Contacts of the helix formed by residues 176 - 187 (chain A) in PDB entry 2O71
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 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LEU 3.4 9.9 + - - -
112A ASN* 3.1 27.7 - - - +
113A SER 3.2 13.0 - - - +
114A SER* 4.3 1.8 - - - +
115A PRO* 4.6 2.0 - - - -
167A TRP* 3.6 3.4 - - - -
173A LYS 3.2 23.6 - - - +
174A GLN* 2.8 11.9 + - - -
175A ALA* 1.3 74.5 - - - +
177A PHE* 1.3 59.9 + - - +
178A GLN* 3.3 14.6 + - - +
179A SER* 3.0 28.7 + - - -
180A LEU* 3.0 16.6 + - - +
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Residues in contact with PHE 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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110A ILE* 3.4 29.2 - - + +
111A LEU* 3.6 7.4 + - - -
113A SER* 3.1 24.4 + - - -
114A SER 4.0 0.9 - - - -
115A PRO* 3.7 18.8 - - + -
119A GLN* 3.1 41.7 - - + -
176A THR* 1.3 72.5 - - - +
178A GLN* 1.3 64.6 + - - +
180A LEU* 3.3 22.0 + - + +
181A HIS* 3.0 24.1 + - - +
194A LEU* 4.0 15.9 - - + +
197A MET* 4.0 17.3 - - + -
198A LEU* 4.0 33.4 - - + -
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Residues in contact with GLN 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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111A LEU* 3.0 31.3 + - + +
112A ASN* 5.2 4.7 - - - +
176A THR* 3.1 6.9 - - - +
177A PHE* 1.3 78.2 - - - +
179A SER* 1.3 60.7 + - - +
181A HIS* 3.3 13.0 + - - +
182A ASN* 2.9 58.7 + - - +
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Residues in contact with SER 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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138A LEU* 3.5 15.3 - - - +
167A TRP* 3.7 19.3 - - - -
174A GLN 2.8 22.9 + - - -
176A THR* 3.0 13.4 + - - -
178A GLN* 1.3 77.0 - - - +
180A LEU* 1.3 59.0 + - - +
182A ASN* 3.1 14.2 + - - +
183A GLY 2.8 23.9 + - - -
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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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115A PRO* 4.2 21.1 - - + -
123A LEU* 4.0 17.5 - - + -
134A MET* 3.6 23.3 - - + +
138A LEU* 4.1 5.6 - - + -
164A PHE* 3.9 15.0 - - + -
167A TRP* 3.5 22.9 - - + -
176A THR 3.0 15.9 + - - +
177A PHE* 3.3 32.7 + - + +
179A SER* 1.3 75.1 - - - +
181A HIS* 1.3 58.2 + - - +
183A GLY* 3.0 2.6 + - - -
184A LEU* 2.8 33.8 + - - +
194A LEU* 4.1 15.3 - - + -
197A MET* 6.0 0.4 - - + -
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Residues in contact with HIS 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 PHE 3.0 13.6 + - - +
178A GLN* 3.4 18.4 + - - +
180A LEU* 1.3 77.1 - - - +
182A ASN* 1.3 67.0 + - - +
184A LEU* 3.5 5.5 + - - +
185A ARG* 3.2 24.0 + - + +
191A PRO* 3.5 37.0 + - + +
194A LEU* 3.6 19.9 - - + +
195A LEU* 6.5 1.6 - - + -
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Residues in contact with ASN 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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138A LEU* 5.7 0.7 - - + -
178A GLN* 2.9 46.6 + - - +
179A SER* 3.1 11.8 + - - +
181A HIS* 1.3 75.3 + - - +
183A GLY* 1.3 66.3 + - - +
185A ARG* 3.4 8.3 + - - +
186A ALA* 3.0 21.4 + - - +
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Residues in contact with GLY 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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134A MET* 3.9 14.4 - - - +
137A SER* 4.0 16.6 - - - -
138A LEU* 4.1 11.2 - - - +
179A SER 2.8 13.0 + - - -
180A LEU 3.0 3.5 + - - -
182A ASN* 1.3 75.1 - - - +
184A LEU* 1.3 64.4 + - - +
186A ALA* 2.9 19.1 + - - +
187A VAL* 3.2 10.6 + - - +
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Residues in contact with LEU 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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123A LEU* 5.1 1.6 - - + -
127A LEU* 3.9 16.6 - - + -
134A MET* 3.7 24.6 - - + +
180A LEU 2.8 15.2 + - - +
181A HIS* 3.7 4.5 - - - +
183A GLY* 1.3 74.5 - - - +
185A ARG* 1.3 60.9 + - - +
187A VAL* 3.2 11.0 + - - +
189A VAL* 2.9 61.0 + - + +
191A PRO* 4.0 18.2 - - + +
193A LEU* 4.5 9.9 - - + -
194A LEU* 3.6 40.8 - - + -
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Residues in contact with ARG 185 (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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181A HIS* 3.2 15.8 + - + +
182A ASN* 3.6 11.4 - - - +
183A GLY 3.2 0.6 - - - -
184A LEU* 1.3 79.5 - - - +
186A ALA* 1.3 64.5 + - - +
188A GLU* 3.2 14.3 + - - +
189A VAL 4.4 5.2 - - - +
191A PRO* 5.1 8.2 - - + +
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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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137A SER* 4.0 23.6 - - - +
182A ASN 3.0 12.8 + - - +
183A GLY* 2.9 14.3 + - - +
185A ARG* 1.3 77.8 - - - +
187A VAL* 1.3 58.4 + - + +
188A GLU* 3.5 7.3 + - - +
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Residues in contact with VAL 187 (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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130A GLU* 4.1 15.5 - - + +
133A PRO* 3.5 20.9 - - + +
134A MET* 3.3 42.8 - - + +
137A SER* 5.5 0.4 - - - -
183A GLY 3.2 8.2 + - - +
184A LEU* 3.2 16.6 + - + +
186A ALA* 1.3 79.3 - - + +
188A GLU* 1.3 72.9 + - - +
189A VAL* 3.0 24.7 + - + +
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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