Contacts of the helix formed by residues 166 - 176 (chain B) in PDB entry 3QGT
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 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B GLY* 1.3 74.8 - - - -
167B SER* 1.3 70.9 + - - +
168B VAL 3.2 2.7 - - - -
169B VAL 2.7 3.1 + - - -
170B TYR* 2.7 26.6 + - - -
610B NDP 3.2 39.5 - - - -
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Residues in contact with SER 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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40B LEU* 4.0 18.0 - - - +
166B GLY* 1.3 71.5 - - - +
168B VAL* 1.3 64.4 + - - +
170B TYR* 3.2 5.9 + - - +
171B GLN* 3.0 22.2 + - - +
195B VAL* 4.3 18.0 - - - +
196B PHE 3.0 24.8 + - - -
198B PRO* 4.4 3.2 - - - +
610B NDP 2.9 22.8 + - - -
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Residues in contact with VAL 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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166B GLY 3.0 0.4 + - - -
167B SER* 1.3 82.4 + - - +
169B VAL* 1.3 64.6 + - - +
171B GLN* 3.3 10.7 + - - +
172B GLU* 3.2 28.4 + - - +
610B NDP 3.0 63.1 + - + +
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Residues in contact with VAL 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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103B VAL* 4.9 5.4 - - + +
104B MET 4.3 3.1 - - - -
105B GLY* 4.1 25.4 - - - +
127B LEU* 4.5 14.6 - - + -
163B ILE* 3.7 15.9 - - + -
165B GLY* 3.8 4.7 - - - -
166B GLY 2.7 17.0 + - - +
168B VAL* 1.3 73.2 - - + +
170B TYR* 1.3 64.1 + - - +
172B GLU* 3.3 9.1 - - - +
173B PHE* 3.0 54.1 + - + -
610B NDP 3.3 22.4 - - - +
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Residues in contact with TYR 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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13B ALA* 4.7 9.4 - - + -
14B ILE 2.7 26.9 + - - -
15B CYS* 3.4 9.9 - - + +
40B LEU* 3.9 19.3 - - + -
163B ILE* 3.1 26.7 - - + -
164B ILE 3.2 5.4 + - - -
165B GLY* 3.6 11.7 - - - -
166B GLY 2.7 36.0 + - - -
167B SER 3.5 6.5 - - - +
169B VAL* 1.3 74.9 - - - +
171B GLN* 1.3 68.6 + - - +
173B PHE* 3.1 4.9 + - - +
174B LEU* 3.0 25.7 + - + +
179B ILE* 6.3 0.4 - - + -
197B PHE* 3.8 27.4 - + + -
198B PRO* 4.0 12.3 - - + -
609B CP6 3.2 13.7 + - - -
610B NDP 3.5 13.0 - + - -
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Residues in contact with GLN 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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167B SER 3.0 9.3 + - - +
168B VAL* 3.5 11.9 - - - +
170B TYR* 1.3 76.7 - - - +
172B GLU* 1.3 64.6 + - - +
174B LEU* 2.8 17.8 + - - +
175B GLU* 2.9 56.5 + - - +
198B PRO* 3.0 37.9 - - + +
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Residues in contact with GLU 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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127B LEU* 3.0 32.9 - - - +
146B VAL* 3.0 23.1 - - + +
168B VAL* 3.2 22.4 - - - +
169B VAL* 3.3 9.8 - - - +
171B GLN* 1.3 77.2 - - - +
173B PHE* 1.3 70.4 + - + +
174B LEU 3.1 0.2 + - - -
175B GLU* 3.2 13.8 + - - +
176B LYS* 3.0 36.8 + - + +
610B NDP 3.3 27.6 + - - -
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Residues in contact with PHE 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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11B ILE* 4.8 5.4 - - + -
103B VAL* 4.4 5.8 - - + -
127B LEU* 4.4 16.4 - - + -
146B VAL* 4.1 13.0 - - + -
149B LEU* 3.4 34.8 - - + -
150B ILE* 6.2 0.7 - - + -
163B ILE* 3.8 22.9 - - + -
169B VAL* 3.0 44.6 - - + +
170B TYR* 3.1 6.7 + - - +
172B GLU* 1.3 86.6 - - + +
174B LEU* 1.3 57.9 + - - +
177B LYS 3.5 1.6 + - - -
178B LEU* 2.9 67.1 + - + +
179B ILE* 3.8 21.1 - - + +
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Residues in contact with LEU 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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13B ALA* 5.7 1.1 - - + -
170B TYR* 3.0 16.6 + - + +
171B GLN* 2.8 12.0 + - - +
173B PHE* 1.3 76.3 - - - +
175B GLU* 1.3 64.7 - - - +
177B LYS* 2.9 20.2 + - - +
179B ILE* 3.6 24.2 - - + -
182B ILE* 3.9 12.8 - - + -
197B PHE* 4.1 22.9 - - + -
198B PRO* 3.9 30.3 - - + +
200B ILE* 5.1 5.4 - - + -
204B GLU* 5.2 4.8 - - - +
205B TYR* 3.8 31.5 + - + +
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Residues in contact with GLU 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 GLN* 2.9 53.5 + - - +
172B GLU* 3.6 15.5 + - - +
174B LEU* 1.3 77.3 - - - +
176B LYS* 1.3 61.3 + - + +
177B LYS* 2.9 23.5 + - - +
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Residues in contact with LYS 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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145B LYS* 5.3 5.5 - - - +
146B VAL* 4.6 24.7 - - + +
147B GLU* 3.6 34.1 + - + +
172B GLU* 3.0 22.4 + - - +
175B GLU* 1.3 78.4 - - + +
177B LYS* 1.3 70.0 + - - +
178B LEU* 3.5 24.1 + - + +
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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