Contacts of the helix formed by residues 162 - 179 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B GLY* 1.3 76.3 - - - -
163B ILE* 1.3 65.6 + - - +
164B ALA* 3.9 6.9 + - - +
165B ALA* 3.2 24.0 + - - +
166B ARG* 3.1 28.1 + - - +
195C LYS* 3.4 42.4 - - + +
196C GLY* 4.6 4.5 - - - -
197C HIS* 4.7 7.9 - - + -
385C ASP* 5.9 0.2 - - - -
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Residues in contact with ILE 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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162B THR* 1.3 74.4 - - - +
164B ALA* 1.3 61.6 + - - +
166B ARG* 3.4 17.9 + - - +
167B ALA* 3.2 23.0 + - - +
188B PHE* 4.7 7.9 - - + -
191B LEU* 3.8 6.9 - - + +
192B MET* 3.9 34.5 - - + -
194C GLN* 5.4 10.6 - - + +
195C LYS 5.2 0.2 + - - -
197C HIS* 5.0 10.7 - - + -
210C LEU* 6.2 1.1 - - + -
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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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162B THR* 3.2 6.7 + - - +
163B ILE* 1.3 76.0 - - - +
165B ALA* 1.3 59.7 + - - +
167B ALA* 3.3 2.3 + - - +
168B GLN* 2.9 29.5 + - - +
188B PHE* 3.6 28.7 - - + -
206B LEU* 4.1 22.2 - - + -
197C HIS* 5.6 5.2 - - + +
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Residues in contact with ALA 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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118B PRO* 6.4 2.5 - - + -
150B TYR* 5.3 0.9 - - - +
161B GLY* 5.0 4.0 - - - -
162B THR* 3.2 29.0 + - - +
164B ALA* 1.3 80.3 - - - +
166B ARG* 1.3 62.4 + - + +
168B GLN* 3.3 7.6 + - - +
169B VAL* 3.1 28.5 + - + +
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Residues in contact with ARG 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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150B TYR* 3.4 37.5 - - + +
154B GLN* 3.1 25.8 - - - +
159B ASP* 2.6 36.9 + - - +
161B GLY* 3.6 21.4 + - - +
162B THR* 3.1 20.9 + - - +
163B ILE* 3.7 14.0 - - - +
165B ALA* 1.3 77.7 - - + +
167B ALA* 1.3 61.2 + - - +
169B VAL* 3.3 5.2 + - - +
170B CYS* 3.1 25.8 + - - -
191B LEU* 3.9 22.0 - - + -
194C GLN* 5.4 4.8 + - - -
385C ASP* 4.4 17.6 + - - -
388C LYS* 5.9 2.2 - - - +
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Residues in contact with ALA 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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163B ILE 3.2 9.5 + - - +
164B ALA 3.8 0.7 - - - +
165B ALA 3.3 0.2 - - - -
166B ARG* 1.3 75.1 - - - +
168B GLN* 1.3 60.3 + - - +
170B CYS* 3.4 1.6 + - - +
171B GLN* 2.8 31.0 + - - +
184B ILE* 5.6 2.9 - - + -
187B GLN* 3.8 20.0 - - + +
188B PHE* 3.5 35.4 - - + +
191B LEU* 3.5 20.1 - - + +
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Residues in contact with GLN 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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164B ALA 2.9 17.6 + - - +
165B ALA* 3.6 8.5 - - - +
167B ALA* 1.3 73.6 - - - +
169B VAL* 1.3 60.9 + - - +
171B GLN* 3.5 16.7 - - - +
172B GLN* 2.9 31.9 + - - +
184B ILE* 5.9 1.3 - - + +
188B PHE* 5.6 0.2 - - - -
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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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113B VAL* 4.2 11.0 - - + +
116B TYR* 3.6 42.4 - - + +
118B PRO* 4.3 10.8 - - + -
150B TYR* 3.7 30.3 - - + -
165B ALA* 3.1 17.2 + - + +
166B ARG 3.4 7.4 - - - +
168B GLN* 1.3 76.6 - - + +
170B CYS* 1.3 63.4 + - - +
172B GLN* 3.3 6.7 + - - +
173B ALA* 3.1 21.1 + - - +
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Residues in contact with CYS 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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113B VAL* 4.3 4.9 - - - -
146B GLU* 3.4 49.5 - - + +
147B VAL* 3.8 11.7 - - + -
150B TYR* 3.9 19.1 - - - -
166B ARG 3.1 16.2 + - - +
167B ALA 3.8 2.7 - - - +
169B VAL* 1.3 79.5 - - - +
171B GLN* 1.3 61.8 + - - +
173B ALA* 3.3 10.1 + - - +
174B GLU* 3.1 17.0 + - - +
187B GLN* 3.6 20.6 - - + -
191B LEU* 5.5 1.3 - - - -
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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 ALA 2.8 17.5 + - - +
168B GLN* 3.5 15.2 - - - +
170B CYS* 1.3 77.0 - - - +
172B GLN* 1.3 57.3 + - - +
174B GLU* 3.0 4.5 + - - +
175B HIS* 2.9 50.6 + - + +
182B CYS* 2.9 29.4 + - - +
183B GLY* 3.5 16.0 - - - +
184B ILE* 3.5 24.3 - - + +
187B GLN* 3.9 15.0 - - + +
240B ARG* 5.3 1.2 - - - +
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Residues in contact with GLN 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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116B TYR* 3.8 35.0 + - + -
168B GLN 2.9 17.6 + - - +
169B VAL* 3.8 5.4 - - - +
171B GLN* 1.3 73.2 - - - +
173B ALA* 1.3 60.2 + - - +
175B HIS* 4.1 11.7 + - - +
176B SER* 2.8 43.4 + - - +
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Residues in contact with ALA 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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108B ASN 5.0 0.3 - - - +
109B TYR* 4.4 6.5 - - - +
112B GLY* 3.6 36.6 - - - -
113B VAL* 3.8 12.8 - - + +
116B TYR* 4.4 3.3 - - - -
146B GLU* 4.2 4.7 - - + +
169B VAL 3.1 12.3 + - - +
170B CYS 3.3 12.1 - - - +
171B GLN 3.1 0.2 - - - -
172B GLN* 1.3 76.7 - - - +
174B GLU* 1.3 57.4 + - - +
177B PHE* 2.9 34.0 + - - +
178B ALA* 3.5 2.3 + - - +
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Residues in contact with GLU 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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109B TYR* 3.5 5.3 + - - -
142B SER* 3.0 26.9 + - - -
146B GLU* 2.7 32.6 + - - +
170B CYS 3.1 8.3 + - - +
171B GLN 3.0 9.3 + - - +
173B ALA* 1.3 76.2 - - - +
175B HIS* 1.3 61.2 + - - +
178B ALA* 3.2 23.0 - - - +
179B GLY 3.2 0.3 + - - -
180B MET* 3.2 52.6 + - + +
182B CYS* 3.5 22.0 - - + +
187B GLN* 4.2 3.8 + - - +
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Residues in contact with HIS 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 44.6 + - + +
172B GLN* 3.7 15.5 + - - +
174B GLU* 1.3 77.2 - - - +
176B SER* 1.3 61.7 + - - +
179B GLY* 3.2 24.6 + - - -
180B MET 3.6 7.2 - - - -
181B PRO* 3.4 26.2 - - + +
182B CYS* 2.8 37.3 + - - -
240B ARG* 4.2 7.9 - - - -
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Residues in contact with SER 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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101B PRO* 3.9 13.9 - - - +
116B TYR* 3.4 23.5 + - - -
172B GLN* 2.8 36.5 + - - -
175B HIS* 1.3 76.1 - - - +
177B PHE* 1.3 68.8 + - - +
178B ALA 3.6 0.2 - - - -
179B GLY* 4.5 1.7 + - - -
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Residues in contact with PHE 177 (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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99B LEU* 3.4 26.5 - - + -
100B GLU* 3.7 7.9 - - - -
101B PRO* 3.6 43.2 - - + +
108B ASN* 3.3 47.8 + - - +
111B LYS* 4.0 12.3 - - + -
112B GLY* 3.6 20.0 - - - -
115B GLN* 3.9 17.3 - - + -
116B TYR* 3.8 25.8 - + - -
173B ALA 2.9 15.4 + - - +
176B SER* 1.3 88.8 - - - +
178B ALA* 1.3 59.6 + - - +
179B GLY 3.7 0.7 - - - -
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Residues in contact with ALA 178 (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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108B ASN* 5.2 1.6 - - + +
109B TYR* 3.4 38.8 - - + +
173B ALA 3.5 0.6 + - - +
174B GLU* 3.2 25.2 + - - +
177B PHE* 1.3 77.9 - - - +
179B GLY* 1.3 61.1 + - - +
180B MET* 3.2 7.5 + - + +
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Residues in contact with GLY 179 (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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174B GLU 3.2 2.8 + - - -
175B HIS 3.2 15.1 + - - -
176B SER 4.5 1.5 + - - -
177B PHE 3.7 2.0 - - - +
178B ALA* 1.3 76.5 - - - +
180B MET* 1.3 57.9 + - - +
181B PRO* 3.4 10.3 - - - +
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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