Contacts of the strand formed by residues 283 - 296 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A SER* 4.2 5.2 - - - -
247A LEU* 3.7 36.1 - - + -
281A GLY 3.7 1.7 + - - +
282A SER* 1.3 77.6 - - - +
284A PRO* 1.3 71.2 - - + +
285A MET 3.4 2.4 + - - -
330A GLN* 3.3 11.5 + - - +
331A VAL* 2.9 36.2 + - + +
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Residues in contact with PRO 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A SER* 2.6 34.7 + - - +
202A GLU* 4.0 32.8 - - + +
283A ALA* 1.3 84.9 - - + +
285A MET* 1.3 63.8 + - - +
286A HIS* 3.4 5.6 + - - +
328A PRO* 4.4 14.8 - - + -
329A VAL 3.7 6.3 - - - +
330A GLN* 3.8 14.8 - - - +
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Residues in contact with MET 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A PRO* 3.7 23.3 - - + -
196A ILE 3.5 11.0 - - - +
247A LEU* 3.9 12.3 - - + -
279A CYS* 5.4 0.2 - - - -
283A ALA 3.4 3.6 + - - -
284A PRO* 1.3 71.0 - - - +
286A HIS* 1.3 61.6 + - - +
287A GLY* 3.7 17.5 - - - +
288A PHE* 3.4 36.6 - - + -
325A LEU* 4.3 10.8 - - + +
328A PRO* 3.2 5.5 - - - +
329A VAL* 2.8 42.2 + - + +
331A VAL* 3.9 23.3 - - + -
337A VAL* 4.2 7.0 - - + -
361A VAL* 4.1 23.6 - - + -
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Residues in contact with HIS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE* 2.9 14.9 + - + +
197A SER* 3.5 9.0 - - - -
198A ASP* 2.8 42.8 + - - +
201A LEU* 4.1 7.4 - - + -
202A GLU* 3.0 35.3 + - + +
205A LEU* 4.5 2.9 - - + +
231A MET* 3.3 33.4 - - + +
284A PRO* 3.6 14.6 + - - +
285A MET* 1.3 72.8 - - - +
287A GLY* 1.3 58.5 + - - +
324A TYR* 3.4 19.0 - - + -
325A LEU* 2.8 26.5 + - - -
328A PRO* 4.0 17.1 - - + +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A PRO* 3.4 5.4 - - - +
196A ILE* 2.8 33.5 + - - +
285A MET* 3.6 9.5 - - - +
286A HIS* 1.3 80.7 - - - +
288A PHE* 1.3 60.9 + - - -
323A LEU 3.2 11.9 - - - -
325A LEU* 3.7 18.4 - - - +
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ILE* 3.8 28.5 - - + -
194A ALA 3.3 9.0 - - - +
195A PRO* 3.8 18.8 - - + -
196A ILE* 3.7 7.4 - - - +
275A PHE* 3.6 22.0 - + - -
285A MET* 3.4 24.0 - - + -
287A GLY* 1.3 75.7 - - - -
289A ALA* 1.3 59.2 + - - +
322A LEU* 3.6 3.1 - - - +
323A LEU* 2.8 48.5 + - + +
325A LEU* 4.0 11.7 - - + -
337A VAL* 3.6 26.5 - - + -
357A LEU* 3.8 31.0 - - + -
359A TYR* 4.0 15.9 - + + -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A PHE 3.8 0.2 - - - +
193A ILE* 3.4 4.3 - - - +
194A ALA 3.0 29.6 + - - -
196A ILE* 3.8 9.3 - - + +
241A LEU* 3.6 30.5 - - + -
288A PHE* 1.3 74.5 - - - +
290A ILE* 1.3 62.7 + - - +
291A TRP* 4.0 18.6 - - + -
320A GLN* 4.5 4.0 - - + -
321A ALA 3.4 4.7 - - - -
322A LEU* 3.8 10.1 - - + -
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLY* 4.0 23.2 - - - +
191A LEU* 4.5 4.7 - - + -
192A PHE 3.0 14.1 - - - +
193A ILE* 3.9 8.3 - - + -
236A ILE* 6.2 0.2 - - + -
253A PHE* 3.8 9.0 - - + -
288A PHE 4.3 0.2 - - - -
289A ALA* 1.3 78.1 - - - +
291A TRP* 1.3 66.4 + - - +
320A GLN* 3.8 3.1 - - - +
321A ALA* 2.9 51.1 + - + +
323A LEU* 4.3 11.4 - - + -
341A ILE* 3.8 25.4 - - + -
343A LEU* 4.2 28.5 - - + -
353A LEU* 5.1 1.3 - - + -
355A VAL* 4.9 8.5 - - + -
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Residues in contact with TRP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLY* 5.8 2.5 - - - -
191A LEU* 3.4 8.6 - - - +
192A PHE* 2.9 52.9 + + + +
194A ALA* 3.9 16.4 - - + -
246A VAL* 4.4 6.1 - - + -
250A PRO* 3.6 40.6 - - + -
289A ALA* 4.0 22.9 - - + -
290A ILE* 1.3 82.5 - - - +
292A PHE* 1.3 72.8 + - - +
308A SER* 4.9 0.9 + - - -
309A THR* 3.4 20.6 - - - +
310A SER* 3.3 37.5 - - - -
311A PRO* 3.6 30.5 - - + -
312A PHE* 5.0 0.9 - + - -
319A LYS 4.9 1.1 - - - +
320A GLN* 4.0 11.2 - - + +
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Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A MET* 3.8 28.9 - - + -
158A GLY 3.6 18.4 - - - -
160A GLY* 4.4 4.5 - - - -
161A LEU* 3.5 39.9 - - + -
190A GLU 3.1 15.7 - - - +
191A LEU* 4.0 7.4 - - + -
192A PHE* 4.3 1.3 - - - -
291A TRP* 1.3 86.0 - - - +
293A GLN* 1.3 71.4 + - - +
294A VAL* 4.3 2.9 - - + -
307A LEU* 5.2 3.4 - - + -
308A SER* 4.4 0.2 + - - -
309A THR* 2.9 52.7 + - + -
318A TRP* 3.7 41.7 - + + -
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ALA* 3.2 3.8 - - - +
190A GLU* 2.8 58.9 + - + +
192A PHE* 3.7 27.8 - - + -
291A TRP* 6.2 0.2 - - + -
292A PHE* 1.3 78.0 - - - +
294A VAL* 1.3 66.8 + - - +
295A THR* 4.4 5.0 + - - +
306A VAL* 3.7 27.1 - - + +
307A LEU 3.1 14.6 - - - +
308A SER* 4.0 12.4 + - - +
313A HIS* 6.0 1.0 - - - -
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TRP* 4.8 1.3 - - + -
157A MET* 3.9 42.2 - - + -
186A PRO* 3.7 23.8 - - + -
188A SER 3.2 8.5 - - - +
189A ALA* 3.9 17.3 - - + -
292A PHE* 4.3 6.1 - - + -
293A GLN* 1.3 79.5 - - - +
295A THR* 1.3 64.8 + - - +
296A PHE* 4.3 4.6 - - + -
305A LEU 3.9 0.3 - - - +
306A VAL* 3.4 4.0 - - - +
307A LEU* 2.8 54.1 + - + +
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A PRO* 3.7 4.0 - - - -
187A ALA* 2.7 36.9 + - + +
188A SER* 3.0 25.2 + - - -
190A GLU* 4.3 13.0 + - - -
293A GLN* 4.4 4.0 + - - -
294A VAL* 1.3 77.8 + - - +
296A PHE* 1.3 68.7 + - - +
297A PRO* 4.8 0.9 - - + -
304A PRO* 3.9 17.7 - - + -
305A LEU 3.5 5.4 - - - +
306A VAL* 4.2 15.1 - - + +
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Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 4.3 16.2 - - + -
70A TYR* 3.7 55.9 - + - -
73A GLY* 4.1 25.4 - - - +
74A ILE* 5.6 0.4 - - + -
185A LEU* 4.1 17.7 - - + -
186A PRO* 3.7 31.2 - - + -
294A VAL* 4.3 11.7 - - + -
295A THR* 1.3 77.2 - - - +
297A PRO* 1.3 76.5 - - + +
304A PRO* 3.2 6.2 - - - +
305A LEU* 2.8 51.9 + - + +
307A LEU* 4.4 3.4 - - + -
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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