Contacts of the strand formed by residues 282 - 291 (chain A) in PDB entry 2O9C
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 GLN 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A PRO* 6.0 3.8 - - - +
217A THR* 5.1 0.7 - - - -
278A VAL* 3.3 4.8 - - - -
279A VAL 2.9 35.8 + - - +
280A GLY 3.2 3.3 - - - +
281A GLY* 1.3 78.7 - - - +
283A LEU* 1.3 74.5 + - + +
284A TRP* 3.2 2.0 + - - +
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Residues in contact with LEU 283 (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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178A PHE* 3.5 42.9 - - + +
213A ARG* 3.8 35.7 - - + +
216A TYR* 3.9 15.3 - - + +
217A THR* 3.8 15.8 + - - +
276A SER* 3.7 32.5 - - - +
277A VAL 3.8 4.7 - - - +
278A VAL* 4.2 4.9 - - + +
282A GLN* 1.3 82.6 + - + +
284A TRP* 1.3 60.2 + - - +
285A GLY 3.7 14.6 - - - +
286A LEU* 4.3 4.3 - - + -
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Residues in contact with TRP 284 (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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153A LEU* 4.1 16.4 - - + -
175A LEU* 3.9 30.7 - - + -
177A LYS* 3.6 38.0 - - + +
178A PHE* 3.0 25.5 + - - +
187A ILE* 4.0 22.4 - - + -
277A VAL* 2.8 30.2 + - + +
279A VAL* 3.8 30.7 - - + -
282A GLN* 3.2 2.7 + - - +
283A LEU* 1.3 74.1 - - - +
285A GLY* 1.3 64.9 + - - +
316A VAL* 3.5 22.0 - - + +
320A GLU* 2.7 35.6 + - - -
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Residues in contact with GLY 285 (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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175A LEU* 5.3 0.2 - - - -
176A TYR 3.0 14.4 - - - -
178A PHE* 3.6 10.2 - - - -
277A VAL* 2.9 29.7 + - - +
283A LEU* 3.5 4.9 - - - +
284A TRP* 1.3 90.7 - - - +
286A LEU* 1.3 70.8 + - - +
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Residues in contact with LEU 286 (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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175A LEU* 3.5 9.1 - - - +
176A TYR* 2.8 41.4 + - + +
178A PHE* 4.1 10.3 - - + -
208A ILE* 3.8 29.2 - - + -
216A TYR* 4.5 10.3 - - + -
222A ARG* 3.6 23.6 - - - +
274A SER* 4.1 9.6 - - - +
275A VAL 3.4 3.6 - - - +
276A SER* 3.9 13.9 - - - +
277A VAL* 4.5 0.4 - - - +
283A LEU* 4.3 7.9 - - + -
285A GLY* 1.3 84.1 - - - +
287A ILE* 1.3 66.9 + - - +
288A ALA* 3.5 3.0 + - + +
328A LBV 3.9 22.7 - - + -
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Residues in contact with ILE 287 (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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160A ALA* 5.7 2.7 - - + -
161A THR* 5.8 2.5 - - + -
164A VAL* 4.2 20.0 - - + -
173A VAL* 3.9 24.2 - - + -
174A MET 3.4 4.5 - - - +
175A LEU* 4.0 17.3 - - + -
273A LEU 3.9 0.5 - - - +
274A SER* 3.0 5.8 - - - -
275A VAL* 2.9 50.5 + - + +
277A VAL* 4.2 5.1 - - + +
286A LEU* 1.3 68.5 - - - +
288A ALA* 1.3 58.7 + - - +
289A CYS* 4.1 6.4 + - - -
305A LEU* 5.0 3.1 - - + +
308A LEU* 3.9 28.0 - - + -
309A GLY* 4.2 15.7 - - - +
312A LEU* 3.9 15.0 - - + -
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Residues in contact with ALA 288 (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 VAL* 3.5 0.9 - - - -
174A MET* 2.8 66.1 + - + +
176A TYR* 4.8 7.9 - - + -
273A LEU 3.8 3.4 - - - -
274A SER* 4.0 4.3 - - - -
286A LEU* 3.5 9.4 + - + +
287A ILE* 1.3 72.3 - - - +
289A CYS* 1.3 60.6 + - - +
290A HIS* 5.6 1.3 - - - +
328A LBV 4.2 25.6 - - + +
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Residues in contact with CYS 289 (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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164A VAL* 4.1 11.2 - - - -
170A PHE* 3.5 40.4 - - + -
172A ARG 3.2 6.3 - - - +
173A VAL* 4.0 21.1 - - - -
272A SER* 3.3 6.8 + - - -
273A LEU* 2.8 50.3 + - - +
287A ILE* 4.2 9.2 - - - -
288A ALA* 1.3 76.7 - - - +
290A HIS* 1.3 67.8 + - - +
305A LEU* 4.8 1.3 - - - -
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Residues in contact with HIS 290 (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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170A PHE* 3.6 7.0 - - - -
171A ASP* 3.2 7.4 + - + -
172A ARG* 2.8 58.1 + - + +
174A MET* 3.6 15.6 - - + +
198A PHE* 4.4 5.5 - + - -
264A LEU* 4.6 0.6 - - - +
267A MET* 3.6 24.6 - - + +
269A VAL* 3.5 27.1 - - + +
271A SER 3.4 4.7 - - - -
272A SER* 3.9 12.2 + - - -
288A ALA* 5.3 1.0 - - + +
289A CYS* 1.3 86.9 - - - +
291A HIS* 1.3 61.9 + - - +
328A LBV 2.8 32.8 + - - +
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Residues in contact with HIS 291 (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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169A GLY 3.3 24.7 - - - -
170A PHE* 3.5 15.9 - + + -
171A ASP* 3.2 31.9 + - - -
269A VAL* 3.8 3.6 - - - +
270A GLY 2.8 23.2 + - - -
271A SER* 2.8 21.5 + - - +
290A HIS* 1.3 75.9 - - - +
292A GLN* 1.3 61.5 + - - +
293A THR* 3.5 34.6 + - - +
294A PRO 4.8 0.2 - - - -
295A TYR* 3.8 23.7 - + + +
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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