Contacts of the helix formed by residues 162 - 177 (chain C) in PDB entry 6GR2
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161C GLY* 1.3 76.0 - - - -
163C ILE* 1.3 68.5 + - - +
164C ALA* 3.4 23.0 + - + +
165C ALA* 3.1 27.1 + - + +
166C ARG* 3.3 16.1 + - - +
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Residues in contact with ILE 163 (chain C).
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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162C THR* 1.3 75.7 + - - +
164C ALA* 1.3 67.4 + - - +
166C ARG* 3.0 36.9 + - - +
167C ALA* 3.0 11.8 + - - +
188C PHE* 5.0 6.7 - - + -
191C LEU* 4.1 23.8 - - + +
192C MET* 3.4 44.4 - - + -
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Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C THR* 3.2 14.4 + - + +
163C ILE* 1.3 78.3 - - - +
165C ALA* 1.3 57.3 + - - +
167C ALA* 3.3 3.4 + - - +
168C GLN* 2.9 38.4 + - - +
188C PHE* 4.4 13.1 - - + -
206C LEU* 3.3 34.5 - - + -
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Residues in contact with ALA 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C PRO* 6.2 3.4 - - + -
150C TYR* 5.1 1.8 - - - +
161C GLY* 4.9 4.7 - - - -
162C THR* 3.1 26.7 + - + +
164C ALA* 1.3 79.2 - - - +
166C ARG* 1.3 53.5 + - + +
168C GLN* 3.2 11.6 + - - +
169C VAL* 2.7 42.3 + - + +
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Residues in contact with ARG 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C TYR* 3.2 43.7 - - + +
154C GLN* 3.3 24.3 + - - +
159C ASP* 2.9 32.4 + - - +
161C GLY 4.0 12.4 + - - -
162C THR 3.6 11.3 + - - +
163C ILE* 3.0 33.0 + - - +
165C ALA* 1.3 77.5 - - + +
167C ALA* 1.3 62.4 + - - +
169C VAL* 3.2 2.8 + - - +
170C CYS* 2.9 28.5 + - - -
191C LEU* 4.0 22.3 - - + +
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C ILE 3.0 9.5 + - - +
164C ALA 3.7 7.4 - - - +
166C ARG* 1.3 75.7 - - - +
168C GLN* 1.3 58.5 + - - +
170C CYS* 3.2 4.0 + - - +
171C GLN* 2.7 29.6 + - - +
184C ILE* 4.9 8.3 - - + -
187C GLN* 3.9 20.0 - - + +
188C PHE* 4.2 25.1 - - + +
191C LEU* 3.4 20.5 - - + +
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Residues in contact with GLN 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ALA* 2.9 27.4 + - - +
165C ALA* 3.7 10.8 - - - +
167C ALA* 1.3 71.7 - - - +
169C VAL* 1.3 62.0 + - - +
171C GLN* 3.6 20.0 - - - +
172C GLN* 2.8 29.1 + - - +
184C ILE* 4.3 11.6 - - + +
206C LEU* 3.5 26.5 - - - +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 4.5 8.3 - - + +
116C TYR* 3.6 40.0 - - + +
117C TYR 4.4 1.6 - - - +
118C PRO* 4.3 11.9 - - + -
150C TYR* 3.6 30.7 - - + -
165C ALA* 2.7 26.5 + - + +
166C ARG 3.5 3.8 - - - +
168C GLN* 1.3 70.3 - - - +
170C CYS* 1.3 67.3 + - - +
172C GLN* 3.1 9.2 + - - +
173C ALA* 3.1 21.0 + - - +
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Residues in contact with CYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 4.7 4.9 - - - -
146C GLU* 3.5 51.2 - - + +
147C VAL* 3.9 11.2 - - + -
150C TYR* 3.8 22.2 - - - -
166C ARG 2.9 18.3 + - - +
167C ALA 3.7 7.0 - - - +
169C VAL* 1.3 77.8 - - - +
171C GLN* 1.3 61.6 + - - +
173C ALA* 3.5 7.1 + - - +
174C GLU* 3.3 16.5 + - - +
187C GLN* 3.7 17.0 - - + -
191C LEU* 5.5 1.1 - - - -
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Residues in contact with GLN 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ALA 2.7 19.9 + - - +
168C GLN* 3.6 13.1 - - - +
170C CYS* 1.3 72.9 - - - +
172C GLN* 1.3 64.8 + - - +
174C GLU* 3.2 3.2 + - - +
175C HIS* 3.0 50.6 + - + +
182C CYS* 2.9 25.5 + - - +
183C GLY* 3.4 20.8 - - - +
184C ILE* 3.1 25.0 - - + +
187C GLN* 4.1 14.3 - - - +
240C ARG* 4.7 3.8 - - - +
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Residues in contact with GLN 172 (chain C).
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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116C TYR* 3.6 33.2 + - + -
168C GLN 2.8 18.6 + - - +
169C VAL* 3.1 8.7 + - - +
171C GLN* 1.3 75.5 - - - +
173C ALA* 1.3 57.0 + - - +
175C HIS* 3.1 16.3 + - - +
176C SER* 2.8 55.0 + - - -
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Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TYR* 4.1 7.2 - - - +
112C GLY* 3.3 36.1 - - - +
113C VAL* 3.5 13.5 - - + +
116C TYR* 3.8 11.8 - - - -
146C GLU* 5.5 1.6 - - + -
169C VAL 3.1 10.7 + - - +
170C CYS 3.8 8.3 - - - +
171C GLN 3.3 0.4 - - - -
172C GLN* 1.3 76.8 - - - +
174C GLU* 1.3 56.7 + - - +
177C PHE* 2.7 36.0 + - - +
178C ALA* 3.5 0.9 + - - +
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TYR* 4.4 3.3 + - + +
142C SER* 3.4 21.2 + - - -
146C GLU* 2.6 32.3 + - - +
170C CYS 3.3 6.4 + - - +
171C GLN 3.2 7.7 + - - +
173C ALA* 1.3 79.0 - - - +
175C HIS* 1.3 62.1 + - - +
178C ALA* 3.4 13.9 + - + +
179C GLY 3.2 7.6 + - - -
180C MET* 3.1 49.1 + - + +
182C CYS* 3.5 21.6 - - - +
186C ASP* 5.6 1.6 - - - +
187C GLN* 2.9 18.8 + - - -
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Residues in contact with HIS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C GLN* 3.0 36.7 + - + +
172C GLN* 3.4 20.5 + - - +
174C GLU* 1.3 80.0 - - - +
176C SER* 1.3 65.4 + - - +
179C GLY* 3.4 17.0 + - - -
180C MET 3.4 20.4 + - - -
181C PRO* 3.5 15.3 - - + +
182C CYS* 2.8 32.9 + - - -
240C ARG* 4.9 7.2 - - - -
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Residues in contact with SER 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PRO* 4.2 11.6 - - - +
116C TYR* 2.9 25.2 + - - -
172C GLN* 2.8 43.7 + - - -
175C HIS* 1.3 75.7 - - - +
177C PHE* 1.3 63.9 + - - +
179C GLY* 4.4 2.0 + - - -
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Residues in contact with PHE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LEU* 3.6 24.7 - - + -
100C GLU 3.6 9.9 - - - -
101C PRO* 3.5 51.4 - - + +
108C ASN* 3.4 42.6 + - + +
109C TYR* 5.4 0.2 - - - -
111C LYS* 4.2 9.2 - - + -
112C GLY* 3.4 21.3 - - - -
115C GLN* 4.0 20.6 - - + -
116C TYR* 3.8 27.1 - + - -
173C ALA 2.7 17.9 + - - +
176C SER* 1.3 80.6 - - - +
178C ALA* 1.3 58.8 + - - +
179C GLY 3.6 0.4 - - - -
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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