Contacts of the helix formed by residues 173 - 186 (chain A) in PDB entry 2G2Y
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 LYS 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLY 4.2 15.5 - - - +
129A THR 2.8 23.3 + - - +
130A GLY 4.4 1.6 - - - +
131A ALA* 3.8 22.2 - - + +
171A GLY 3.5 2.0 + - - -
172A HIS* 1.3 70.2 - - - +
174A GLU* 1.3 79.9 + - + +
176A VAL* 3.2 2.9 + - - +
177A GLU* 3.1 45.2 + - - +
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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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129A THR* 4.8 1.9 - - - +
154A GLN* 2.9 23.7 + - - +
172A HIS* 4.1 1.4 - - - +
173A LYS* 1.3 95.4 + - + +
175A ALA* 1.3 58.2 + - - +
177A GLU* 3.2 18.8 + - - +
178A ARG* 3.0 51.9 + - - +
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Residues in contact with ALA 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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150A ALA* 4.1 2.6 - - - +
151A ALA 4.2 0.7 - - - +
154A GLN* 3.5 16.8 + - + +
155A VAL 3.9 10.5 - - - +
156A VAL* 3.7 24.2 - - + +
172A HIS 3.1 7.5 + - - +
174A GLU* 1.3 78.6 - - - +
176A VAL* 1.3 60.0 + - - +
178A ARG* 3.3 27.2 + - - +
179A ALA* 2.8 30.3 + - - +
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Residues in contact with VAL 176 (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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131A ALA* 3.5 25.1 - - + +
132A MET 4.3 0.4 - - - +
133A ALA* 3.9 31.1 - - + +
156A VAL* 3.8 13.9 - - + -
169A ILE* 4.1 4.9 - - + +
170A ALA* 3.6 8.7 - - - -
171A GLY* 3.4 29.6 - - - +
172A HIS 2.9 13.2 + - - +
173A LYS 3.6 7.9 - - - +
175A ALA* 1.3 77.1 - - - +
177A GLU* 1.3 58.2 + - + +
179A ALA* 3.7 1.3 - - - +
180A GLY* 2.9 25.8 + - - -
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Residues in contact with GLU 177 (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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173A LYS* 3.1 49.3 + - - +
174A GLU* 3.3 18.4 - - - +
175A ALA 3.2 0.2 - - - -
176A VAL* 1.3 74.5 - - + +
178A ARG* 1.3 66.9 + - + +
179A ALA 3.1 0.5 + - - -
180A GLY* 3.2 3.2 + - - -
181A ALA* 3.1 21.1 + - - +
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Residues in contact with ARG 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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150A ALA* 3.1 37.2 + - + +
151A ALA 3.1 14.6 + - - -
152A GLU* 4.2 14.0 + - - +
154A GLN* 2.4 32.4 + - - +
174A GLU* 3.0 25.4 + - - +
175A ALA* 3.3 19.7 + - - +
177A GLU* 1.3 77.9 - - + +
179A ALA* 1.3 57.8 + - - +
181A ALA* 3.3 7.2 + - - +
182A ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 179 (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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146A ALA* 4.4 3.9 - - - +
147A CYS* 4.3 12.8 - - - -
150A ALA* 3.7 15.3 - - + -
156A VAL* 3.9 12.1 - - + -
169A ILE* 3.7 17.9 - - + -
175A ALA 2.8 17.8 + - - +
176A VAL 3.7 3.8 - - - +
178A ARG* 1.3 74.3 - - - +
180A GLY* 1.3 67.4 + - - +
182A ALA* 3.3 3.1 + - - +
183A CYS* 2.9 29.5 + - - -
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Residues in contact with GLY 180 (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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133A ALA* 5.8 2.0 - - - -
135A ILE* 4.4 5.8 - - - -
169A ILE* 4.3 1.7 - - - +
176A VAL 2.9 15.5 + - - -
177A GLU* 3.2 3.5 + - - -
179A ALA* 1.3 75.4 - - - +
181A ALA* 1.3 56.8 + - - +
183A CYS* 3.0 8.4 + - - +
184A LYS* 2.9 31.2 + - - +
191A ALA* 4.0 22.4 - - - +
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Residues in contact with ALA 181 (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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177A GLU 3.1 12.1 + - - +
178A ARG* 3.5 11.0 - - - +
180A GLY* 1.3 74.1 - - - +
182A ALA* 1.3 58.2 + - - +
184A LYS* 3.1 9.9 + - - +
185A ALA* 2.8 29.3 + - - +
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Residues in contact with ALA 182 (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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146A ALA* 3.9 26.7 - - + +
149A GLU* 5.2 8.3 - - + +
150A ALA* 5.2 2.7 - - + -
178A ARG 3.0 16.3 + - - +
179A ALA 3.7 4.3 - - - +
181A ALA* 1.3 77.1 - - - +
183A CYS* 1.3 57.1 + - - +
185A ALA* 3.3 8.7 + - - +
186A ALA* 3.0 28.4 + - - +
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Residues in contact with CYS 183 (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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135A ILE* 3.9 43.7 - - + -
138A LEU* 3.9 14.2 - - + +
143A ILE* 4.2 12.3 - - - -
146A ALA* 3.8 18.6 - - - -
147A CYS* 5.5 0.4 - - - -
169A ILE* 5.3 2.2 - - - -
179A ALA* 2.9 20.6 + - - +
180A GLY 3.0 9.4 + - - +
182A ALA* 1.3 75.0 - - - +
184A LYS* 1.3 66.0 + - - +
186A ALA* 3.1 10.8 + - - +
187A GLY 3.2 0.9 + - - -
188A ALA* 3.0 23.3 + - + +
191A ALA* 5.3 0.4 - - + -
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Residues in contact with LYS 184 (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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180A GLY 2.9 15.4 + - - +
181A ALA* 3.5 10.8 - - - +
183A CYS* 1.3 77.4 - - - +
185A ALA* 1.3 61.1 + - - +
187A GLY* 3.0 15.2 + - - -
188A ALA* 3.7 22.1 + - - +
189A LYS 3.7 17.5 + - - +
190A ARG* 4.5 6.4 - - - +
191A ALA* 4.5 20.9 - - + +
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Residues in contact with ALA 185 (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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181A ALA 2.8 16.8 + - - +
182A ALA* 3.6 10.5 - - - +
183A CYS 3.2 0.4 - - - -
184A LYS* 1.3 77.1 - - - +
186A ALA* 1.3 59.2 + - - +
187A GLY 3.2 1.1 + - - -
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Residues in contact with ALA 186 (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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138A LEU* 4.1 26.1 - - + +
142A SER* 4.8 10.5 - - - +
145A LYS* 6.2 2.7 - - - +
146A ALA* 5.6 1.3 - - + -
182A ALA 3.0 16.5 + - - +
183A CYS* 3.6 6.1 - - - +
184A LYS 3.1 0.6 - - - -
185A ALA* 1.3 76.2 - - - +
187A GLY* 1.3 58.4 + - - +
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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