Contacts of the helix formed by residues 181 - 194 (chain A) in PDB entry 2OOR
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 GLY 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A GLY 3.6 5.1 + - - -
180A VAL* 1.3 73.8 - - - +
182A VAL* 1.3 65.2 - - - -
183A ALA 3.4 2.0 - - - -
184A GLY 4.2 2.4 - - - +
185A LEU* 3.1 31.6 + - - +
204A ARG* 4.3 3.6 - - - -
264A THR* 4.6 0.4 + - - -
500A NAD 3.5 38.9 + - - -
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Residues in contact with VAL 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 SER* 3.3 47.3 - - - +
141A SER* 3.4 13.9 - - - +
142A ASN* 3.6 17.3 - - + +
181A GLY* 1.3 72.8 - - - +
183A ALA* 1.3 62.1 + - - +
185A LEU* 4.0 8.9 - - + +
186A GLN* 3.4 21.5 + - - +
500A NAD 3.0 33.6 + - + +
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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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141A SER* 3.2 33.7 + - - +
142A ASN* 4.7 0.2 - - - +
144A ALA* 4.9 1.3 - - + -
145A GLY* 3.2 19.9 - - - +
181A GLY* 3.4 0.4 - - - -
182A VAL* 1.3 80.2 - - - +
184A GLY* 1.3 59.0 + - - +
186A GLN 3.4 1.4 + - - -
187A ALA* 3.0 24.7 + - - +
264A THR* 4.4 10.1 - - + -
293A LEU* 4.3 15.3 - - + -
500A NAD 4.7 1.0 + - - -
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Residues in contact with GLY 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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177A VAL* 3.6 12.3 - - - +
179A GLY 3.6 22.8 + - - -
180A VAL* 4.2 2.5 - - - -
181A GLY 3.6 6.6 + - - +
182A VAL 3.5 0.2 - - - -
183A ALA* 1.3 76.4 - - - +
185A LEU* 1.3 58.5 + - - +
187A ALA* 3.4 4.3 + - - +
188A ILE* 3.1 35.1 + - - +
264A THR* 4.0 9.1 + - - +
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Residues in contact with LEU 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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180A VAL* 3.3 24.4 - - + +
181A GLY 3.1 29.3 + - - +
182A VAL* 4.0 7.9 - - + +
183A ALA 3.4 0.2 - - - -
184A GLY* 1.3 75.5 - - - +
186A GLN* 1.3 61.0 + - - +
188A ILE* 3.3 3.2 + - - -
189A ALA* 3.2 19.9 + - - +
210A GLN* 3.7 45.1 - - + +
214A LEU* 3.4 34.4 - - + +
500A NAD 6.4 1.3 - - - -
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Residues in contact with GLN 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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142A ASN* 3.0 54.5 + - - +
145A GLY 4.2 0.9 - - - -
146A TYR* 3.6 15.7 - - + +
182A VAL 3.4 5.1 + - - +
183A ALA 3.4 7.5 + - - +
185A LEU* 1.3 76.3 - - - +
187A ALA* 1.3 59.1 + - - +
189A ALA* 3.9 13.3 - - - +
190A THR* 2.8 53.7 + - - -
193A ARG* 5.7 2.1 + - - -
161B PRO* 5.3 2.1 - - - +
163B MET* 3.7 25.1 - - + +
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Residues in contact with ALA 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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145A GLY* 3.5 18.5 + - - +
149A VAL* 3.4 6.4 - - - +
177A VAL* 4.6 7.9 - - + +
183A ALA 3.0 16.8 + - - +
184A GLY* 3.6 11.0 - - - +
185A LEU 3.3 0.2 - - - -
186A GLN* 1.3 75.2 - - - +
188A ILE* 1.3 62.8 + - - +
191A ALA* 3.1 26.9 + - - +
262A ILE* 4.0 31.4 - - + +
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Residues in contact with ILE 188 (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 VAL* 3.6 17.5 - - + -
180A VAL* 3.8 24.9 - - + -
184A GLY 3.1 18.1 + - - +
185A LEU* 3.6 8.7 - - - +
186A GLN 3.3 0.2 - - - -
187A ALA* 1.3 73.7 - - - +
189A ALA* 1.3 61.3 + - - +
191A ALA* 3.4 1.7 + - - +
192A LYS* 2.9 38.6 + - + +
198A VAL* 3.9 20.1 - - + +
200A ALA* 4.0 9.9 - - + -
211A VAL* 3.8 20.4 - - + +
214A LEU* 3.7 33.7 - - + +
216A GLY* 4.6 8.1 - - - +
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Residues in contact with ALA 189 (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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185A LEU 3.2 12.3 + - - +
186A GLN* 3.9 18.4 - - - +
187A ALA 3.5 0.2 - - - -
188A ILE* 1.3 79.8 - - - +
190A THR* 1.3 57.0 + - - +
192A LYS* 3.5 5.9 + - - +
193A ARG* 2.8 38.0 + - + +
214A LEU* 4.5 19.5 - - + +
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Residues in contact with THR 190 (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 TYR* 3.6 40.9 - - + +
149A VAL* 3.9 26.0 - - + +
150A ILE* 4.7 2.2 - - + -
186A GLN* 2.8 35.5 + - - -
189A ALA* 1.3 74.1 - - - +
191A ALA* 1.3 65.2 + - - +
193A ARG* 3.4 12.7 - - - +
194A LEU* 3.2 23.4 + - - +
161B PRO* 5.5 0.5 - - - +
194B LEU* 4.1 13.2 - - + -
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Residues in contact with ALA 191 (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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149A VAL* 3.9 17.4 - - + +
160A PHE* 4.3 2.9 - - + -
175A VAL* 4.1 24.0 - - + -
187A ALA 3.1 21.4 + - - +
190A THR* 1.3 78.0 - - - +
192A LYS* 1.3 60.5 + - - +
194A LEU* 3.3 9.4 + - - +
195A GLY 3.4 0.2 + - - -
196A ALA* 3.1 25.8 + - - +
198A VAL* 3.6 19.1 - - + -
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Residues in contact with LYS 192 (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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188A ILE* 2.9 23.4 + - + +
189A ALA* 3.8 5.2 - - - +
191A ALA* 1.3 74.3 - - - +
193A ARG* 1.3 64.6 + - - +
195A GLY* 3.1 13.2 + - - -
196A ALA 3.8 19.3 - - - -
197A VAL* 5.3 1.3 - - - +
198A VAL* 3.6 20.0 - - + +
214A LEU 3.2 26.2 - - - +
215A GLY* 3.1 31.5 + - - -
216A GLY 4.1 1.6 - - - +
193B ARG* 5.2 0.3 + - - -
100C ALA* 6.2 0.2 - - - +
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Residues in contact with ARG 193 (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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186A GLN* 5.7 2.0 + - - -
189A ALA* 2.8 28.0 + - + +
190A THR* 3.4 14.8 - - - +
192A LYS* 1.3 73.6 - - - +
194A LEU* 1.3 57.1 + - - +
195A GLY 3.4 0.5 + - - -
161B PRO* 3.7 31.7 - - - +
162B MET 4.8 5.9 + - - +
192B LYS 4.9 0.6 + - - -
193B ARG* 3.0 55.8 + - - +
194B LEU* 3.8 18.2 - - + +
195B GLY* 3.6 17.0 - - - -
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Residues in contact with LEU 194 (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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149A VAL* 4.1 18.6 - - + -
150A ILE* 5.0 4.0 - - + -
153A ALA* 4.6 4.9 - - + -
160A PHE* 3.4 34.1 - - + +
161A PRO* 3.2 30.9 - - + +
190A THR 3.2 5.5 + - - +
191A ALA 3.8 2.5 - - - +
192A LYS 3.2 0.4 - - - -
193A ARG* 1.3 77.5 - - - +
195A GLY* 1.3 57.3 + - - +
196A ALA 3.5 1.6 - - - -
146B TYR* 4.6 6.5 - - + -
150B ILE* 4.3 20.0 - - + -
190B THR* 4.0 20.4 - - + -
193B ARG* 3.8 12.7 + - + +
194B LEU* 3.8 40.2 - - + -
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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