Contacts of the strand formed by residues 286 - 298 (chain F) in PDB entry 2W3S
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 LEU 286 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278F ILE* 3.5 36.6 - - + -
279F GLY 3.5 4.0 - - - +
280F ALA* 4.2 1.6 - - + -
284F GLY 3.8 0.6 + - - -
285F LYS* 1.3 74.8 - - - +
287F LEU* 1.3 61.1 + - - +
288F GLY 4.7 2.5 - - - +
319F TYR* 3.8 25.8 - - + -
320F PHE 3.9 10.0 - - - +
321F VAL* 3.8 22.0 - - + -
322F PRO* 3.0 21.4 - - - +
353F MET* 5.0 1.1 - - + -
357F ILE* 3.7 26.7 - - + -
360F LEU* 3.8 13.9 - - + -
371F LEU* 5.8 0.4 - - + -
375F ASN* 2.7 25.6 + - - +
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Residues in contact with LEU 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F ALA* 3.7 29.6 - - + +
155F LEU* 6.2 0.2 - - - -
157F GLY 4.7 3.6 - - - +
158F ALA* 4.1 20.4 - - + -
159F ALA 4.6 1.8 - - - +
279F GLY* 2.8 11.5 + - - +
280F ALA 3.7 23.3 - - - +
281F ASP* 3.6 24.7 - - - +
285F LYS* 3.1 6.3 + - + +
286F LEU* 1.3 75.0 - - - +
288F GLY* 1.3 58.5 + - - +
322F PRO* 3.3 29.5 - - + +
323F ALA* 3.4 3.6 + - - +
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Residues in contact with GLY 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F VAL* 4.3 8.3 - - - -
154F ALA* 4.7 4.5 - - - -
155F LEU* 3.5 7.7 - - - +
278F ILE* 3.5 2.9 - - - +
279F GLY* 3.0 27.6 + - - +
286F LEU* 3.7 2.0 - - - +
287F LEU* 1.3 82.9 - - - +
289F ALA* 1.3 61.4 + - - +
321F VAL* 3.7 5.0 - - - +
323F ALA* 2.9 17.9 - - - -
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Residues in contact with ALA 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F VAL* 3.3 6.1 - - - +
277F ARG 3.3 6.5 - - - +
278F ILE* 4.2 12.1 - - + +
288F GLY* 1.3 73.9 - - - +
290F ASP* 1.3 60.2 + - - +
291F PHE* 3.7 27.4 - - + -
321F VAL* 3.5 8.6 - - + +
323F ALA 2.8 9.5 + - - -
324F LEU* 3.1 8.2 - - + +
325F ARG 2.9 25.0 + - - +
353F MET* 3.9 15.5 - - + -
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Residues in contact with ASP 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F VAL* 3.8 13.6 - - + +
155F LEU* 4.0 2.7 - - + -
275F ARG 3.8 0.5 - - - +
276F TYR* 3.2 6.1 - - - +
277F ARG* 2.7 72.7 + - + +
289F ALA* 1.3 74.8 - - - +
291F PHE* 1.3 65.2 + - - +
292F VAL* 5.4 4.9 - - - +
325F ARG* 2.7 53.3 + - - +
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Residues in contact with PHE 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F ILE* 4.2 13.7 - - + -
275F ARG 3.4 1.3 - - - -
276F TYR* 3.8 25.4 - - + -
278F ILE* 5.9 0.4 - - + -
289F ALA* 3.7 16.2 - - + -
290F ASP* 1.3 77.6 - - - +
292F VAL* 1.3 65.2 + - - +
293F HIS* 4.2 16.8 - - + +
315F ALA* 3.4 30.3 - - + -
324F LEU* 4.5 7.0 - - + -
325F ARG* 2.8 18.3 + - - +
326F ILE* 3.4 8.4 - - + -
327F GLU* 3.0 24.5 + - - +
349F GLY 5.6 0.4 - - - -
352F GLY* 3.6 23.6 - - - -
353F MET* 3.5 40.6 - - + -
356F ALA* 4.2 5.6 - - + -
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Residues in contact with VAL 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273F ARG 3.3 1.4 - - - +
274F ILE* 3.2 8.0 - - - +
275F ARG* 2.7 83.4 + - + +
290F ASP* 5.4 6.1 - - - +
291F PHE* 1.3 78.1 - - - +
293F HIS* 1.3 62.8 + - - +
294F LEU* 3.9 21.3 - - + -
325F ARG* 5.9 2.2 - - - +
327F GLU* 3.5 30.5 - - + +
329F HIS* 4.2 5.4 - - + +
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Residues in contact with HIS 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F PHE* 4.0 15.0 - + + -
273F ARG 3.5 2.7 - - - -
274F ILE* 3.7 34.7 - - + +
291F PHE* 4.4 13.8 - - + +
292F VAL* 1.3 74.8 - - - +
294F LEU* 1.3 61.0 + - - +
295F ALA* 4.0 1.1 - - + +
311F ALA* 3.6 40.7 - - + +
312F MET* 4.3 5.6 - - - +
315F ALA* 4.3 6.6 - - + +
326F ILE* 3.6 25.2 - - + +
327F GLU 2.8 14.9 + - - +
328F SER* 4.1 11.1 + - - +
329F HIS* 2.9 32.3 + - - +
349F GLY* 4.3 9.3 + - - -
352F GLY* 5.6 0.2 - - - -
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Residues in contact with LEU 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F LEU* 4.0 10.1 - - + +
133F LEU* 3.8 29.6 - - + -
271F ASP 3.8 0.3 - - - +
272F PHE* 3.3 5.8 - - - -
273F ARG* 2.7 78.8 + - + +
275F ARG* 4.7 11.7 - - - +
292F VAL* 3.9 11.9 - - + -
293F HIS* 1.3 73.0 - - - +
295F ALA* 1.3 62.9 + - - +
329F HIS* 3.1 44.6 - - + +
331F LEU* 3.9 13.5 - - + -
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Residues in contact with ALA 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F LEU* 3.9 2.7 - - - -
270F HIS* 4.5 7.2 - - + -
271F ASP 3.6 4.7 - - - +
272F PHE* 3.6 33.0 - - + -
293F HIS* 4.0 0.8 - - + -
294F LEU* 1.3 74.7 - - - +
296F ARG* 1.3 58.6 + - - +
297F CYS* 3.8 2.9 - - - -
308F CYS* 3.7 20.6 - - - -
328F SER* 5.9 0.7 - - - +
329F HIS 2.9 12.6 + - - +
331F LEU* 3.0 33.6 + - - +
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Residues in contact with ARG 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F LEU 2.8 29.7 + - - -
128F THR* 4.6 6.5 - - - +
129F LEU* 3.6 19.4 - - + +
270F HIS* 3.3 9.4 - - - -
271F ASP* 3.0 49.4 + - - +
295F ALA* 1.3 69.1 - - - +
297F CYS* 1.3 54.0 + - - +
298F GLY 4.5 0.9 - - - +
331F LEU 4.1 2.5 - - - -
333F THR* 3.3 22.9 + - + +
335F THR* 3.3 26.3 + - - +
336F GLN 5.7 0.7 - - - -
338F ASN* 2.4 38.6 + - - +
682F TRP* 4.0 35.5 - - - +
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Residues in contact with CYS 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F PHE* 3.6 17.9 - - + -
270F HIS* 3.7 14.1 - - - -
295F ALA* 4.1 5.6 - - - -
296F ARG* 1.3 74.3 - - - +
298F GLY* 1.3 59.8 + - - +
300F SER 3.7 4.0 - - - +
304F SER* 3.3 33.4 + - - +
308F CYS* 4.8 1.3 - - - -
330F ARG* 3.8 36.8 - - - -
331F LEU 3.0 16.4 + - - +
337F SER* 3.6 1.7 - - - -
338F ASN* 2.9 24.8 + - - -
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Residues in contact with GLY 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F PHE* 3.3 16.5 - - - -
296F ARG* 3.5 3.2 - - - +
297F CYS* 1.3 78.6 - - - +
299F TRP* 1.3 63.7 + - - -
300F SER 3.3 2.0 - - - -
331F LEU 4.1 0.4 + - - -
332F ARG* 3.4 0.2 - - - +
333F THR* 3.0 33.1 + - - -
335F THR* 3.3 7.4 - - - -
336F GLN 3.3 20.1 + - - -
338F ASN* 4.6 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