Contacts of the strand formed by residues 264 - 270 (chain B) in PDB entry 4CEV
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 ILE 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B PHE* 3.5 19.4 - - + -
119B ILE* 4.1 6.3 - - + -
221B VAL* 3.4 27.8 - - + +
223B LEU* 4.1 16.2 - - + -
258B LEU* 4.0 40.4 + - + +
262B GLN 3.8 1.3 - - - -
263B ILE* 1.3 82.1 - - + +
265B THR* 1.3 59.7 + - - +
266B SER 3.3 27.8 - - - +
267B ALA* 4.5 0.9 - - + -
293B LEU* 4.0 19.5 - - + -
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Residues in contact with THR 265 (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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2B LYS* 6.1 0.5 - - - +
91B PHE* 3.2 20.9 - - - -
92B PRO* 3.8 8.1 - - - +
113B TYR* 3.3 30.5 + - + +
116B LEU* 4.3 2.8 - - - +
219B ASP 4.9 1.8 - - - +
220B GLY* 3.4 15.2 - - - -
221B VAL 2.8 31.2 + - - -
263B ILE 3.8 9.6 - - - +
264B ILE* 1.3 74.5 - - - +
266B SER* 1.3 59.6 + - - -
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Residues in contact with SER 266 (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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91B PHE* 3.4 10.4 - - - -
92B PRO* 3.6 25.8 - - - -
105B THR* 5.6 0.7 - - - -
109B VAL* 3.8 20.7 - - - +
221B VAL 3.6 0.6 + - - -
222B HIS* 2.8 36.6 + - - +
223B LEU 2.9 22.2 + - - -
264B ILE* 3.3 5.5 - - - +
265B THR* 1.3 79.7 + - - +
267B ALA* 1.3 65.2 + - - +
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Residues in contact with ALA 267 (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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91B PHE* 3.5 15.6 - - + -
92B PRO 3.2 10.9 + - - +
93B LEU* 3.4 6.0 - - + -
94B VAL* 2.9 24.4 + - - +
105B THR* 5.0 0.5 - - - +
222B HIS* 3.8 5.9 + - - -
223B LEU* 3.2 22.0 - - + +
264B ILE* 4.5 0.4 - - + -
266B SER* 1.3 79.5 - - - +
268B GLU* 1.3 63.5 + - - +
269B PHE* 4.2 8.3 - - + -
293B LEU* 4.0 17.5 - - + -
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Residues in contact with GLU 268 (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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94B VAL* 3.0 21.9 - - + +
101B ILE* 3.9 6.6 - - - +
102B ALA* 3.2 29.1 + - - +
105B THR* 2.7 28.4 + - - -
222B HIS* 2.8 27.3 + - + +
223B LEU 3.0 5.7 + - - +
224B SER* 2.9 23.6 + - - +
225B LEU* 2.9 27.9 + - - +
267B ALA* 1.3 76.7 - - - +
269B PHE* 1.3 66.5 + - - +
270B VAL* 3.9 13.9 - - + -
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Residues in contact with PHE 269 (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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27B MET* 3.6 14.8 - - - +
93B LEU* 4.1 15.5 - - + -
94B VAL 3.0 7.1 + - - +
95B LEU* 3.8 1.6 - - + -
96B GLY 3.0 22.3 + - - -
223B LEU* 4.2 11.9 - - + -
225B LEU* 3.3 38.1 - - + -
227B LEU* 4.3 13.9 - - + -
255B MET* 4.6 3.4 - - - -
267B ALA* 4.2 7.2 - - + -
268B GLU* 1.3 76.7 - - - +
270B VAL* 1.3 61.2 + - - +
286B ALA* 4.2 7.9 - - + -
289B LEU* 4.1 15.5 - - + -
290B MET* 3.5 49.8 - - + -
293B LEU* 4.0 26.0 - - + -
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Residues in contact with VAL 270 (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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96B GLY* 4.5 1.1 - - - -
97B GLY 3.4 8.3 - - - +
98B ASP 4.3 0.7 - - - +
99B HIS* 3.5 37.5 - - + +
101B ILE* 3.8 36.1 - - + -
225B LEU 2.9 10.1 + - - +
226B ASP* 3.5 22.2 - - + -
227B LEU* 3.2 24.7 + - - +
268B GLU* 4.2 16.6 - - + -
269B PHE* 1.3 77.9 - - - +
271B GLU* 1.3 72.7 + - + +
272B VAL* 3.3 4.8 + - - -
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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