Contacts of the strand formed by residues 287 - 295 (chain B) in PDB entry 4WLU
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 TYR 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ILE* 3.7 23.3 - - + -
149B PRO* 4.0 20.9 + - + +
152B ALA* 3.2 27.9 - - + +
153B GLU* 4.5 9.9 + - - -
156B LYS* 4.8 4.9 + - - -
161B TYR* 4.3 4.1 + - - -
166B ILE* 6.3 0.2 - - + -
277B PHE* 3.5 28.7 - - + -
278B VAL 3.3 6.1 - - - +
279B LYS* 3.6 39.4 - - + +
280B SER* 4.0 0.9 - - - +
285B CYS* 3.3 16.0 - - - +
286B THR* 1.3 93.7 - - + +
288B PHE* 1.3 66.2 + - - +
323B LEU* 5.1 1.2 - - - +
327B ILE* 3.6 28.1 - - + +
331B GLU* 3.8 15.6 + - - -
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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
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197B ILE* 4.2 9.6 - - + -
198B GLY* 3.6 23.1 - - - -
206B ILE* 5.2 2.0 - - + -
276B SER 3.7 1.7 - - - +
277B PHE* 3.6 12.4 - - - -
278B VAL* 3.0 29.1 + - - +
280B SER* 3.5 20.8 + - - +
282B GLU* 4.9 0.7 - - + -
283B THR* 3.5 37.7 - - + +
285B CYS* 4.4 3.4 - - + +
287B TYR* 1.3 76.4 - - - +
289B SER* 1.3 87.3 + - - +
290B THR* 3.7 21.1 + - + -
305B ILE* 4.1 17.0 - - + -
316B ILE* 4.7 13.2 - - + -
319B ALA* 6.3 0.2 - - + -
320B ILE* 5.2 2.9 - - + -
323B LEU* 4.0 24.0 - - + -
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Residues in contact with SER 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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170B THR* 3.7 14.4 + - - -
196B VAL 3.9 10.9 + - - -
197B ILE* 3.2 11.2 - - - +
198B GLY 2.7 47.2 + - - -
199B GLY* 4.6 0.9 - - - -
275B CYS* 4.1 0.7 - - - +
276B SER 3.3 31.2 + - - -
277B PHE* 3.7 8.5 - - - -
288B PHE* 1.3 73.2 - - - +
290B THR* 1.3 65.5 + - - +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 4.2 5.2 - - + -
275B CYS* 3.3 15.9 - - - -
276B SER 3.4 3.6 + - - -
280B SER* 4.9 0.2 + - - -
282B GLU* 4.3 5.0 - - + +
288B PHE* 3.7 23.5 + - + -
289B SER* 1.3 80.9 + - - +
291B PRO* 1.3 74.3 - - + +
292B LEU* 3.3 15.6 - - - +
302B ASN* 2.6 36.8 + - - -
304B GLY* 3.7 24.0 - - - +
305B ILE* 3.9 9.4 - - + -
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Residues in contact with PRO 291 (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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195B PRO* 4.4 15.3 - - + -
197B ILE* 4.1 11.0 - - + -
208B LEU* 6.0 0.9 - - + -
211B GLN* 5.4 3.4 - - - +
273B VAL* 3.9 18.2 - - + -
274B GLU 3.8 6.1 - - - +
275B CYS* 3.8 22.2 - - - -
290B THR* 1.3 89.6 - - - +
292B LEU* 1.3 61.1 + - - +
302B ASN* 3.8 0.7 - - - +
303B LEU* 3.0 36.6 + - + +
304B GLY 3.5 15.7 - - - +
305B ILE 5.8 0.4 - - - +
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Residues in contact with LEU 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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167B PHE* 4.4 5.2 - - + -
273B VAL* 3.3 7.9 - - - +
274B GLU 2.8 36.0 + - - +
276B SER* 3.9 18.2 - - - +
278B VAL* 3.7 36.8 - - + -
290B THR* 3.3 18.2 - - - +
291B PRO* 1.3 73.5 - - - +
293B LEU* 1.3 63.4 + - - +
294B LEU* 3.3 14.0 + - + +
299B ILE* 4.0 19.5 - - + -
301B LYS 3.6 4.5 - - - +
302B ASN* 3.5 41.1 - - + +
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Residues in contact with LEU 293 (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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271B GLY* 3.8 28.7 - - - +
272B VAL 3.5 16.8 - - - +
273B VAL* 4.3 8.3 - - + -
292B LEU* 1.3 70.6 - - - +
294B LEU* 1.3 60.1 + - - +
299B ILE* 3.8 2.4 - - - +
300B GLU* 2.7 49.2 + - + +
301B LYS* 2.8 41.0 + - + +
303B LEU* 4.0 14.4 - - + +
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Residues in contact with LEU 294 (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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167B PHE* 4.0 26.2 - - + -
258B PHE* 4.6 9.0 - - + -
261B SER* 4.3 0.2 - - - -
262B LEU* 4.1 29.4 - - + +
265B ALA* 3.6 18.8 - - + +
269B LYS 4.9 3.6 - - - +
271B GLY 5.6 0.5 + - - -
272B VAL* 2.9 34.2 + - + +
274B GLU* 4.1 22.2 - - + +
292B LEU* 3.9 24.2 - - + +
293B LEU* 1.3 88.1 - - - +
295B GLY* 1.3 59.7 + - - +
298B GLY 3.3 11.9 - - - +
299B ILE* 4.6 1.1 - - - -
300B GLU* 4.1 2.2 - - - +
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Residues in contact with GLY 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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262B LEU* 5.0 0.9 - - - +
265B ALA* 3.6 23.5 - - - +
266B MET* 4.0 6.8 + - - +
269B LYS 5.6 1.1 - - - -
294B LEU* 1.3 75.8 - - - +
296B LYS* 1.3 60.6 + - - -
297B LYS 3.2 3.4 - - - -
298B GLY* 2.7 24.6 + - - +
300B GLU* 3.5 14.3 + - - -
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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