Contacts of the strand formed by residues 243 - 254 (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 LEU 243 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241U GLU* 3.5 26.2 - - - +
242U ASN* 1.3 77.7 - - - +
244U MET* 1.3 64.6 + - - +
245U LEU* 4.1 25.5 + - + +
266U VAL 3.9 1.6 - - - +
267U VAL* 3.4 5.6 - - - -
268U THR* 3.3 26.0 + - - +
12V ARG* 4.0 43.5 - - + +
13V SER* 5.7 0.2 - - - -
112V ARG* 3.3 40.4 - - + +
114V VAL* 4.3 4.0 - - + -
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Residues in contact with MET 244 (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* 1.3 74.9 - - - +
245U LEU* 1.3 62.9 + - - +
246U CYS* 4.2 5.6 - - - -
262U LEU* 3.6 31.2 - - + -
266U VAL 3.6 3.8 - - - +
267U VAL* 3.6 34.5 - - + -
269U ILE* 5.8 1.1 - - + -
276U PHE* 3.7 26.2 - - + -
279U ALA* 5.0 1.6 - - + -
60V LEU* 4.3 7.0 - - + -
62V VAL* 4.1 26.0 - - + -
111V LEU* 4.4 10.3 - - + -
112V ARG 2.8 13.9 + - - +
113V ILE* 3.5 16.9 - - + +
114V VAL* 2.9 28.8 + - - +
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Residues in contact with LEU 245 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243U LEU* 4.1 24.9 - - + +
244U MET* 1.3 77.6 - - - +
246U CYS* 1.3 62.5 + - - +
265U GLY* 3.2 1.7 - - - -
266U VAL* 3.0 34.9 + - + +
9V LEU* 3.2 43.3 - - + +
10V TYR* 3.6 16.0 - - + -
12V ARG* 3.8 17.7 - - + +
13V SER* 3.6 36.3 - - - +
114V VAL* 3.6 15.0 - - + -
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Residues in contact with CYS 246 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244U MET* 4.2 11.2 - - - -
245U LEU* 1.3 77.9 - - - +
247U LEU* 1.3 65.3 + - - +
262U LEU* 4.0 38.8 - - - -
263U LYS 3.3 13.9 - - - +
264U ASP 3.8 0.4 - - - -
265U GLY* 3.7 7.6 - - - -
276U PHE* 4.1 5.2 - - + -
9V LEU* 3.7 10.0 - - - +
10V TYR* 3.7 13.0 - - - -
113V ILE* 4.3 3.4 - - - -
114V VAL 3.1 12.8 + - - +
115V ALA* 3.3 6.7 - - - -
116V CYS* 3.0 20.4 + - - +
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Residues in contact with LEU 247 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246U CYS* 1.3 78.9 - - - +
248U TYR* 1.3 60.2 + - - +
262U LEU* 3.3 7.6 - - - +
263U LYS* 2.9 37.5 + - + +
264U ASP* 4.1 25.4 - - + +
7V TYR* 3.6 34.1 - - + -
9V LEU* 6.1 0.7 - - + -
10V TYR* 4.3 11.7 - - + +
115V ALA* 4.2 3.1 - - - -
116V CYS* 3.0 21.3 - - + +
117V ASN 3.6 6.1 - - - +
118V SER* 4.3 21.3 - - - +
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Residues in contact with TYR 248 (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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247U LEU* 1.3 74.8 - - - +
249U ASP* 1.3 67.2 + - - +
250U LYS* 4.6 2.9 - - - +
251U VAL* 4.5 14.8 - - + -
261U SER 3.7 4.3 - - - +
262U LEU* 4.3 10.3 - - + +
263U LYS* 5.5 0.4 - - - -
71V PHE* 3.4 15.2 - - - -
74V ASP* 3.4 21.3 + - - -
76V TRP* 3.5 32.8 - + - -
115V ALA* 3.3 37.5 - - + -
116V CYS 2.9 8.6 + - - -
117V ASN* 3.3 39.8 + - - +
118V SER* 2.9 22.1 + - - -
119V LYS* 3.7 4.3 + - - -
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Residues in contact with ASP 249 (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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247U LEU 4.3 0.2 + - - -
248U TYR* 1.3 74.2 - - - +
250U LYS* 1.3 66.9 + - + +
261U SER* 2.8 23.9 + - - +
263U LYS* 3.3 35.2 - - - +
118V SER* 3.0 23.8 + - - -
119V LYS* 3.1 21.1 + - - +
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Residues in contact with LYS 250 (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 2.0 - - - -
249U ASP* 1.3 84.1 - - - +
251U VAL* 1.3 70.5 + - - +
252U THR* 3.6 26.7 - - + -
259U LYS 4.6 0.4 - - - -
260U CYS* 3.4 2.9 - - - -
261U SER* 2.9 45.8 + - - +
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Residues in contact with VAL 251 (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* 4.5 13.6 - - + -
250U LYS* 1.3 81.8 - - - +
252U THR* 1.3 69.8 + - - +
258U TRP* 3.9 30.7 - - + -
259U LYS 3.4 8.3 - - - +
260U CYS* 4.3 9.0 - - + -
76V TRP* 3.8 43.9 - - + +
78V PHE* 3.9 19.5 - - + -
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Residues in contact with THR 252 (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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20N T 5.0 12.1 - - - +
250U LYS* 3.6 28.9 - - + -
251U VAL* 1.3 80.2 - - - +
253U ARG* 1.3 65.7 + - - +
254U THR* 6.0 0.4 - - - -
258U TRP* 3.4 8.7 - - - -
259U LYS* 2.9 49.7 + - - +
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Residues in contact with ARG 253 (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* 5.7 1.5 + - - -
105O ARG* 4.0 16.6 - - - +
46T T 4.9 0.4 - - - -
47T A 3.3 32.1 + - - -
252U THR* 1.3 80.1 - - - +
254U THR* 1.3 67.9 + - - +
255U LYS* 2.8 39.3 + - - +
257U ARG 3.2 9.9 - - - +
258U TRP* 3.7 46.0 - - + +
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Residues in contact with THR 254 (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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19N G 4.7 20.2 + - - +
20N T 6.2 4.8 - - + +
252U THR* 6.0 0.3 - - - -
253U ARG* 1.3 77.8 + - - +
255U LYS* 1.3 80.2 + - + +
257U ARG* 3.0 29.1 + - - +
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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