Contacts of the strand formed by residues 283 - 296 (chain B) in PDB entry 4Y2H
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B SER* 4.8 1.3 - - - +
247B LEU* 3.6 36.3 - - + -
281B GLY 3.4 6.3 + - - +
282B SER* 1.3 77.8 - - - +
284B PRO* 1.3 72.5 - - + +
285B MET 3.4 0.5 + - - -
330B GLN* 3.2 11.8 + - - +
331B VAL* 2.9 32.8 + - + +
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Residues in contact with PRO 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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197B SER* 2.4 40.0 + - - +
202B GLU* 3.5 30.7 - - + +
283B ALA* 1.3 83.4 - - + +
285B MET* 1.3 61.8 + - - +
286B HIS* 3.8 13.6 + - + +
328B PRO* 5.1 7.9 - - + -
329B VAL 3.8 4.3 - - - +
330B GLN* 3.7 17.2 - - - +
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Residues in contact with MET 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PRO* 3.8 19.3 - - + -
196B ILE 3.6 9.9 - - - +
247B LEU* 3.9 13.0 - - + -
279B CYS* 5.5 0.2 - - - -
283B ALA 3.4 2.0 + - - -
284B PRO* 1.3 70.4 - - - +
286B HIS* 1.3 63.2 + - - +
287B GLY 3.6 19.5 - - - +
288B PHE* 3.6 34.1 - - + -
325B LEU* 4.0 14.1 - - + +
328B PRO* 3.4 4.7 - - - +
329B VAL* 2.6 42.4 + - + +
331B VAL* 4.0 23.8 - - + -
337B VAL* 4.4 4.9 - - + -
361B VAL* 3.9 24.9 - - + -
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Residues in contact with HIS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ILE* 3.0 10.1 + - + +
197B SER* 3.6 14.3 - - - -
198B ASP 2.9 44.0 + - - +
201B LEU* 3.7 30.3 - - + -
202B GLU* 4.0 27.0 + - + +
205B LEU* 4.7 2.5 - - + +
231B MET* 3.4 14.6 - - + +
284B PRO* 3.9 9.7 + - + +
285B MET* 1.3 73.7 - - - +
287B GLY* 1.3 58.3 + - - +
324B TYR* 3.4 14.5 - - + -
325B LEU* 2.9 27.0 + - - +
328B PRO* 4.0 27.1 - - + +
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PRO* 3.4 6.2 - - - +
196B ILE* 2.9 29.0 + - - +
285B MET* 3.6 9.6 - - - +
286B HIS* 1.3 80.3 - - - +
288B PHE* 1.3 64.0 + - - -
323B LEU 3.2 11.9 - - - -
324B TYR* 5.1 0.2 - - - -
325B LEU* 3.6 17.9 - - - -
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ILE* 3.7 29.4 - - + -
194B ALA 3.3 14.4 - - - +
195B PRO* 3.9 9.4 - - + -
196B ILE* 3.7 7.2 - - - +
275B PHE* 3.8 13.9 - + - -
285B MET* 3.6 17.7 - - + -
287B GLY* 1.3 77.4 - - - -
289B ALA* 1.3 58.2 + - - +
322B LEU* 3.5 3.1 - - - +
323B LEU* 2.8 45.2 + - + +
325B LEU* 3.8 15.7 - - + -
337B VAL* 3.6 27.6 - - + -
357B LEU* 3.6 33.7 - - + -
359B TYR* 3.7 25.1 - + + -
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE 3.9 0.2 - - - +
193B ILE* 3.3 6.6 - - - +
194B ALA 3.0 28.5 + - - -
196B ILE* 3.6 23.0 - - + +
241B LEU* 4.0 5.2 - - + -
288B PHE* 1.3 74.6 - - - +
290B ILE* 1.3 61.7 + - - +
291B TRP* 3.9 17.4 - - + -
311B PRO* 5.7 0.7 - - + -
320B GLN* 4.3 6.5 - - + -
321B ALA 3.4 4.5 - - - +
322B LEU* 3.7 20.6 - - + -
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLY* 3.9 23.4 - - - +
191B LEU* 5.0 2.2 - - + -
192B PHE 3.2 12.8 - - - +
193B ILE* 3.9 11.7 - - + -
236B ILE* 6.0 0.2 - - + -
253B PHE* 4.1 6.7 - - + -
289B ALA* 1.3 78.3 - - - +
291B TRP* 1.3 67.5 + - - +
320B GLN* 3.8 2.3 - - - +
321B ALA* 2.8 51.6 + - + +
323B LEU* 4.2 13.0 - - + -
341B ILE* 3.6 26.0 - - + -
343B LEU* 4.3 26.5 - - + -
353B LEU* 4.9 1.8 - - + -
355B VAL* 4.7 10.5 - - + -
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Residues in contact with TRP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLY* 5.8 2.0 - - - -
191B LEU* 3.5 9.2 - - - +
192B PHE* 2.9 53.0 + + + +
193B ILE 4.8 0.4 - - - -
194B ALA* 3.9 17.5 - - + -
246B VAL* 4.7 3.8 - - + -
250B PRO* 3.5 41.1 - - + -
289B ALA* 3.9 23.1 - - + -
290B ILE* 1.3 82.1 - - - +
292B PHE* 1.3 75.1 + - - +
308B SER* 5.2 0.4 - - - -
309B THR* 3.5 21.8 - - - +
310B SER* 3.4 32.0 - - - -
311B PRO* 3.6 34.5 - - + -
312B PHE* 5.0 0.7 - + - -
319B LYS 4.8 1.8 - - - +
320B GLN* 4.0 10.3 - - + +
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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
----------------------------------------------------------
157B MET* 3.8 30.3 - - + -
158B GLY 3.6 17.9 - - - -
160B GLY* 4.4 3.6 - - - -
161B LEU* 3.5 44.2 - - + -
190B GLU 3.0 14.4 - - - +
191B LEU* 4.1 3.4 - - + -
192B PHE* 4.5 1.6 - - - -
291B TRP* 1.3 90.1 - - - +
293B GLN* 1.3 71.3 + - - +
294B VAL* 4.3 2.0 - - + -
307B LEU* 5.3 3.1 - - + -
308B SER* 4.6 0.2 + - - -
309B THR* 2.7 53.7 + - + -
318B TRP* 3.6 43.3 - + + -
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Residues in contact with GLN 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA* 3.2 5.4 - - - +
190B GLU* 2.7 67.0 + - + +
192B PHE* 3.8 26.4 - - + -
291B TRP* 6.1 0.2 - - + -
292B PHE* 1.3 78.3 - - - +
294B VAL* 1.3 65.4 + - - +
295B THR* 4.9 3.0 + - - +
306B VAL* 3.6 29.0 - - + +
307B LEU 3.1 14.6 - - - +
308B SER* 3.9 12.4 + - - +
313B HIS* 5.5 3.5 - - - -
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TRP* 4.8 1.6 - - + -
157B MET* 3.9 37.2 - - + -
186B PRO* 3.8 23.8 - - + -
188B SER 3.2 9.2 - - - +
189B ALA* 4.0 15.3 - - + +
292B PHE* 4.3 6.1 - - + -
293B GLN* 1.3 78.5 - - - +
295B THR* 1.3 62.3 + - - +
296B PHE* 4.3 6.0 - - + -
305B LEU 3.9 0.5 - - - +
306B VAL* 3.5 3.3 - - - +
307B LEU* 2.8 63.1 + - + +
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Residues in contact with THR 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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186B PRO* 3.4 4.8 - - - +
187B ALA* 2.9 28.1 + - + +
188B SER* 3.1 26.4 + - - -
190B GLU* 4.3 12.5 + - - -
293B GLN* 4.9 1.2 + - - +
294B VAL* 1.3 75.1 + - - +
296B PHE* 1.3 66.5 + - - +
297B PRO* 3.9 1.6 - - + -
304B PRO* 3.7 28.5 - - + -
305B LEU 3.5 6.7 - - - +
306B VAL* 4.3 15.3 - - + +
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Residues in contact with PHE 296 (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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69B ALA 3.9 10.1 - - - -
70B TYR* 3.6 59.2 - + - -
73B GLY* 4.0 24.9 - - - -
74B ILE 5.2 0.4 - - - -
153B VAL* 5.3 0.2 - - + -
185B LEU* 3.9 24.0 - - + -
186B PRO* 3.9 15.5 - - + -
294B VAL* 4.3 17.9 - - + -
295B THR* 1.3 76.5 - - - +
297B PRO* 1.3 75.4 - - + +
304B PRO* 3.3 7.3 - - - +
305B LEU* 2.9 55.7 + - + +
307B LEU* 4.4 7.0 - - + -
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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
------------------------------------------------------------
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