG* 3.6 24.7 - - + +
197A ALA* 3.6 30.3 - - - -
200A ASN* 3.8 15.9 - - - +
203A MET* 3.9 8.6 - - - +
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Residues in contact with PHE 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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143A ALA* 3.5 42.6 - - + -
144A THR* 4.0 16.6 - - + -
166A GLU 2.9 14.8 + - - +
167A GLU* 3.4 17.9 - - - +
169A MET* 1.3 76.4 - - - +
171A LEU* 1.3 62.5 + - + +
173A LYS* 3.0 43.0 + - + +
174A PHE* 3.8 26.4 - + - -
30B ALA* 4.7 11.2 - - + -
308B GLU* 3.4 43.3 - - + -
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Residues in contact with LEU 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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143A ALA* 3.9 13.7 - - + -
147A GLY* 3.7 30.5 - - - +
150A TYR* 5.5 1.3 - - + -
155A VAL* 4.2 10.3 - - + -
157A VAL* 3.4 32.1 - - + -
167A GLU 2.7 21.6 + - - +
168A GLY* 3.2 8.7 + - - +
170A PHE* 1.3 75.1 - - + +
172A THR* 1.3 56.1 + - - +
173A LYS 3.1 0.7 - - - -
174A PHE* 3.0 10.0 + - - -
175A ALA* 2.9 26.6 + - + +
178A VAL* 3.8 10.5 - - + -
242A PHE* 3.7 39.7 - - + -
244A PHE* 4.6 1.3 - - + -
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Residues in contact with THR 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 GLY 3.3 8.7 + - - +
169A MET 2.7 19.4 + - - +
171A LEU* 1.3 71.4 - - - +
173A LYS* 1.3 60.6 + - - +
174A PHE* 3.0 7.2 + - - -
175A ALA 3.9 13.6 - - - +
178A VAL* 3.7 11.4 - - + -
200A ASN* 3.1 19.2 + - - +
202A LYS* 3.8 35.6 + - + +
203A MET* 3.4 33.2 - - + -
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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