Contacts of the helix formed by residues 280 - 292 (chain B) in PDB entry 1W98
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 PRO 280 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B GLU* 3.5 24.9 - - + +
114B ARG* 6.3 0.4 - - - +
278B GLU 3.7 8.1 - - - +
279B PHE* 1.3 88.6 - - + +
281B TYR* 1.3 57.8 + - + +
283B ILE* 2.8 51.0 + - + +
284B LEU 3.1 7.8 + - - -
304B TYR* 6.0 0.2 - - - +
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Residues in contact with TYR 281 (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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109B GLU* 3.5 6.2 + - + +
114B ARG* 3.3 53.0 + - + +
155B GLN* 3.2 25.7 + - - -
156B ASP* 2.8 27.0 + - + -
159B ASP* 4.7 2.1 + - - +
229B LEU 3.1 27.4 - - - +
230B THR* 3.8 13.2 - - - -
231B ILE* 3.6 32.0 - - + +
234B TRP* 3.8 10.2 - - + +
277B LEU* 4.1 17.5 - - + +
279B PHE 4.2 6.1 - - - -
280B PRO* 1.3 72.7 - - - +
282B GLY* 1.3 57.0 + - - +
284B LEU* 3.3 8.3 + - + +
285B ALA* 3.1 27.4 + - - +
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Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLU* 3.1 16.7 + - - -
234B TRP* 3.5 21.2 - - - -
238B TYR* 2.7 29.1 + - - -
281B TYR* 1.3 75.3 - - - +
283B ILE* 1.3 56.8 - - - +
285B ALA 4.0 0.4 - - - -
286B ALA* 3.0 19.8 + - - +
304B TYR* 3.8 9.9 - - - -
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Residues in contact with ILE 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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279B PHE* 4.1 8.3 - - + -
280B PRO* 2.8 38.5 + - + +
282B GLY* 1.3 77.3 - - - +
284B LEU* 1.3 53.3 + - - +
285B ALA 3.2 0.2 - - - -
286B ALA* 3.6 0.9 - - - +
287B SER* 2.6 41.8 + - - -
304B TYR* 4.8 13.4 + - + -
308B ASP* 3.2 29.6 - - + +
309B ILE* 3.6 20.2 - - + -
312B CYS* 3.4 28.9 - - + -
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 3.5 32.3 - - + -
267B LEU* 3.4 18.9 - - + +
270B CYS* 4.8 8.7 - - + -
271B VAL* 5.4 0.9 - - + +
276B CYS* 3.9 30.1 - - + +
279B PHE* 4.2 16.4 - - + +
280B PRO 3.1 5.6 + - - +
281B TYR* 3.4 11.4 - - + +
283B ILE* 1.3 76.7 - - - +
285B ALA* 1.3 57.8 - - - +
287B SER* 3.8 1.6 - - - -
288B ALA* 3.0 24.9 + - - +
312B CYS* 3.8 16.4 - - - -
315B TRP* 3.6 32.1 - - + -
316B MET* 4.0 4.6 - - + +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 3.5 24.5 - - + +
234B TRP* 3.7 17.0 - - + -
235B LEU* 4.0 10.5 - - - +
238B TYR* 3.7 10.9 - - + -
267B LEU* 4.0 16.3 - - + +
281B TYR 3.1 10.6 + - - +
282B GLY 4.0 0.4 - - - +
284B LEU* 1.3 82.6 - - - +
286B ALA* 1.3 60.0 + - - +
288B ALA* 3.6 1.9 + - - +
289B LEU* 3.1 23.6 + - - +
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Residues in contact with ALA 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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238B TYR* 3.5 9.2 - - + -
282B GLY 3.0 20.3 + - - +
283B ILE 3.2 0.6 + - - +
285B ALA* 1.3 76.5 - - - +
287B SER* 1.3 59.2 + - - +
289B LEU* 3.4 3.0 + - - +
290B TYR* 2.9 24.1 + - - +
298B MET* 3.3 18.7 - - + +
302B SER* 3.7 22.7 - - - +
304B TYR* 4.1 2.2 - - + -
309B ILE* 3.6 22.7 - - + -
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 2.6 24.9 + - - +
284B LEU 3.8 0.4 - - - -
286B ALA* 1.3 73.6 - - - +
288B ALA* 1.3 64.6 + - - +
290B TYR* 3.4 7.9 - - - +
291B HIS* 2.9 29.5 + - - -
309B ILE* 3.8 11.4 + - - +
312B CYS* 3.1 34.2 - - - +
313B VAL* 4.1 14.1 - - - -
316B MET* 3.6 12.6 - - - -
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Residues in contact with ALA 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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263B ILE* 3.7 13.0 - - + +
266B LEU* 4.0 8.3 - - + -
267B LEU* 3.6 26.5 - - + -
284B LEU 3.0 17.2 + - - +
285B ALA 3.9 2.2 - - - +
287B SER* 1.3 75.3 - - - +
289B LEU* 1.3 65.0 + - - +
291B HIS* 3.2 12.5 + - - +
292B PHE* 3.3 18.7 + - - -
316B MET* 3.3 21.2 - - + -
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Residues in contact with LEU 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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235B LEU* 4.6 7.0 - - + -
238B TYR* 4.6 15.5 - - + -
239B MET* 4.2 15.5 - - - -
242B ALA* 5.7 2.0 - - + -
263B ILE* 3.7 31.6 - - + +
285B ALA 3.1 16.4 + - - +
286B ALA 3.7 1.1 - - - +
287B SER 3.3 0.2 - - - -
288B ALA* 1.3 78.6 - - - +
290B TYR* 1.3 57.0 - - - +
292B PHE* 2.9 14.2 + - - +
293B SER* 2.8 27.9 + - - +
297B LEU* 4.6 10.3 - - + -
298B MET* 3.6 28.5 - - + +
301B VAL* 3.5 31.0 - - + -
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Residues in contact with TYR 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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286B ALA 2.9 18.4 + - - +
287B SER* 3.4 8.3 - - - +
289B LEU* 1.3 76.4 - - - +
291B HIS* 1.3 68.0 + + - +
293B SER* 2.9 32.2 + - - +
294B SER* 3.4 9.4 - - - -
295B SER* 3.4 39.3 - - - -
298B MET* 4.1 9.9 - - + -
306B TRP* 3.7 29.9 + + - -
309B ILE* 4.8 1.3 - - + -
313B VAL* 3.6 37.7 - - + -
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Residues in contact with HIS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 4.2 11.7 - - + -
287B SER 2.9 22.1 + - - -
288B ALA 3.2 9.6 + - - +
290B TYR* 1.3 85.9 - + - +
292B PHE* 1.3 59.8 + - + +
293B SER 3.3 0.8 + - - -
313B VAL* 3.4 45.5 + - + +
316B MET* 3.3 24.1 - - + +
317B VAL* 4.0 11.2 + - - +
320B ALA* 3.5 25.2 - - + +
321B MET* 6.1 2.7 - - + -
324B ARG* 3.2 18.9 + - - -
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Residues in contact with PHE 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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259B ILE* 5.7 4.0 - - + -
262B GLN* 3.7 35.9 - - + -
263B ILE* 4.1 26.5 - - + -
266B LEU* 3.6 26.7 - - + -
288B ALA 3.3 14.7 + - - +
289B LEU 2.9 8.9 + - - +
291B HIS* 1.3 80.0 - - + +
293B SER* 1.3 61.8 + - - +
320B ALA* 6.2 0.4 - - - -
323B ILE* 4.1 15.0 - - + -
324B ARG* 3.5 39.2 + - - +
328B SER* 3.8 20.9 - - - -
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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