Contacts of the helix formed by residues 162 - 178 (chain A) in PDB entry 6Q3W
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A GLY* 1.3 77.1 - - - -
163A ILE* 1.3 64.4 + - - +
164A ALA* 3.5 8.8 + - - +
165A ALA* 3.4 23.1 + - - +
166A ARG* 3.3 26.1 + - - +
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Residues in contact with ILE 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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162A THR* 1.3 73.1 - - - +
164A ALA* 1.3 59.7 + - - +
166A ARG* 3.3 23.7 + - - +
167A ALA* 3.0 22.7 + - - +
188A PHE* 5.0 3.5 - - + -
191A LEU* 3.5 14.5 - - + +
192A MET* 4.4 28.0 - - + -
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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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162A THR* 3.2 8.6 + - - +
163A ILE* 1.3 76.5 - - - +
165A ALA* 1.3 59.6 + - - +
167A ALA* 3.2 3.8 + - - +
168A GLN* 3.0 36.5 + - - +
184A ILE* 4.5 0.8 - - + +
188A PHE* 3.8 30.6 - - + -
206A LEU* 3.9 25.6 - - + -
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Residues in contact with ALA 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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118A PRO* 6.5 0.4 - - + -
150A TYR* 5.2 1.6 - - - +
161A GLY* 5.1 4.3 - - - -
162A THR* 3.4 25.1 + - - +
164A ALA* 1.3 79.0 - - - +
166A ARG* 1.3 57.3 + - + +
168A GLN* 3.4 15.3 + - - +
169A VAL* 3.1 32.5 + - + +
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Residues in contact with ARG 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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150A TYR* 3.4 37.4 - - + +
154A GLN* 3.2 25.0 + - - +
159A ASP* 2.9 34.5 + - - +
160A SER* 5.7 0.4 - - - +
161A GLY 3.7 17.7 + - - -
162A THR 3.3 10.7 + - - +
163A ILE* 3.3 24.4 + - - +
164A ALA 3.2 0.6 - - - -
165A ALA* 1.3 75.8 - - + +
167A ALA* 1.3 64.1 + - - +
169A VAL* 3.4 2.9 + - - +
170A CYS* 3.2 27.2 + - - -
191A LEU* 4.0 19.6 - - + +
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Residues in contact with ALA 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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163A ILE 3.0 9.6 + - - +
164A ALA 3.5 8.1 - - - +
166A ARG* 1.3 76.3 - - - +
168A GLN* 1.3 57.7 + - - +
170A CYS* 3.3 3.6 + - - +
171A GLN* 2.8 29.2 + - - +
184A ILE* 4.0 21.9 - - + +
187A GLN* 3.7 17.8 - - + +
188A PHE* 4.0 13.7 - - + +
191A LEU* 3.5 20.3 - - + +
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Residues in contact with GLN 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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164A ALA* 3.0 21.3 + - - +
165A ALA* 3.8 14.2 - - - +
166A ARG 3.2 0.4 - - - -
167A ALA* 1.3 73.6 - - - +
169A VAL* 1.3 55.6 + - - +
171A GLN* 3.3 19.4 + - - +
172A GLN* 2.8 34.8 + - - +
184A ILE* 4.1 12.6 - - + +
206A LEU* 3.9 26.1 - - - +
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Residues in contact with VAL 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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113A VAL* 4.3 11.7 - - + +
116A TYR* 3.6 39.8 - - + +
118A PRO* 4.2 11.0 - - + -
150A TYR* 3.6 30.7 - - + +
165A ALA 3.1 17.4 + - - +
166A ARG 3.6 7.4 - - - +
168A GLN* 1.3 76.8 - - + +
170A CYS* 1.3 63.8 + - - +
172A GLN* 3.2 7.5 + - - +
173A ALA* 3.0 21.1 + - - +
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Residues in contact with CYS 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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113A VAL* 4.5 3.8 - - - -
146A GLU* 3.4 50.6 - - + +
147A VAL* 4.0 10.8 - - + -
150A TYR* 3.8 19.3 - - - -
166A ARG* 3.2 17.1 + - - -
167A ALA* 3.7 2.7 - - - +
169A VAL* 1.3 79.7 - - - +
171A GLN* 1.3 63.1 + - - +
173A ALA* 3.3 9.8 + - - +
174A GLU* 3.1 17.2 + - - +
187A GLN* 3.5 21.8 - - + -
191A LEU* 5.6 0.7 - - - -
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Residues in contact with GLN 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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167A ALA 2.8 16.2 + - - +
168A GLN* 3.5 22.9 - - - +
170A CYS* 1.3 75.7 - - - +
172A GLN* 1.3 61.1 + - - +
174A GLU* 3.1 2.9 + - - +
175A HIS* 2.9 51.4 + - + +
182A CYS* 2.8 31.5 + - - -
183A GLY* 3.3 20.4 - - - +
184A ILE* 3.7 10.7 - - - +
187A GLN* 3.9 15.4 - - - +
240A ARG* 4.9 1.8 - - - +
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Residues in contact with GLN 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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116A TYR* 3.6 34.7 + - + -
168A GLN 2.8 20.8 + - - +
169A VAL* 3.2 8.2 + - - +
171A GLN* 1.3 72.5 - - - +
173A ALA* 1.3 57.3 + - - +
175A HIS* 3.8 13.7 + - - +
176A SER* 2.8 49.7 + - - -
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Residues in contact with ALA 173 (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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108A ASN 5.0 0.6 - - - +
109A TYR* 4.3 6.3 - - - +
112A GLY* 3.4 37.5 - - - -
113A VAL* 3.6 13.7 - - + +
116A TYR* 4.1 5.3 - - - -
146A GLU* 4.6 4.0 - - + -
169A VAL 3.0 12.0 + - - +
170A CYS 3.4 10.3 - - - +
171A GLN 3.2 0.2 - - - -
172A GLN* 1.3 78.2 - - - +
174A GLU* 1.3 56.8 + - - +
177A PHE* 2.8 33.4 + - - +
178A ALA* 3.4 1.9 + - - +
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Residues in contact with GLU 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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109A TYR* 3.2 16.4 - - - -
142A SER* 3.1 23.0 + - - -
146A GLU* 2.6 32.3 + - - +
170A CYS 3.1 9.0 + - - +
171A GLN 3.1 9.5 + - - +
173A ALA* 1.3 76.8 - - - +
175A HIS* 1.3 61.8 + - - +
178A ALA* 3.2 9.8 + - - +
179A GLY 3.2 8.1 + - - -
180A MET* 3.1 52.8 + - + +
182A CYS* 3.5 23.2 - - - +
186A ASP* 5.3 3.6 - - - +
187A GLN* 4.5 3.7 + - - -
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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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171A GLN* 2.9 41.7 + - + +
172A GLN* 3.3 20.8 + - - +
174A GLU* 1.3 77.1 - - - +
176A SER* 1.3 57.8 + - - +
179A GLY* 3.3 23.4 + - - -
180A MET 3.5 10.9 + - - -
181A PRO* 3.2 31.4 - - + +
182A CYS* 2.7 29.9 + - - -
240A ARG* 3.8 11.4 - - - -
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Residues in contact with SER 176 (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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101A PRO* 3.5 15.8 - - - +
116A TYR* 3.2 29.9 + - - -
172A GLN* 2.8 35.2 + - - -
175A HIS* 1.3 74.8 - - - +
177A PHE* 1.3 62.7 + - - +
179A GLY* 4.5 1.7 + - - -
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Residues in contact with PHE 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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99A LEU* 3.4 22.2 - - + -
100A GLU 3.7 9.2 - - - -
101A PRO* 3.6 43.0 - - + +
108A ASN* 3.3 50.5 + - - +
111A LYS* 3.8 19.1 - - + -
112A GLY* 3.5 16.4 - - - -
115A GLN* 3.9 19.3 - - + -
116A TYR* 3.9 28.7 - + - -
173A ALA 2.8 13.5 + - - +
176A SER* 1.3 85.0 - - - +
178A ALA* 1.3 61.5 + - - +
179A GLY 3.6 0.7 - - - -
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Residues in contact with ALA 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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108A ASN* 5.1 2.7 - - + +
109A TYR* 3.4 39.9 - - + +
173A ALA 3.4 0.8 + - - -
174A GLU* 3.2 21.8 + - - +
177A PHE* 1.3 78.1 - - - +
179A GLY* 1.3 65.3 + - - +
180A MET* 3.1 6.4 + - + +
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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