Contacts of the strand formed by residues 278 - 289 (chain B) in PDB entry 4OIA
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 GLU 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B PHE* 4.6 15.6 - - + -
195B LEU* 3.6 23.6 - - + +
274B THR* 3.8 1.4 + - - -
275B LEU 2.9 31.5 + - - +
276B GLY 3.5 0.2 - - - -
277B GLY* 1.3 82.6 - - - +
279B ASN* 1.3 66.0 + - - +
280B ARG* 2.6 37.9 + - - +
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Residues in contact with ASN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 4.8 0.7 - - - -
273B VAL 3.3 13.0 - - - +
274B THR* 3.7 13.9 + - - -
277B GLY 4.4 7.3 - - - +
278B GLU* 1.3 81.2 - - - +
280B ARG* 1.3 73.0 + - - +
281B GLU* 6.2 0.4 - - - +
1L NAG 3.4 33.9 + - + +
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 3.4 31.1 + - + +
196B SER 3.0 23.7 + - - -
197B PRO* 2.8 37.4 + - - +
198B ASP 3.4 10.5 + - - +
199B ALA* 5.4 0.7 - - - -
200B PRO* 4.1 22.1 - - + +
220B LEU* 4.6 6.3 - - + -
271B CYS 4.0 0.2 - - - +
272B ASN* 3.2 3.6 - - - +
273B VAL* 2.9 35.2 + - - +
278B GLU* 2.6 34.0 + - - +
279B ASN* 1.3 84.0 - - - +
281B GLU* 1.3 60.5 + - - +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA* 5.0 3.8 - - - +
200B PRO* 4.6 2.3 - - - +
270B VAL* 4.4 3.5 - - - +
271B CYS 3.3 13.2 - - - +
272B ASN* 3.0 30.1 + - + +
279B ASN* 6.2 0.4 - - - +
280B ARG* 1.3 75.7 - - - +
282B THR* 1.3 67.5 + - - +
283B ARG* 3.3 47.9 + - + +
1L NAG 3.9 14.5 - - + +
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Residues in contact with THR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B ALA* 3.4 13.9 - - + +
200B PRO* 2.9 48.4 + - - +
202B LEU* 4.3 10.0 - - + +
269B LEU 3.6 3.3 - - - +
271B CYS* 2.9 36.2 + - - +
281B GLU* 1.3 71.5 + - - +
283B ARG* 1.3 70.7 + - - +
284B GLU* 4.2 13.4 + - + -
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B GLN* 3.7 37.4 + - + +
269B LEU 3.5 3.8 - - - +
270B VAL* 3.4 27.3 - - + +
281B GLU* 3.3 38.9 + - + -
282B THR* 1.3 78.7 - - - +
284B GLU* 1.3 70.6 + - - +
285B ASN* 4.4 0.7 + - - -
1L NAG 5.3 7.9 + - - -
2L NAG 6.2 2.0 - - - -
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Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B LEU* 3.6 43.7 + - + +
204B ALA* 3.8 28.3 - - + +
268B GLN* 3.4 3.5 - - - -
269B LEU* 2.9 35.9 + - + +
282B THR* 4.6 8.3 - - + -
283B ARG* 1.3 82.1 - - - +
285B ASN* 1.3 66.9 + - - +
286B VAL* 3.6 0.9 + - - +
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ALA* 5.1 4.5 - - - +
205B PRO 4.6 5.5 - - - +
206B ARG* 4.6 3.6 - - - +
267B ARG 3.7 5.9 - - - +
268B GLN* 3.0 30.4 + - - +
283B ARG 5.8 0.7 - - - -
284B GLU* 1.3 77.0 + - - +
286B VAL* 1.3 61.3 + - - +
287B THR* 5.7 2.7 - - + -
2313B NAG 1.4 68.6 + - - +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B ALA* 6.5 0.7 - - + -
205B PRO* 3.7 21.5 - - + +
206B ARG 4.1 5.4 - - - +
207B LEU 4.6 0.2 - - - -
208B LEU* 4.4 26.0 - - + +
235B LEU* 5.1 5.2 - - + -
266B ALA* 4.3 0.2 - - - -
267B ARG* 3.0 52.8 + - + +
268B GLN* 3.9 7.2 - - - +
269B LEU* 4.2 27.6 - - + -
284B GLU 4.6 0.9 - - - +
285B ASN* 1.3 76.0 - - - +
287B THR* 1.3 69.9 + - - +
288B ILE* 5.0 4.7 - - + +
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ARG 3.4 15.2 + - - +
207B LEU* 3.3 13.3 - - - +
208B LEU 3.1 20.0 + - - -
265B GLY* 3.9 19.1 - - - +
266B ALA* 5.1 1.6 - - - -
285B ASN* 5.7 2.7 - - + -
286B VAL* 1.3 80.5 - - - +
288B ILE* 1.3 64.3 + - - +
289B TYR* 3.9 1.5 + - - -
358B VAL* 5.2 3.4 + - - +
359B ASP* 3.2 40.6 - - + +
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Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 3.2 26.9 - - + +
210B VAL* 3.8 15.9 - - + -
235B LEU* 4.0 15.3 - - + -
259B ALA* 3.6 33.7 - - + -
262B GLU* 5.1 1.3 - - - +
263B GLN 3.5 18.8 - - - +
264B GLU* 3.2 22.0 - - + +
265B GLY* 2.9 29.3 + - - +
266B ALA 5.0 0.2 - - - +
267B ARG* 3.7 27.6 - - + -
286B VAL* 4.1 5.1 + - + -
287B THR* 1.3 75.5 - - - +
289B TYR* 1.3 59.7 + - - +
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Residues in contact with TYR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B LEU* 3.7 38.4 - - + +
208B LEU 3.1 10.3 + - - -
209B GLU* 3.4 40.6 + - + +
210B VAL* 3.4 27.4 + - - +
264B GLU* 4.8 2.0 - - - -
287B THR* 4.1 1.1 - - - +
288B ILE* 1.3 75.0 - - - +
290B SER* 1.3 63.0 + - - +
291B PHE* 3.7 32.2 + + + -
356B LEU* 5.4 0.4 - - + -
358B VAL* 3.7 34.5 - - + -
363B LEU* 3.2 30.3 - - + +
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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