Contacts of the helix formed by residues 161 - 172 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B GLY 3.8 0.4 - - - -
160B GLY* 1.3 80.9 - - - +
162B ASP* 1.3 65.6 + - - -
163B ALA* 3.3 3.4 - - - -
164B ALA* 3.3 4.8 + - - +
165B VAL* 3.2 23.0 + - - +
188B ARG* 3.5 27.9 - - - +
189B ALA* 3.6 10.6 - - - +
244B PHE 5.0 3.3 + - - -
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Residues in contact with ASP 162 (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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161B GLY* 1.3 72.5 - - - -
163B ALA* 1.3 57.0 + - - +
165B VAL* 3.1 7.7 - - - +
166B GLU* 2.9 54.1 + - - +
188B ARG* 5.0 0.2 - - - +
189B ALA* 3.3 5.9 - - - +
190B ASN* 2.9 39.4 + - - +
193B ALA* 4.8 2.1 - - - +
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Residues in contact with ALA 163 (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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161B GLY* 3.3 0.8 - - - -
162B ASP* 1.3 74.4 - - - +
164B ALA* 1.3 66.8 + - - +
166B GLU* 4.9 4.0 - - - -
167B GLU* 2.9 33.6 + - + +
244B PHE* 4.0 24.5 - - + +
291B ARG* 5.9 4.3 - - - +
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Residues in contact with ALA 164 (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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157B VAL* 3.7 16.0 - - + +
159B GLY* 3.4 40.6 - - - +
160B GLY* 3.7 2.5 - - - +
161B GLY 3.3 11.1 + - - +
163B ALA* 1.3 78.4 - - - +
165B VAL* 1.3 59.7 + - + +
167B GLU* 4.3 0.2 - - - +
168B GLY* 2.9 26.7 + - - -
180B VAL* 5.0 4.3 - - + +
244B PHE* 3.7 20.0 + - + +
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Residues in contact with VAL 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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160B GLY 4.9 0.2 - - - +
161B GLY 3.2 14.3 + - - +
162B ASP* 3.1 17.3 - - - +
164B ALA* 1.3 78.2 - - + +
166B GLU* 1.3 64.0 + - - +
168B GLY* 3.5 0.8 + - - -
169B MET* 3.1 31.2 + - + +
180B VAL* 6.0 2.0 - - + -
187B LEU* 4.1 26.7 - - + -
189B ALA* 3.5 24.9 - - + -
193B ALA* 3.7 22.7 - - + -
194B GLN* 5.0 2.7 - - + -
197B ALA* 4.7 11.7 - - + -
203B MET* 4.4 6.1 - - - +
205B PHE* 4.9 8.5 - - + -
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Residues in contact with GLU 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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162B ASP* 2.9 43.6 + - - +
163B ALA* 4.4 2.8 + - - +
165B VAL* 1.3 72.8 - - - +
167B GLU* 1.3 60.0 + - - +
169B MET* 3.4 21.5 + - + +
170B PHE* 3.1 25.6 + - - +
193B ALA* 4.2 17.1 - - + +
196B ARG* 4.8 10.3 + - - +
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Residues in contact with GLU 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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309A ARG* 4.8 17.6 + - - -
141B THR 4.7 0.2 - - - +
142B CYS* 4.0 3.8 - - - -
143B ALA* 3.1 39.5 + - + +
144B THR* 4.4 4.1 + - - -
163B ALA* 2.9 21.8 + - - +
166B GLU* 1.3 75.0 - - - +
168B GLY* 1.3 54.9 + - - +
170B PHE* 3.3 14.7 + - - +
171B LEU* 2.7 39.9 + - - +
244B PHE* 3.0 38.5 - - + -
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Residues in contact with GLY 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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157B VAL* 4.1 19.7 - - - +
164B ALA 2.9 21.0 + - - -
167B GLU* 1.3 75.7 - - - +
169B MET* 1.3 60.9 + - - +
171B LEU* 3.2 14.2 + - - +
172B THR* 3.3 15.4 + - - +
178B VAL* 3.9 3.8 - - - +
203B MET* 3.8 19.5 - - - -
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Residues in contact with MET 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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312A ALA* 6.4 1.8 - - + -
165B VAL 3.1 22.1 + - - +
166B GLU* 3.6 15.9 - - + +
167B GLU 3.3 0.2 - - - -
168B GLY* 1.3 72.2 - - - +
170B PHE* 1.3 61.0 + - - +
172B THR* 2.4 29.1 + - - -
173B LYS* 3.9 3.5 + - - +
193B ALA* 3.9 18.8 - - + +
196B ARG* 3.3 49.1 - - - +
197B ALA* 3.6 23.1 - - + -
200B ASN* 4.2 9.6 - - - +
203B MET* 3.6 20.6 - - - -
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Residues in contact with PHE 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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30A ALA* 3.9 21.3 - - + -
308A GLU* 3.4 42.8 - - + +
143B ALA* 3.8 21.3 - - + -
144B THR* 3.7 31.9 - - + -
166B GLU 3.1 14.3 + - - +
167B GLU* 3.3 19.7 - - - +
169B MET* 1.3 75.8 - - - +
171B LEU* 1.3 57.3 + - - +
173B LYS* 2.9 45.8 + - + +
174B PHE* 3.5 21.8 - + - -
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Residues in contact with LEU 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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143B ALA* 3.9 10.1 - - + -
147B GLY* 3.7 20.2 - - - +
150B TYR* 5.4 2.0 - - + -
155B VAL* 4.2 10.1 - - + -
157B VAL* 3.6 26.0 - - + -
167B GLU 2.7 24.6 + - - +
168B GLY 3.2 6.0 + - - +
170B PHE* 1.3 72.0 - - - +
172B THR* 1.3 56.5 + - - +
174B PHE* 3.1 11.5 + - + +
175B ALA* 3.0 27.4 + - + +
178B VAL* 3.8 12.8 - - + -
242B PHE* 3.6 58.3 - - + -
244B PHE* 4.6 2.0 - - + -
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Residues in contact with THR 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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168B GLY 3.3 7.5 + - - +
169B MET 2.4 24.7 + - - -
171B LEU* 1.3 71.9 - - - +
173B LYS* 1.3 59.4 + - - +
174B PHE 3.0 6.2 + - - -
175B ALA 4.2 4.5 - - - -
178B VAL* 3.8 13.2 - - + -
200B ASN* 3.0 28.3 + - - +
202B LYS* 3.0 55.0 + - + +
203B MET* 3.6 22.4 - - + -
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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