Contacts of the strand formed by residues 283 - 296 (chain B) in PDB entry 4PAR
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 ALA 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B LYS 3.3 16.6 - - - +
274B ARG* 4.0 32.8 - - - +
275B VAL 4.0 2.9 - - - -
276B LYS* 5.1 1.1 - - - +
282B ARG* 1.3 75.3 - - - +
284B MET* 1.3 68.5 + - - +
285B TYR* 4.5 13.0 - - + +
9E A 4.7 7.9 - - - +
10E C 3.1 20.8 + - - +
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Residues in contact with MET 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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172B TYR* 3.6 36.8 - - + +
190B VAL* 3.7 23.1 - - + -
191B LEU 3.7 6.3 - - - +
192B LYS* 3.9 23.1 - - + -
274B ARG* 3.3 2.9 - - - +
275B VAL* 2.8 40.2 + - + +
277B ASP* 3.6 44.2 - - + +
282B ARG* 3.6 4.0 - - - +
283B ALA* 1.3 86.1 - - - +
285B TYR* 1.3 71.1 + - - +
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Residues in contact with TYR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B VAL* 3.4 3.3 - - - +
191B LEU* 3.0 37.0 + - + +
192B LYS 4.5 0.4 - - - -
193B THR* 4.0 23.8 - - - -
194B THR* 3.6 34.0 - - + +
197B VAL* 5.0 6.7 - - + -
225B PHE* 4.2 16.2 - + + -
272B PHE* 3.7 32.8 - - + -
273B ALA 3.2 3.6 - - - +
274B ARG* 3.4 60.3 + - + -
283B ALA* 4.5 7.9 - - + +
284B MET* 1.3 84.5 - - - +
286B ARG* 1.3 61.2 + - - +
9E A 4.3 5.5 + - - -
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Residues in contact with ARG 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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48B GLN* 5.2 3.4 + - - -
63B TYR* 6.3 0.8 - - - -
111B ASP* 2.8 39.1 + - - -
112B ILE 5.8 1.3 - - - -
113B ILE* 4.1 19.6 - - - +
188B ASN* 2.6 43.0 + - - +
189B VAL 3.5 6.3 - - - +
190B VAL* 3.6 27.2 - - + +
272B PHE* 3.1 4.8 - - - -
273B ALA* 2.8 36.4 + - + +
275B VAL* 4.2 14.6 - - + -
284B MET 4.2 0.6 - - - -
285B TYR* 1.3 73.0 - - - +
287B PHE* 1.3 70.7 + - - +
288B MET* 3.3 25.8 + - + +
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ILE* 3.4 39.3 - - + -
184B SER 3.7 12.8 - - - -
185B LEU* 3.1 24.8 - - + +
189B VAL* 3.0 18.4 + - + +
270B ILE* 4.2 5.6 - - + -
271B VAL 3.6 8.5 - - - -
272B PHE* 3.8 31.9 - + + -
286B ARG* 1.3 73.8 - - - +
288B MET* 1.3 65.6 + - - +
289B GLY* 3.3 37.5 - - - -
309B SER 3.4 21.5 - - - -
310B GLU* 4.1 6.5 - - - -
311B VAL* 4.0 21.1 - - + -
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Residues in contact with MET 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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112B ILE 5.8 6.1 - - - +
113B ILE* 6.2 2.9 - - + -
185B LEU* 3.6 15.3 - - + +
228B LEU* 4.0 21.8 - - + -
238B ILE* 4.2 12.3 - - + -
245B ILE* 5.4 0.2 - - + -
271B VAL* 2.8 22.9 + - + +
273B ALA* 3.7 20.9 - - + +
275B VAL* 6.5 0.2 - - - -
286B ARG* 3.7 40.8 - - - +
287B PHE* 1.3 77.1 - - - +
289B GLY* 1.3 58.4 + - - +
291B TYR* 3.0 27.8 + - + +
306B ARG* 3.7 9.9 + - - -
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Residues in contact with GLY 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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185B LEU* 3.9 3.1 - - - +
270B ILE* 3.9 0.4 - - - -
271B VAL 3.0 25.6 + - - -
287B PHE* 3.3 33.4 - - - -
288B MET* 1.3 80.0 - - - +
290B LEU* 1.3 60.9 + - - -
291B TYR* 3.4 11.7 - - - -
306B ARG* 4.5 1.8 - - - -
308B LYS 3.6 8.3 - - - -
309B SER* 4.9 0.4 - - - -
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Residues in contact with LEU 290 (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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221B THR* 4.5 3.8 - - + +
268B LYS* 4.2 22.0 - - + +
269B ARG 3.4 22.7 - - - +
270B ILE* 3.7 19.7 - - + +
287B PHE* 4.3 1.8 - - - -
289B GLY* 1.3 71.2 - - - -
291B TYR* 1.3 65.1 + - - +
306B ARG* 3.5 1.9 - - - -
307B VAL* 2.9 35.4 + - + +
308B LYS* 2.9 53.8 + - + +
311B VAL* 3.7 18.4 - - + -
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Residues in contact with TYR 291 (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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238B ILE* 3.8 13.0 - - - +
242B GLY* 2.6 26.3 + - - -
243B LEU 3.7 6.1 - - - -
245B ILE* 3.5 31.6 - - + +
268B LYS* 3.4 5.0 - - - +
269B ARG* 2.9 37.0 + - + +
271B VAL* 3.6 16.2 - - + -
288B MET* 3.0 33.9 + - + +
289B GLY* 3.4 14.8 - - - -
290B LEU* 1.3 75.9 - - - +
292B GLU* 1.3 60.2 + - - +
304B TRP* 3.9 24.2 - - + -
305B LYS 3.2 8.1 - - - +
306B ARG* 3.4 31.9 + - + -
307B VAL* 4.6 2.2 - - - -
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Residues in contact with GLU 292 (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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267B GLN* 3.4 16.5 - - + +
268B LYS* 4.4 20.9 - - + +
291B TYR* 1.3 74.8 - - - +
293B PHE* 1.3 77.4 + - - +
294B GLN* 3.5 0.9 + - - +
304B TRP* 3.5 3.5 - - - -
305B LYS* 2.7 36.3 + - + +
307B VAL* 4.3 25.0 - - + +
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Residues in contact with PHE 293 (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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262B TRP* 3.7 30.7 - - + -
263B LYS* 4.6 10.1 - - + -
267B GLN* 2.7 49.7 + - - +
292B GLU* 1.3 84.8 - - - +
294B GLN* 1.3 64.5 + - - +
295B LYS* 3.4 22.4 - - - -
296B ALA* 3.4 33.7 - - + -
302B ALA* 4.2 10.3 - - + -
303B VAL 4.2 2.0 - - - -
304B TRP* 3.4 38.5 - + + -
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Residues in contact with GLN 294 (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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292B GLU 4.6 2.7 - - - +
293B PHE* 1.3 85.7 - - - +
295B LYS* 1.3 92.6 + - + +
303B VAL* 3.0 29.3 + - + +
305B LYS* 3.3 41.9 - - + +
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Residues in contact with LYS 295 (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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293B PHE* 3.4 11.5 - - - -
294B GLN* 1.3 106.8 + - + +
296B ALA* 1.3 60.2 + - - +
297B ASP* 5.1 9.0 - - + +
301B GLY 3.9 0.9 - - - +
302B ALA* 3.8 0.5 - - - -
303B VAL* 3.1 40.5 + - + +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 4.0 33.5 - - + +
262B TRP* 4.1 19.5 - - + -
263B LYS* 5.9 1.8 - - + -
293B PHE* 3.4 20.2 - - + -
295B LYS* 1.3 74.7 - - - +
297B ASP* 1.3 62.2 + - - +
301B GLY 3.3 5.4 - - - +
302B ALA* 4.7 0.2 - - - -
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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