Contacts of the strand formed by residues 273 - 288 (chain B) in PDB entry 6Q2J
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 CYS 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A CYS* 2.0 53.6 - - + -
275A VAL* 5.0 2.0 - - + -
244B CYS* 4.1 3.4 - - - -
258B LYS* 5.5 0.6 - - - +
271B ALA 4.4 7.6 - - - -
272B PRO* 1.3 77.3 - - - +
274B CYS* 1.3 63.0 + - - +
275B VAL* 3.5 12.6 + - + +
307B CYS* 3.4 1.0 - - - -
308B ILE 2.9 33.5 + - - +
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Residues in contact with CYS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 4.5 12.3 + - - -
211B CYS* 2.0 56.3 - - + -
240B CYS* 3.7 24.3 - - - +
241B ILE 5.0 1.3 - - - -
242B GLY 5.2 12.3 - - - +
243B ALA 5.3 0.4 - - - +
244B CYS* 3.9 10.3 - - - -
273B CYS* 1.3 70.6 - - - +
275B VAL* 1.3 61.0 + - - +
276B PRO* 4.7 1.0 - - - +
305B CYS* 3.7 12.8 - - - -
306B HIS 3.5 4.9 - - - -
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 5.8 2.0 - - - +
273A CYS* 4.9 1.6 - - + -
275A VAL* 3.8 28.0 - - + -
308A ILE* 4.2 23.6 - - + +
273B CYS* 3.5 15.2 + - + +
274B CYS* 1.3 79.4 - - - +
276B PRO* 1.3 79.9 - - + +
305B CYS* 3.3 5.0 - - - -
306B HIS* 2.9 41.0 + - + +
308B ILE* 3.7 24.2 - - + -
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Residues in contact with PRO 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A HIS* 4.4 13.9 - - + +
258A LYS* 5.4 5.2 - - - +
308A ILE* 5.0 10.4 - - + +
240B CYS* 5.1 3.1 - - + +
274B CYS 4.7 1.6 - - - +
275B VAL* 1.3 102.0 - - + +
277B ALA* 1.3 60.9 + - - +
278B SER 4.5 2.0 - - - +
279B TYR* 3.6 45.5 + - + +
302B ALA* 3.9 22.0 - - + -
304B ASP 3.5 7.2 - - - +
305B CYS* 3.6 8.7 - - - -
306B HIS* 4.4 2.6 + - - -
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL 3.9 0.4 + - - -
276B PRO* 1.3 75.0 - - - +
278B SER* 1.3 59.9 + - - +
279B TYR* 4.9 6.2 - - - -
304B ASP* 2.9 28.8 + - - +
306B HIS* 3.5 28.5 - - + +
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B PRO* 4.5 0.5 - - - +
277B ALA* 1.3 80.4 + - - +
279B TYR* 1.3 70.4 + - - +
302B ALA* 3.9 1.2 - - - -
303B LYS* 3.0 44.9 + - - +
304B ASP* 3.3 15.8 + - - -
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN* 3.0 32.0 + - + -
254A HIS* 4.1 14.9 - + + -
308A ILE* 3.3 21.4 - - + +
276B PRO* 3.6 40.9 + - + +
277B ALA 4.9 6.5 - - - -
278B SER* 1.3 81.6 - - - +
280B ASN* 1.3 66.5 + - - +
281B PRO* 4.1 4.7 - - - +
298B ASP 4.2 17.8 - - - +
299B ASP* 4.3 19.7 - - + -
301B LEU 3.3 17.7 - - - +
302B ALA* 3.9 7.6 - - - -
303B LYS* 4.7 2.0 - - - +
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Residues in contact with ASN 280 (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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238B THR* 6.4 0.2 - - - +
279B TYR* 1.3 77.7 - - - +
281B PRO* 1.3 74.7 - - + +
298B ASP 4.8 1.1 - - - -
300B LEU 3.9 2.8 + - - -
301B LEU* 2.5 50.1 + - + +
302B ALA 3.9 8.9 + - - -
303B LYS* 3.8 38.3 - - - +
146D ALA* 6.5 0.9 - - + -
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Residues in contact with PRO 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR 4.1 4.7 - - - +
280B ASN* 1.3 96.1 - - + +
282B MET* 1.3 62.0 + - - +
296B THR* 4.0 17.3 - - + -
297B TYR 3.2 15.9 - - - +
298B ASP* 4.3 14.3 - - - +
301B LEU* 4.3 5.4 - - - +
146D ALA* 5.4 5.4 - - - +
149D ALA* 3.9 23.8 - - + +
150D SER* 5.4 2.7 - - - +
153D LYS* 5.0 17.9 - - + +
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Residues in contact with MET 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PRO* 4.0 22.9 - - + -
235B VAL* 3.8 28.7 - - + -
236B GLN 4.7 5.4 - - - +
281B PRO* 1.3 76.4 - - - +
283B VAL* 1.3 66.8 + - - +
284B LEU* 3.9 14.1 + - + +
296B THR* 3.6 1.1 - - - -
297B TYR* 2.9 35.2 + - - +
300B LEU* 3.7 37.9 - - + +
301B LEU* 3.9 21.3 - - + -
139D VAL 5.4 0.2 - - - +
145D ASN* 3.4 29.4 - - - +
149D ALA* 4.8 2.0 - - - -
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PRO* 4.3 1.2 - - - +
282B MET* 1.3 78.3 - - - +
284B LEU* 1.3 75.2 + - - +
285B ILE* 5.4 0.2 - - + -
294B LEU* 4.3 9.2 - - + -
295B GLN 3.2 10.5 - - - +
296B THR* 3.4 21.3 - - - +
139D VAL* 3.3 25.6 - - + +
145D ASN* 3.5 13.8 + - - +
148D LEU* 4.1 15.7 - - + +
149D ALA* 3.6 30.7 - - + +
152D LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 5.8 0.4 - - + -
225B TRP* 3.7 29.4 - - + -
228B TRP* 4.5 0.4 - - + -
229B VAL* 3.7 31.2 - - + -
231B SER 3.7 4.7 - - - +
232B PRO* 4.5 7.6 - - + -
235B VAL* 6.4 0.7 - - + -
282B MET* 4.0 21.8 - - + +
283B VAL* 1.3 82.2 - - - +
285B ILE* 1.3 66.7 + - - +
286B GLN* 4.1 7.6 + - + +
294B LEU* 3.6 3.3 - - - -
295B GLN* 2.9 33.1 + - - +
297B TYR* 4.5 21.5 - - + -
300B LEU* 3.9 24.0 - - + -
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Residues in contact with ILE 285 (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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229B VAL* 3.3 5.0 - - - -
230B LEU* 2.6 50.3 + - + -
231B SER* 2.9 35.2 + - - +
283B VAL* 5.4 0.2 - - + -
284B LEU* 1.3 76.3 - - - +
286B GLN* 1.3 58.0 + - - +
292B VAL* 3.7 27.6 - - + -
293B SER 3.4 4.7 - - - +
294B LEU* 3.7 23.8 - - + -
132D LEU* 5.7 2.7 - - + -
135D ALA* 3.9 36.3 - - + +
136D GLU* 4.7 2.7 - - + +
139D VAL* 4.6 8.7 - - + -
201D SER* 6.4 0.2 - - - -
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Residues in contact with GLN 286 (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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228B TRP* 3.3 23.7 - - + +
284B LEU* 4.8 5.3 - - + +
285B ILE* 1.3 78.4 - - - +
287B LYS* 1.3 61.9 + - - +
288B THR* 3.3 17.7 + - + +
292B VAL* 3.4 4.9 - - - +
293B SER 2.9 35.1 + - - +
295B GLN* 3.4 34.6 - - + +
297B TYR* 2.4 40.2 + - - -
551F ILE* 3.3 24.2 - - + +
594F HIS 3.5 8.5 + - - +
595F GLU* 5.2 1.2 - - - +
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Residues in contact with LYS 287 (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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226B ALA 5.3 5.4 - - - +
227B ASP 4.8 16.6 + - - +
228B TRP* 3.7 8.5 + - - -
229B VAL 5.2 3.1 - - - +
230B LEU* 4.1 35.4 - - + +
285B ILE 4.2 0.2 + - - -
286B GLN* 1.3 70.2 - - - +
288B THR* 1.3 66.7 + - - +
291B GLY 3.6 5.8 - - - +
292B VAL* 4.7 11.2 - - + +
549F LYS 5.0 1.2 - - - +
550F GLY* 4.8 5.0 - - - -
551F ILE* 4.1 16.2 + - - +
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Residues in contact with THR 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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286B GLN* 3.3 30.7 + - + +
287B LYS* 1.3 80.1 - - - +
289B ASP* 1.3 65.8 + - - +
290B THR* 3.6 10.5 + - - -
291B GLY* 2.9 31.0 + - - +
292B VAL* 4.2 1.2 + - - -
293B SER* 4.3 17.0 - - - -
549F LYS 5.3 2.7 - - - +
551F ILE* 3.9 19.7 - - + -
595F GLU* 4.3 20.4 - - - +
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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
------------------------------------------------------------
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