Contacts of the strand formed by residues 273 - 288 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A CYS* 4.1 3.6 - - - -
258A LYS* 5.5 1.2 - - - +
271A ALA 4.4 7.2 - - - -
272A PRO* 1.3 75.4 - - - +
274A CYS* 1.3 63.6 + - - +
275A VAL* 3.5 12.8 + - + +
307A CYS* 3.4 0.5 - - - -
308A ILE 2.9 34.0 + - - +
273B CYS* 2.0 54.3 - - + -
275B VAL* 4.9 2.0 - - + -
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Residues in contact with CYS 274 (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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211A CYS* 2.0 55.9 - - + -
240A CYS* 3.7 23.9 - - - +
241A ILE 5.0 1.3 - - - -
242A GLY 5.2 12.1 - - - +
243A ALA 5.3 0.4 - - - +
244A CYS* 3.9 9.6 - - - -
273A CYS* 1.3 72.2 - - - +
275A VAL* 1.3 61.5 + - - +
276A PRO* 4.7 0.9 - - - +
305A CYS* 3.7 12.1 - - - -
306A HIS 3.5 5.2 - - - -
258B LYS* 4.5 13.2 + - - -
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A CYS* 4.1 13.9 - - + +
274A CYS* 1.3 79.1 - - - +
276A PRO* 1.3 79.0 - - + +
305A CYS* 3.3 4.8 - - - -
306A HIS* 2.9 40.8 + - + +
308A ILE* 3.7 23.8 - - + -
258B LYS* 5.8 2.0 - - - +
273B CYS* 5.0 1.3 - - + -
275B VAL* 3.8 27.8 - - + -
308B ILE* 4.2 23.3 - - + +
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Residues in contact with PRO 276 (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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240A CYS* 5.1 2.7 - - + +
274A CYS 4.7 1.3 - - - +
275A VAL* 1.3 99.4 - - + +
277A ALA* 1.3 60.5 + - - +
278A SER 4.5 2.5 - - - +
279A TYR* 3.6 46.6 + - + +
302A ALA* 3.9 22.7 - - + -
304A ASP 3.5 7.4 - - - +
305A CYS* 3.6 8.7 - - - -
306A HIS* 4.4 2.5 + - - -
254B HIS* 4.4 13.9 - - + +
258B LYS* 5.5 5.2 - - - +
308B ILE* 5.0 10.4 - - + +
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO* 1.3 75.1 - - - +
278A SER* 1.3 60.0 + - - +
279A TYR* 4.9 6.2 - - - -
304A ASP* 2.9 28.0 + - - +
306A HIS* 3.5 28.3 - - + +
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Residues in contact with SER 278 (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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276A PRO* 4.5 0.5 - - - +
277A ALA* 1.3 81.5 + - - +
279A TYR* 1.3 69.5 + - - +
302A ALA* 3.9 1.0 - - - -
303A LYS* 3.0 44.7 + - - +
304A ASP* 3.3 15.8 + - - -
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Residues in contact with TYR 279 (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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276A PRO* 3.6 40.8 + - + +
277A ALA 4.9 6.1 - - - -
278A SER* 1.3 81.7 - - - +
280A ASN* 1.3 65.5 + - - +
281A PRO* 4.1 4.5 - - - +
298A ASP 4.2 17.5 - - - +
299A ASP* 4.3 19.5 - - + -
301A LEU 3.3 17.9 - - - +
302A ALA* 3.9 7.4 - - - -
303A LYS* 4.7 2.3 - - - +
252B ASN* 2.9 31.9 + - + -
254B HIS* 4.1 15.2 - + + -
308B ILE* 3.3 20.8 - - + +
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Residues in contact with ASN 280 (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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279A TYR* 1.3 77.8 - - - +
281A PRO* 1.3 73.9 - - + +
298A ASP 4.8 1.1 - - - -
300A LEU 3.9 2.9 + - - -
301A LEU* 2.5 50.5 + - + +
302A ALA 3.9 8.5 + - - -
303A LYS* 3.8 37.3 - - - +
146C ALA* 6.5 1.1 - - + -
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Residues in contact with PRO 281 (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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279A TYR 4.1 4.9 - - - +
280A ASN* 1.3 96.2 - - + +
282A MET* 1.3 62.6 + - - +
296A THR* 4.0 16.4 - - + -
297A TYR 3.2 15.5 - - - +
298A ASP* 4.3 14.5 - - - +
301A LEU* 4.3 5.5 - - - +
146C ALA* 5.4 5.0 - - - +
149C ALA* 3.9 24.6 - - + +
150C SER* 5.4 2.7 - - - +
153C LYS* 5.0 17.5 - - + +
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Residues in contact with MET 282 (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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232A PRO* 4.0 23.1 - - + -
235A VAL* 3.8 28.0 - - + -
236A GLN 4.7 5.2 - - - +
281A PRO* 1.3 76.2 - - - +
283A VAL* 1.3 66.5 + - - +
284A LEU* 3.9 14.0 + - + +
296A THR* 3.6 0.8 - - - -
297A TYR* 2.9 34.8 + - - +
300A LEU* 3.7 37.2 - - + +
301A LEU* 3.9 22.0 - - + -
139C VAL 5.4 0.4 - - - +
145C ASN* 3.4 30.1 - - - +
149C ALA* 4.8 2.0 - - - -
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Residues in contact with VAL 283 (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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232A PRO* 4.3 1.2 - - - +
282A MET* 1.3 78.5 - - - +
284A LEU* 1.3 75.2 + - - +
285A ILE* 5.4 0.2 - - + -
294A LEU* 4.3 8.7 - - + -
295A GLN 3.2 10.3 - - - +
296A THR* 3.4 21.3 - - - +
139C VAL* 3.3 25.6 - - + +
145C ASN* 3.5 13.4 + - - +
148C LEU* 4.1 15.5 - - + +
149C ALA* 3.6 31.2 - - + +
152C LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 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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220A LEU* 5.8 0.2 - - + -
225A TRP* 3.7 28.3 - - + -
228A TRP* 4.5 0.4 - - + -
229A VAL* 3.7 30.1 - - + -
231A SER 3.7 4.9 - - - +
232A PRO* 4.5 7.4 - - + -
282A MET* 4.0 22.7 - - + +
283A VAL* 1.3 82.7 - - - +
285A ILE* 1.3 66.5 + - - +
286A GLN* 4.1 6.9 + - + +
294A LEU* 3.6 3.1 - - - -
295A GLN* 2.9 33.1 + - - +
297A TYR* 4.5 21.8 - - + -
300A LEU* 3.9 24.0 - - + -
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Residues in contact with ILE 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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229A VAL* 3.3 4.9 - - - -
230A LEU* 2.6 51.1 + - + -
231A SER* 2.9 36.9 + - - +
283A VAL* 5.4 0.4 - - + -
284A LEU* 1.3 77.5 - - - +
286A GLN* 1.3 59.2 + - - +
292A VAL* 3.7 27.6 - - + -
293A SER 3.4 3.8 - - - +
294A LEU* 3.7 24.0 - - + -
132C LEU* 5.7 2.7 - - + -
135C ALA* 3.9 36.3 - - + +
136C GLU* 4.7 2.5 - - + +
139C VAL* 4.6 8.3 - - + -
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Residues in contact with GLN 286 (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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228A TRP* 3.3 23.9 - - + +
229A VAL* 5.4 0.2 - - - -
284A LEU* 4.8 5.5 - - + +
285A ILE* 1.3 77.7 - - - +
287A LYS* 1.3 61.3 + - - +
288A THR* 3.3 18.8 + - + +
292A VAL* 3.4 4.4 - - - +
293A SER* 2.9 35.2 + - - +
295A GLN* 3.3 34.5 - - + +
297A TYR* 2.4 40.2 + - - -
551E ILE* 3.3 23.6 - - + +
594E HIS 3.5 8.6 + - - +
595E GLU* 5.2 1.4 - - - +
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Residues in contact with LYS 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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226A ALA 5.3 6.8 + - - +
227A ASP 4.8 15.9 - - - +
228A TRP* 3.7 8.2 + - - -
229A VAL 5.2 3.8 - - - +
230A LEU* 4.1 35.4 - - + +
285A ILE 4.2 0.4 + - - -
286A GLN* 1.3 69.2 - - - +
288A THR* 1.3 67.2 + - - +
291A GLY 3.6 6.5 - - - +
292A VAL* 4.7 11.2 - - + +
549E LYS 5.0 1.4 - - - +
550E GLY* 4.8 4.3 - - - -
551E ILE* 4.1 16.6 + - - +
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Residues in contact with THR 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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286A GLN* 3.3 31.1 + - + +
287A LYS* 1.3 79.7 - - - +
289A ASP* 1.3 65.4 + - - +
290A THR* 3.6 10.8 + - - -
291A GLY* 2.9 31.3 + - - +
292A VAL* 4.2 1.2 + - - -
293A SER* 4.3 17.0 - - - -
549E LYS 5.3 2.5 - - - +
551E ILE* 3.9 18.6 - - + -
595E GLU* 4.3 20.6 - - - +
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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