Contacts of the strand formed by residues 286 - 296 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278D ILE* 3.5 35.4 - - + -
279D GLY 3.7 4.5 - - - +
280D ALA* 4.6 1.8 - - + -
284D GLY 5.2 0.2 - - - +
285D LYS* 1.3 76.0 - - - +
287D LEU* 1.3 61.5 + - - +
288D GLY 4.8 2.5 - - - +
319D TYR* 3.8 29.4 - - + -
320D PHE 4.0 11.2 - - - +
321D VAL* 3.8 21.3 - - + -
322D PRO* 3.2 20.8 - - - +
353D MET* 4.9 1.6 - - - -
357D ILE* 3.9 17.5 - - + -
360D LEU* 3.8 19.3 - - + -
375D ASN* 2.9 27.6 + - + +
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Residues in contact with LEU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ALA* 3.7 32.5 - - + +
157D GLY 4.6 3.1 - - - +
158D ALA* 3.6 24.5 - - + -
159D ALA 4.4 0.7 - - - +
279D GLY* 2.8 12.2 + - - +
280D ALA 3.5 9.4 - - - +
281D ASP* 3.4 42.8 - - + +
285D LYS 3.5 0.4 + - - +
286D LEU* 1.3 75.9 - - - +
288D GLY* 1.3 57.9 + - - +
322D PRO* 3.8 9.1 - - + +
323D ALA* 3.6 14.7 + - - +
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Residues in contact with GLY 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D VAL* 4.3 4.3 - - - -
154D ALA* 4.7 4.5 - - - -
155D LEU* 3.7 10.4 - - - +
278D ILE* 3.5 5.5 - - - +
279D GLY* 3.1 26.3 + - - +
286D LEU* 3.7 1.4 - - - +
287D LEU* 1.3 80.1 - - - +
289D ALA* 1.3 62.6 + - - +
321D VAL* 3.7 5.7 - - - +
323D ALA* 2.7 19.5 - - - -
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Residues in contact with ALA 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D VAL* 3.5 4.7 - - - +
277D ARG 3.5 4.9 - - - +
278D ILE* 4.3 11.2 - - + -
288D GLY* 1.3 75.3 - - - +
290D ASP* 1.3 60.7 + - - +
291D PHE* 3.8 24.5 - - + -
321D VAL* 3.9 14.1 - - + -
323D ALA 2.7 9.1 + - - -
324D LEU* 3.1 9.6 - - + +
325D ARG 2.8 26.0 + - - +
353D MET* 4.0 9.2 - - + -
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Residues in contact with ASP 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D VAL* 4.5 7.4 - - + -
155D LEU* 4.2 17.0 - - + +
275D ARG 3.8 0.3 - - - +
276D TYR* 3.2 5.7 - - - +
277D ARG* 2.8 61.4 + - + +
289D ALA* 1.3 73.2 - - - +
291D PHE* 1.3 66.4 + - - +
292D VAL* 5.5 4.9 - - - +
325D ARG* 3.1 58.9 + - - +
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Residues in contact with PHE 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ILE* 4.1 11.4 - - + -
275D ARG 3.3 4.0 - - - -
276D TYR* 3.6 24.0 - - + -
277D ARG 6.1 0.2 - - - -
278D ILE* 5.7 0.7 - - + -
289D ALA* 3.8 18.6 - - + -
290D ASP* 1.3 79.5 + - - +
292D VAL* 1.3 65.8 + - - +
293D HIS* 4.3 11.0 - - + +
315D ALA* 3.5 28.3 - - + -
324D LEU* 4.6 3.6 - - + -
325D ARG* 2.7 17.1 + - - +
326D ILE* 3.3 17.4 - - + -
327D GLU* 2.9 24.6 + - - +
349D GLY 5.8 0.2 - - - -
352D GLY* 3.6 23.8 - - - -
353D MET* 3.5 36.1 - - + -
356D ALA* 4.2 6.7 - - + -
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Residues in contact with VAL 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D ARG 3.5 1.4 - - - +
274D ILE* 3.3 7.1 - - - -
275D ARG* 2.9 68.0 + - + +
290D ASP* 5.5 5.6 - - - +
291D PHE* 1.3 76.3 - - - +
293D HIS* 1.3 64.2 + - - +
294D LEU* 3.9 23.3 - - + -
325D ARG* 6.0 1.3 - - - +
327D GLU* 3.4 30.5 - - - +
329D HIS* 4.2 7.0 - - + +
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Residues in contact with HIS 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D PHE* 4.0 22.2 - + + -
273D ARG 3.7 2.2 - - - -
274D ILE* 3.5 34.1 - - + +
291D PHE* 4.3 11.8 - - + +
292D VAL* 1.3 75.8 - - - +
294D LEU* 1.3 59.3 + - - +
295D ALA* 4.1 0.4 - - + -
308D CYS 5.3 0.2 + - - -
311D ALA* 4.0 33.0 - - + +
312D MET* 4.3 5.3 + - - +
315D ALA* 4.2 10.9 - - + +
326D ILE* 3.5 25.6 - - + +
327D GLU 2.8 13.7 + - - +
328D SER* 4.0 11.8 + - - +
329D HIS* 2.7 36.4 + - - -
349D GLY* 4.2 7.7 + - - -
352D GLY* 5.5 0.4 - - - -
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Residues in contact with LEU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LEU* 4.1 12.9 - - + +
133D LEU* 4.0 27.4 - - + -
271D ASP 3.9 0.2 - - - +
272D PHE* 3.1 8.7 - - - +
273D ARG* 2.8 87.2 + - + +
275D ARG* 4.4 10.1 - - - +
292D VAL* 3.9 13.0 - - + -
293D HIS* 1.3 73.9 - - - +
295D ALA* 1.3 59.7 + - - +
329D HIS* 3.4 37.5 - - + -
331D LEU* 4.2 4.9 - - + -
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LEU* 4.0 4.4 - - - +
270D HIS* 4.7 3.6 - - + -
271D ASP 3.5 4.5 - - - -
272D PHE* 3.7 31.9 - - + -
293D HIS* 5.4 0.7 - - + -
294D LEU* 1.3 74.6 - - - +
296D ARG* 1.3 62.0 + - - +
297D CYS* 3.5 4.5 + - - -
308D CYS* 3.8 19.5 - - - -
328D SER* 5.9 0.2 - - - +
329D HIS 3.0 13.3 + - - +
331D LEU* 3.0 29.2 + - - +
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Residues in contact with ARG 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D LEU 3.1 29.1 + - - -
128D THR* 4.5 7.0 - - - +
129D LEU* 3.7 20.5 - - + +
270D HIS* 3.0 10.4 - - - -
271D ASP* 3.1 45.3 + - - +
295D ALA* 1.3 69.8 - - - +
297D CYS* 1.3 54.2 + - - +
298D GLY 4.0 2.2 - - - +
331D LEU* 4.1 3.1 - - - -
333D THR* 3.2 23.1 + - + +
335D THR* 3.0 30.2 + - - +
336D GLN 5.5 0.4 - - - -
338D ASN* 2.7 38.3 + - - +
682D TRP* 4.1 36.5 - - - -
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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