Contacts of the strand formed by residues 272 - 285 (chain U) in PDB entry 6GYK
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 ASN 272 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2U SER 4.6 17.4 - - - +
267U VAL 3.6 2.9 - - - +
268U THR* 3.6 1.5 - - - +
269U ILE 2.9 34.3 + - - +
270U ASN* 2.9 18.3 + - - +
271U ARG* 1.3 86.0 + - - +
273U ASP* 1.3 64.8 + - - +
274U TYR* 3.7 27.5 + - + +
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Residues in contact with ASP 273 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U ASN* 5.3 9.7 + - - +
6U ALA* 5.6 9.2 - - + +
10U TYR* 3.7 24.2 + - - +
266U VAL* 4.9 7.9 - - + -
267U VAL 3.4 4.0 - - - +
268U THR* 3.5 23.7 + - - +
271U ARG 5.2 1.7 - - - -
272U ASN* 1.3 79.0 + - - +
274U TYR* 1.3 73.8 + - - +
275U THR* 6.3 0.9 - - + -
14V THR* 3.8 23.9 + - - +
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Residues in contact with TYR 274 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2U SER 5.9 2.7 + - - -
3U ASN* 5.8 7.9 - - + +
265U GLY 4.5 0.2 - - - -
266U VAL* 3.1 9.7 - - - +
267U VAL* 2.9 45.3 + - + +
269U ILE* 4.4 19.5 - - + -
272U ASN* 3.7 39.0 + - + +
273U ASP* 1.3 78.8 - - - +
275U THR* 1.3 65.3 - - - +
60V LEU* 4.9 14.1 - - + -
87V VAL* 4.3 29.4 - - + -
106V ILE* 4.2 23.7 - - + +
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Residues in contact with THR 275 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U ASN* 4.7 10.1 + - - +
5U GLU* 4.3 16.6 + - - +
6U ALA* 5.5 13.4 - - + -
9U VAL* 5.7 10.9 - - + +
10U TYR* 5.9 5.6 - - + +
265U GLY 3.3 4.9 - - - -
266U VAL* 4.4 11.4 - - + -
273U ASP* 5.9 0.7 - - + -
274U TYR* 1.3 81.9 - - - +
276U PHE* 1.3 59.3 + - - +
52V LEU* 4.0 16.6 - - + -
55V ASN 5.3 0.2 + - - -
56V THR* 3.9 20.7 - - - +
57V GLN 5.1 0.5 + - - -
58V SER* 3.2 23.7 + - - -
60V LEU* 6.0 0.4 - - - -
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Residues in contact with PHE 276 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244U MET* 4.2 7.6 - - + -
246U CYS* 3.5 29.6 - - + -
262U LEU* 3.9 10.8 - - + -
263U LYS 4.2 0.2 - - - -
264U ASP* 3.2 10.9 - - - -
265U GLY* 2.9 64.8 + - - +
266U VAL 4.2 0.2 - - - -
267U VAL* 3.5 23.8 - - + -
275U THR* 1.3 74.8 - - - +
277U GLN* 1.3 58.0 + - - +
278U LYS 3.2 26.7 - - - +
279U ALA* 3.5 20.0 - - + -
56V THR* 3.9 7.8 - - - +
58V SER* 3.6 15.7 - - - +
60V LEU* 3.6 33.4 - - + -
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Residues in contact with GLN 277 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263U LYS* 2.7 41.7 + - - +
264U ASP* 2.5 46.1 + - - -
276U PHE* 1.3 71.9 - - - +
278U LYS* 1.3 71.2 + - + +
52V LEU 4.6 0.2 - - - +
53V LYS* 3.9 14.0 + - - +
54V ASP 6.2 0.2 - - - -
56V THR* 3.2 41.0 - - - +
57V GLN* 4.4 2.9 - - - -
58V SER 2.9 10.8 + - - +
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Residues in contact with LYS 278 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262U LEU 3.3 7.6 - - - +
263U LYS* 3.0 30.5 - - + +
276U PHE* 3.2 12.3 - - - -
277U GLN* 1.3 92.1 - - + +
279U ALA* 1.3 62.1 + - - +
58V SER 3.4 3.2 + - - -
59V LYS* 3.3 31.6 - - + +
60V LEU 3.3 16.5 + - - -
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Residues in contact with ALA 279 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244U MET* 5.6 2.2 - - + -
260U CYS 4.3 0.2 - - - -
261U SER* 3.6 4.3 - - - -
262U LEU* 2.9 44.7 + - + +
276U PHE* 3.5 24.0 - - + -
278U LYS* 1.3 78.6 - - - +
280U GLN* 1.3 63.4 + - - +
281U VAL* 5.5 0.9 - - + -
59V LYS* 4.0 5.1 - - - +
60V LEU* 3.6 22.7 - - + +
62V VAL* 6.1 2.5 - - + -
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Residues in contact with GLN 280 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259U LYS* 3.6 31.5 - - - +
260U CYS 3.4 10.1 + - - +
261U SER* 3.6 21.3 + - - +
279U ALA* 1.3 77.8 + - - +
281U VAL* 1.3 63.4 + - - +
282U GLU* 4.0 22.9 + - + +
59V LYS* 4.1 12.3 - - - +
60V LEU 3.5 6.7 + - - +
61V THR* 3.7 11.1 - - + +
62V VAL* 3.2 24.8 + - - +
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Residues in contact with VAL 281 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258U TRP* 3.3 1.2 - - + +
259U LYS* 2.9 11.3 - - - +
260U CYS* 2.9 53.5 + - + -
262U LEU* 3.7 29.4 - - + -
279U ALA* 5.5 0.7 - - + -
280U GLN* 1.3 78.6 - - - +
282U GLU* 1.3 63.7 + - - +
283U ALA* 3.8 19.1 - - + +
62V VAL* 3.6 24.0 - - + +
66V LEU* 6.4 0.2 - - + -
78V PHE* 6.0 4.0 - - + -
80V VAL* 5.3 4.7 - - + -
113V ILE* 4.3 19.7 - - + -
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Residues in contact with GLU 282 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257U ARG* 3.9 26.0 + - - +
258U TRP 3.4 5.2 - - - -
259U LYS* 4.3 17.4 + - + +
280U GLN* 4.0 22.1 - - + +
281U VAL* 1.3 76.2 - - - +
283U ALA* 1.3 59.4 + - - +
61V THR* 5.9 1.1 - - + -
62V VAL 3.0 9.3 + - - -
63V LYS* 3.4 55.2 + - + +
64V GLY 3.7 3.2 + - - +
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Residues in contact with ALA 283 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257U ARG* 3.8 4.9 - - - +
258U TRP* 2.9 37.0 + - + +
281U VAL* 3.8 14.1 - - + -
282U GLU* 1.3 75.4 - - - +
284U GLU* 1.3 61.7 + - - +
64V GLY 3.4 13.0 - - - +
66V LEU* 3.6 34.8 - - + +
80V VAL* 4.7 7.0 - - + -
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Residues in contact with GLU 284 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O LYS* 5.3 1.2 + - - -
256U ALA* 3.1 36.2 - - - +
257U ARG* 3.7 19.2 - - - +
283U ALA* 1.3 74.8 - - - +
285U TRP* 1.3 64.2 + - - +
286U VAL* 4.2 1.7 + - - +
64V GLY 3.2 11.3 + - - +
65V ASN* 3.4 14.1 - - - +
66V LEU* 2.5 29.7 + - - +
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Residues in contact with TRP 285 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O ASN* 2.5 38.2 - - - +
105O ARG* 2.9 47.1 - - + -
106O ILE* 3.2 24.5 - - - -
107O ARG* 4.2 10.9 - - + +
110O LYS* 4.7 11.4 - - + -
111O THR 4.5 2.7 - - - -
253U ARG* 5.2 1.3 - - - -
255U LYS 5.3 0.4 - - - -
256U ALA* 3.0 42.7 + - + +
258U TRP* 4.4 7.0 - - + -
283U ALA 4.3 0.4 + - - -
284U GLU* 1.3 79.9 - - - +
286U VAL* 1.3 98.7 + - - +
66V LEU* 3.8 30.2 - - + +
67V ASP 4.9 5.4 + - - -
69V TYR* 3.4 17.5 - + + -
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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