Contacts of the strand formed by residues 257 - 269 (chain U) in PDB entry 5FYW
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 ARG 257 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18N T 5.7 4.8 + - - -
19N G 4.5 7.8 + - - -
253U ARG* 3.2 3.8 - - - -
254U THR* 3.0 38.1 + - - +
255U LYS* 3.3 1.6 + - + -
256U ALA* 1.3 78.4 - - - +
258U TRP* 1.3 66.3 + - - +
259U LYS* 3.2 45.0 + - - +
282U GLU* 4.5 17.6 + - + +
283U ALA 3.7 6.5 - - - +
284U GLU* 3.8 14.6 - - - +
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Residues in contact with TRP 258 (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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93O GLU* 4.2 13.2 - - - -
105O ARG* 5.1 1.8 - - - -
251U VAL* 3.9 15.3 - - + -
252U THR 3.4 15.0 - - - -
253U ARG* 3.7 34.7 - - + +
256U ALA* 3.9 13.0 - - - +
257U ARG* 1.3 80.8 - - - +
259U LYS* 1.3 64.5 + - - +
260U CYS* 4.9 7.6 - - - -
281U VAL 3.5 0.8 - - - +
282U GLU* 3.5 4.3 - - - -
283U ALA* 2.8 42.2 + - + +
285U TRP* 3.8 14.9 - - + +
66V LEU* 3.4 30.3 - - + +
69V TYR* 3.6 43.7 - + - -
76V TRP* 3.8 26.0 - + - -
78V PHE* 4.7 8.1 - + + -
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Residues in contact with LYS 259 (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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18N T 4.5 5.3 + - - -
19N G 3.3 25.5 + - - -
250U LYS 4.1 0.2 - - - +
251U VAL* 3.4 2.9 - - - -
252U THR* 2.9 45.7 + - - +
257U ARG* 3.2 48.1 + - + +
258U TRP* 1.3 78.8 - - - +
260U CYS* 1.3 64.5 + - - +
280U GLN* 3.9 11.0 - - - +
281U VAL 3.0 9.4 - - - +
282U GLU* 4.3 15.9 - - + +
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Residues in contact with CYS 260 (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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250U LYS 3.4 7.9 - - - +
251U VAL* 4.3 9.2 - - + -
258U TRP* 4.9 6.5 - - - -
259U LYS* 1.3 85.6 - - - +
261U SER* 1.3 63.7 + - - +
262U LEU* 3.7 13.6 + - + -
279U ALA 3.4 2.1 - - - +
280U GLN* 3.3 10.8 + - - -
281U VAL* 2.9 60.6 + - + +
78V PHE* 3.7 34.5 - - + -
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Residues in contact with SER 261 (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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248U TYR* 3.7 1.4 - - - -
249U ASP* 2.8 48.3 + - - +
250U LYS* 2.9 33.4 + - - +
260U CYS* 1.3 70.1 - - - +
262U LEU* 1.3 59.3 + - - +
263U LYS* 5.1 0.9 - - - -
279U ALA 3.7 3.6 - - - -
280U GLN* 3.2 19.6 + - - +
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Residues in contact with LEU 262 (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* 3.6 30.1 - - + -
246U CYS* 4.0 19.3 - - - -
247U LEU 3.3 9.4 - - - +
248U TYR* 4.3 13.2 - - + -
260U CYS* 4.2 14.8 - - + +
261U SER* 1.3 75.2 - - - +
263U LYS* 1.3 71.5 + - - +
276U PHE* 4.3 2.0 - - + -
278U LYS* 3.4 4.0 - - - +
279U ALA* 2.8 45.5 + - + +
281U VAL* 3.5 28.0 - - + -
78V PHE* 4.9 4.7 - - + -
113V ILE* 4.3 9.0 - - + -
115V ALA* 4.3 6.3 - - + -
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Residues in contact with LYS 263 (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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246U CYS* 3.3 4.0 - - - +
247U LEU* 2.9 34.6 + - + +
248U TYR 5.6 0.2 - - - -
249U ASP* 3.3 35.6 + - + +
261U SER* 4.7 1.1 - - - +
262U LEU* 1.3 82.3 - - - +
264U ASP* 1.3 83.0 + - - +
265U GLY 3.3 2.4 + - - -
276U PHE* 4.3 2.7 - - - -
277U GLN* 3.2 20.6 + - - +
278U LYS* 2.8 40.5 - - + +
118V SER* 5.9 1.6 - - - -
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Residues in contact with ASP 264 (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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246U CYS* 3.8 0.7 - - - -
247U LEU* 4.1 18.5 + - + +
263U LYS* 1.3 83.7 - - - +
265U GLY* 1.3 53.7 + - - +
276U PHE 3.4 8.7 - - - -
277U GLN* 2.9 34.6 + - - +
10V TYR* 2.7 27.0 + - - +
49V ALA* 4.8 2.9 - - - +
52V LEU* 3.6 28.1 - - + +
53V LYS* 3.6 25.1 - - - +
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Residues in contact with GLY 265 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245U LEU 3.2 13.2 - - - -
246U CYS* 3.7 7.9 - - - -
263U LYS 3.3 1.8 + - - -
264U ASP* 1.3 76.9 - - - +
266U VAL* 1.3 61.9 + - - +
275U THR* 3.4 3.8 - - - -
276U PHE* 2.9 45.5 + - - +
52V LEU* 3.7 12.0 - - - +
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Residues in contact with VAL 266 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10U TYR* 3.7 27.1 - - + +
243U LEU 3.9 1.4 - - - +
244U MET* 3.6 1.2 - - - -
245U LEU* 3.0 29.1 + - + +
265U GLY* 1.3 75.4 - - - +
267U VAL* 1.3 71.8 + - - +
268U THR* 5.7 1.1 - - - +
274U TYR 3.4 13.9 - - - +
275U THR* 4.0 13.5 - - + -
276U PHE* 4.1 1.2 - - - -
10V TYR* 4.0 25.6 - - + -
13V SER* 4.1 23.3 - - - -
15V ILE* 5.9 0.9 - - + -
48V VAL* 5.7 2.5 - - + -
52V LEU* 4.7 6.7 - - + -
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Residues in contact with VAL 267 (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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243U LEU 3.4 15.7 - - - +
244U MET* 3.6 27.6 - - + -
266U VAL* 1.3 74.6 - - - +
268U THR* 1.3 66.3 + - - +
269U ILE* 3.7 25.6 - - + -
272U ASN 3.6 0.3 - - - +
273U ASP* 3.2 6.8 - - - +
274U TYR* 2.9 36.5 + - + +
276U PHE* 3.4 34.3 - - + -
60V LEU* 3.9 10.5 - - + -
111V LEU* 4.0 9.0 - - + -
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Residues in contact with THR 268 (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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10U TYR* 5.4 0.3 + - - -
241U GLU* 4.5 15.7 - - - +
242U ASN* 2.8 34.6 + - - +
243U LEU* 3.3 10.5 + - - -
266U VAL* 5.7 1.0 - - - +
267U VAL* 1.3 76.4 - - - +
269U ILE* 1.3 61.4 + - - +
271U ARG* 4.3 20.4 - - - +
272U ASN 3.2 6.3 - - - +
273U ASP* 2.9 22.5 + - - +
14V THR* 3.2 19.4 + - - +
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Residues in contact with ILE 269 (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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242U ASN* 3.5 3.1 - - - -
244U MET* 5.8 0.4 - - + -
267U VAL* 3.7 26.2 - - + -
268U THR* 1.3 76.3 - - - +
270U ASN* 1.3 76.9 + - - +
271U ARG 3.3 0.7 - - - -
272U ASN* 2.8 26.8 + - - +
274U TYR* 4.4 21.6 - - + -
60V LEU* 5.2 1.8 - - + -
85V VAL* 3.9 35.7 - - + -
106V ILE* 3.6 21.9 - - + +
108V VAL* 3.3 30.1 - - + -
111V LEU* 4.7 9.0 - - + -
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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