Contacts of the helix formed by residues 208 - 223 (chain A) in PDB entry 2OB1
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 HIS 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ASN* 4.9 1.8 + - - +
206A TYR 5.4 1.2 + - - -
207A MET* 1.3 75.7 - - - +
209A ASN* 1.3 68.3 + - - +
210A ASN* 3.2 2.5 - - + +
211A GLU* 3.1 26.7 + - + +
212A SER* 3.0 19.7 + - - -
258A GLU* 4.6 12.9 + - - -
260A PRO* 3.7 28.9 - - + +
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Residues in contact with ASN 209 (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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208A HIS* 1.3 73.8 - - - +
210A ASN* 1.3 62.0 + - - +
212A SER* 3.5 9.1 + - - -
213A GLN* 2.8 40.6 + - - +
260A PRO* 5.1 0.2 - - - +
261A THR* 3.6 18.1 - - + +
264A THR* 5.7 2.7 - - + -
265A TYR* 2.5 44.2 + - + -
274A ARG* 4.5 2.6 - - - +
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Residues in contact with ASN 210 (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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208A HIS* 3.2 1.8 - - + +
209A ASN* 1.3 83.7 + - - +
211A GLU* 1.3 76.1 + - - +
213A GLN* 3.9 2.7 - - - +
214A LEU* 2.9 33.2 + - - +
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Residues in contact with GLU 211 (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 LEU 5.3 0.2 - - - +
177A ASN* 3.2 52.4 - - + +
179A ILE* 4.5 6.6 - - + +
207A MET* 3.5 7.0 - - + +
208A HIS* 3.1 28.6 + - + +
210A ASN* 1.3 92.8 - - - +
212A SER* 1.3 57.5 + - - +
214A LEU* 3.8 4.2 - - - +
215A LEU* 2.9 30.7 + - - +
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Residues in contact with SER 212 (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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204A LEU* 3.8 20.4 - - - +
207A MET* 3.6 19.1 + - - +
208A HIS 3.0 14.3 + - - -
209A ASN* 3.2 13.9 + - - -
211A GLU* 1.3 76.1 - - - +
213A GLN* 1.3 59.4 + - - +
215A LEU* 3.3 2.0 + - - +
216A ILE* 2.9 34.8 + - - +
261A THR* 4.9 0.2 - - - +
274A ARG* 3.1 30.2 + - - -
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Residues in contact with GLN 213 (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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209A ASN* 2.8 29.3 + - - +
210A ASN* 4.0 2.9 - - - +
212A SER* 1.3 78.8 + - - +
214A LEU* 1.3 57.3 + - - +
216A ILE* 3.3 7.2 + - - +
217A ASN* 2.8 69.9 + - - +
265A TYR* 4.4 6.1 + - - -
274A ARG* 2.9 47.6 + - - +
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Residues in contact with LEU 214 (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 ILE* 3.6 30.1 - - + -
210A ASN 2.9 19.2 + - - +
211A GLU* 4.0 0.9 - - - +
213A GLN* 1.3 73.5 - - - +
215A LEU* 1.3 60.3 + - - +
217A ASN* 4.5 9.0 - - + +
218A THR* 2.7 56.1 + - - +
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Residues in contact with LEU 215 (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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104A LEU* 4.2 15.9 - - + -
176A LEU* 4.0 20.4 - - + +
179A ILE* 4.2 13.1 - - + +
182A THR* 3.9 21.5 - - + -
203A LEU* 4.2 7.0 - - + -
204A LEU* 3.9 17.5 - - + -
207A MET* 3.9 22.4 - - + -
211A GLU 2.9 17.7 + - - +
212A SER 3.5 4.5 - - - +
214A LEU* 1.3 77.2 - - - +
216A ILE* 1.3 63.6 + - - +
219A ILE* 3.0 57.7 + - + +
228A TRP* 4.6 2.9 - - + -
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Residues in contact with ILE 216 (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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204A LEU* 4.1 10.5 - - + -
212A SER 2.9 24.3 + - - +
213A GLN* 3.7 10.3 - - - +
215A LEU* 1.3 78.0 - - - +
217A ASN* 1.3 63.7 + - - +
220A MET* 3.1 36.2 + - + +
228A TRP* 3.7 15.4 - - + -
274A ARG* 3.7 37.5 - - + +
275A TRP* 3.5 61.5 - - + +
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Residues in contact with ASN 217 (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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213A GLN* 2.8 54.9 + - - +
214A LEU* 4.0 10.4 - - + +
216A ILE* 1.3 79.8 - - - +
218A THR* 1.3 63.7 + - - +
220A MET* 4.0 8.3 - - - +
221A SER* 3.0 30.1 + - - +
274A ARG 4.5 1.0 - - - +
277A ALA* 5.4 5.9 - - - +
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Residues in contact with THR 218 (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 ILE* 3.0 35.5 - - + +
183A THR* 3.3 21.5 - - + -
214A LEU* 2.7 32.8 + - - +
217A ASN* 1.3 74.6 - - - +
219A ILE* 1.3 64.7 + - - +
221A SER* 3.3 7.3 + - - -
222A LYS* 3.1 24.8 + - + +
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Residues in contact with ILE 219 (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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102A VAL* 5.8 1.6 - - + -
104A LEU* 3.9 28.9 - - + -
179A ILE* 5.2 1.6 - - + -
182A THR* 4.4 2.9 - - + -
183A THR* 6.1 0.4 - - + -
186A LEU* 3.8 22.2 - - + -
198A VAL* 3.8 21.5 - - + -
215A LEU* 3.0 51.0 + - + +
218A THR* 1.3 78.3 - - + +
220A MET* 1.3 63.9 + - - +
222A LYS* 2.9 16.0 + - + +
223A PHE* 3.3 26.8 - - + -
228A TRP* 3.7 15.3 - - + -
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Residues in contact with MET 220 (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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216A ILE* 3.1 37.8 + - + +
217A ASN* 4.0 6.3 - - - +
219A ILE* 1.3 76.3 - - - +
221A SER* 1.3 59.3 + - - +
222A LYS 3.2 0.5 + - - -
223A PHE 3.1 23.4 + - - +
228A TRP* 3.8 11.4 - - + -
274A ARG 5.1 0.4 - - - +
275A TRP* 4.0 21.3 - - + -
277A ALA* 4.1 26.2 - - + -
278A ALA* 4.0 18.6 - - - +
326A ALA* 4.9 0.2 - - - -
328A TRP* 3.4 55.9 + - + +
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Residues in contact with SER 221 (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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192A ARG* 2.8 29.7 + - - -
217A ASN* 3.0 21.4 + - - +
218A THR* 3.6 6.7 - - - -
219A ILE 3.2 0.4 - - - -
220A MET* 1.3 76.3 - - - +
222A LYS* 1.3 49.6 + - - +
223A PHE 3.4 1.1 - - - +
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Residues in contact with LYS 222 (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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183A THR* 3.5 27.6 - - + +
186A LEU* 3.8 33.2 - - + -
187A ASP* 3.0 29.9 + - - +
190A THR* 5.4 0.9 - - - -
192A ARG* 3.3 49.3 + - - +
218A THR* 3.1 21.2 + - + +
219A ILE* 2.9 13.2 + - + +
221A SER* 1.3 75.8 - - - +
223A PHE* 1.3 71.2 + - + +
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Residues in contact with PHE 223 (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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100A GLN* 3.4 16.8 - - - -
102A VAL* 4.9 2.9 - - + -
186A LEU* 4.6 9.0 - - + -
190A THR* 3.3 35.7 - - + -
191A LYS 3.6 11.2 - - - -
192A ARG* 3.5 6.3 - - - +
194A ILE 4.7 0.2 - - - +
196A THR* 3.4 41.5 - - + +
198A VAL* 5.0 0.2 - - + -
219A ILE* 3.3 40.8 - - + -
220A MET 3.1 7.0 + - - +
221A SER 3.4 1.6 - - - +
222A LYS* 1.3 101.7 - - + +
224A SER* 1.3 62.0 + - - +
225A HIS 3.2 7.6 - - - +
328A TRP* 2.8 32.4 + + + +
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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