Contacts of the helix formed by residues 169 - 184 (chain A) in PDB entry 2O7R
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 SER 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLU* 1.4 85.3 - - - +
170A ALA* 1.4 63.6 + - - -
172A GLY* 2.8 12.7 + - - +
173A ASN 3.2 1.9 + - - -
200A ASP 2.9 14.6 + - - -
201A GLU 3.1 14.3 + - - -
203A GLY* 3.0 21.6 + - - +
306A HIS* 2.7 21.4 + - - -
369A 4PA 1.9 47.3 + - - -
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLY 4.4 2.7 - - - +
93A GLY 3.6 2.5 - - - +
94A PHE* 3.4 53.5 - - + +
124A TYR* 4.5 4.7 - - - +
168A GLU 3.2 0.4 + - - -
169A SER* 1.4 71.5 + - - +
171A GLY* 1.3 57.8 + - - +
173A ASN* 3.1 7.5 + - - +
174A ILE* 3.0 29.8 + - - +
369A 4PA 2.7 29.6 + - + +
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Residues in contact with GLY 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 3.4 18.7 - - - +
90A HIS 3.3 22.0 + - - -
167A GLY* 3.4 15.0 - - - -
168A GLU 2.8 9.7 + - - -
170A ALA* 1.3 78.4 - - - +
172A GLY* 1.3 57.9 + - - +
174A ILE* 4.1 5.8 - - - -
175A ALA* 2.8 22.9 + - - +
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Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLY* 3.3 27.1 - - - -
168A GLU 3.4 0.4 - - - -
169A SER 2.8 9.4 + - - -
171A GLY* 1.3 74.0 - - - +
173A ASN* 1.3 61.7 + - - +
175A ALA* 4.2 2.2 - - - -
176A TYR* 2.9 29.5 + - - +
199A LEU* 3.6 9.2 - - - +
200A ASP 4.9 0.2 - - - -
202A PRO* 3.8 16.9 - - - +
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Residues in contact with ASN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 3.7 12.6 - - + -
136A TYR* 2.7 29.7 + - - -
169A SER 3.2 4.0 + - - +
170A ALA 3.1 10.9 + - - +
172A GLY* 1.3 74.9 - - - +
174A ILE* 1.4 64.2 + - - +
176A TYR* 3.2 1.7 + - - +
177A HIS* 3.0 28.2 + - - -
202A PRO* 4.0 2.0 - - - +
203A GLY 2.9 29.4 + - - +
204A PHE* 3.6 20.7 - - - -
231A TRP* 3.8 8.7 - - - -
245A TYR 3.0 23.2 + - - -
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Residues in contact with ILE 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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89A PHE* 3.7 24.2 - - + -
94A PHE* 4.0 11.0 - - + -
124A TYR* 3.6 36.6 - - + +
135A ALA* 3.6 29.2 - - + +
136A TYR* 3.8 23.4 - - + -
139A ALA* 3.9 16.8 - - + -
170A ALA 3.0 15.0 + - - +
171A GLY* 3.6 8.3 - - - +
173A ASN* 1.4 77.4 - - - +
175A ALA* 1.3 52.9 + - - +
177A HIS* 3.4 1.2 + - - +
178A ALA* 2.8 33.4 + - - +
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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
----------------------------------------------------------
89A PHE* 4.3 4.0 - - + -
165A ILE* 3.9 22.4 - - + +
166A MET* 3.6 12.1 - - - +
167A GLY 3.6 21.5 - - - +
171A GLY 2.8 20.4 + - - +
172A GLY 3.7 4.5 - - - +
173A ASN 3.3 0.2 - - - -
174A ILE* 1.3 73.1 - - - +
176A TYR* 1.3 58.2 + - - +
178A ALA* 3.8 1.5 - - - +
179A GLY* 2.9 26.7 + - - -
197A LEU* 4.5 3.1 - - - +
199A LEU* 4.1 10.5 - - + -
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Residues in contact with TYR 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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172A GLY 2.9 18.1 + - - +
173A ASN 3.5 3.1 - - - +
175A ALA* 1.3 76.2 - - - +
177A HIS* 1.3 79.4 + + - +
179A GLY* 3.1 3.8 + - - -
180A LEU* 2.9 62.3 + - + +
197A LEU* 4.8 9.5 - - + +
199A LEU* 3.8 20.5 - - + +
204A PHE* 4.0 15.5 - + + -
248A PRO* 3.8 27.8 + - + +
255A LEU* 4.3 2.6 - - - +
258A PHE* 3.3 29.4 - + - -
261A ILE* 5.6 1.1 - - + -
285A LEU* 3.8 32.2 - - + +
289A LEU* 5.4 4.7 - - + -
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Residues in contact with HIS 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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136A TYR* 3.4 34.7 + + + -
173A ASN* 3.0 44.9 + - - +
176A TYR* 1.3 99.6 - + - +
178A ALA* 1.4 61.7 + - - +
180A LEU* 3.3 17.5 + - + +
181A ARG* 3.0 32.3 + - - +
204A PHE* 4.7 2.6 - - - -
244A GLU* 3.4 25.6 + - + -
245A TYR* 3.6 25.4 + + - -
248A PRO* 5.5 0.8 - - + +
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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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89A PHE* 5.0 1.3 - - + -
136A TYR* 5.2 3.0 - - - +
139A ALA* 3.8 25.4 - - + -
140A MET* 3.7 18.5 - - - +
143A LEU* 4.7 5.8 - - + -
165A ILE* 4.5 11.2 - - + -
174A ILE 2.8 21.4 + - - +
175A ALA* 3.8 7.2 - - - +
177A HIS* 1.4 69.3 - - - +
179A GLY* 1.3 57.0 + - - +
181A ARG* 3.3 1.6 + - - +
182A ALA* 2.8 37.2 + - - +
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Residues in contact with GLY 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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165A ILE* 4.1 6.7 - - - +
175A ALA 2.9 15.8 + - - -
176A TYR 3.1 4.7 + - - -
178A ALA* 1.3 76.3 - - - +
180A LEU* 1.3 57.8 + - - +
182A ALA* 3.3 0.6 + - - -
183A ALA* 2.9 25.6 + - - +
197A LEU* 3.9 25.1 - - - -
261A ILE* 5.4 0.7 - - - -
266A TRP* 3.3 16.7 - - - -
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Residues in contact with LEU 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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176A TYR* 2.9 59.9 + - + +
177A HIS* 3.3 19.5 + - + +
179A GLY* 1.3 76.4 - - - +
181A ARG* 1.3 63.7 + - + +
183A ALA* 3.4 14.1 + - - +
184A ALA* 3.4 12.6 + - - +
197A LEU* 5.9 0.2 - - + -
255A LEU* 6.5 0.2 - - + -
257A SER* 4.0 32.0 + - - +
258A PHE* 4.2 3.4 - - + -
261A ILE* 3.8 25.6 - - + -
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Residues in contact with ARG 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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133A PRO* 5.0 2.8 - - - +
136A TYR* 3.6 27.4 - - - +
137A ASP* 2.9 30.5 + - - +
140A MET* 3.5 45.1 - - + +
177A HIS* 3.0 24.5 + - - +
180A LEU* 1.3 75.8 - - + +
182A ALA* 1.3 65.2 - - - +
184A ALA* 3.3 15.9 + - - +
185A VAL* 3.5 15.8 + - - +
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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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140A MET* 3.8 8.2 - - - +
143A LEU* 4.0 11.0 - - + -
165A ILE* 4.4 1.6 - - + -
178A ALA 2.8 22.4 + - - +
179A GLY 3.7 3.6 - - - +
181A ARG* 1.3 71.1 - - - +
183A ALA* 1.3 67.3 + - - +
185A VAL* 3.0 8.3 + - - +
186A ALA* 3.0 23.2 + - - +
189A LEU* 3.8 10.7 - - + +
194A ILE* 3.7 28.5 - - + -
266A TRP* 4.2 2.6 - - + -
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Residues in contact with ALA 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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179A GLY 2.9 17.8 + - - +
180A LEU* 3.7 7.0 - - - +
181A ARG 3.2 0.4 - - - -
182A ALA* 1.3 76.7 - - - +
184A ALA* 1.3 58.7 + - - +
185A VAL 3.3 0.9 + - - -
186A ALA* 3.4 8.0 + - - +
257A SER* 5.1 2.0 - - - +
260A LYS* 2.9 47.5 + - + +
261A ILE* 4.4 11.2 - - + -
264A LEU* 3.9 9.3 - - + +
266A TRP* 3.6 20.4 - - + -
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Residues in contact with ALA 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 LEU 3.4 8.8 + - - +
181A ARG* 3.3 13.0 + - - +
182A ALA 3.1 0.4 - - - -
183A ALA* 1.3 80.7 - - - +
185A VAL* 1.3 64.6 + - + +
186A ALA 3.6 0.4 - - - -
188A GLU* 5.3 0.7 - - - +
260A LYS* 4.0 14.0 + - - +
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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