Contacts of the strand formed by residues 261 - 267 (chain B) in PDB entry 2V90
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 PHE 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B LEU* 4.3 0.7 - - + -
259B PHE* 3.9 24.2 - + + +
260B GLY* 1.3 78.8 - - - +
262B LEU* 1.3 66.6 + - - +
263B LEU* 3.9 26.4 + - + -
277B LEU* 3.9 27.1 - - + -
279B GLU 3.3 13.5 - - - +
280B VAL* 4.4 2.7 - - - -
281B ASP* 4.1 4.4 + - - -
286B ALA* 3.8 14.1 - - + -
291B MET* 3.8 11.4 - - + -
297B LEU* 5.3 0.7 - - + -
317B ILE* 4.3 22.9 - - + -
326B LEU* 3.7 32.3 - - + -
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Residues in contact with LEU 262 (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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261B PHE* 1.3 73.7 - - - +
263B LEU* 1.3 65.1 + - - +
264B ARG* 4.5 18.6 - - + +
277B LEU* 3.4 5.4 - - - -
278B TRP* 2.8 48.6 + - + -
279B GLU* 2.9 39.5 + - + +
281B ASP* 5.6 0.8 + - - -
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PHE* 3.9 16.0 + - + -
262B LEU* 1.3 81.2 - - - +
264B ARG* 1.3 61.3 + - - +
275B GLN* 3.9 22.2 - - + +
276B PHE 3.3 17.3 - - - +
277B LEU* 4.2 10.8 - - + -
297B LEU* 4.0 16.8 - - + -
310B HIS* 3.3 24.9 + - + +
313B THR* 3.9 25.8 - - + -
314B VAL* 4.0 20.9 - - + -
317B ILE* 4.0 14.1 - - + -
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Residues in contact with ARG 264 (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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262B LEU* 4.0 17.5 + - + +
263B LEU* 1.3 75.8 - - - +
265B GLU* 1.3 72.9 + - - +
266B GLU* 4.2 4.3 - - - -
275B GLN* 3.6 4.9 - - - -
276B PHE* 2.7 42.1 + - - +
278B TRP* 3.6 59.6 - - + +
310B HIS* 4.5 1.3 - - - -
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Residues in contact with GLU 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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264B ARG* 1.3 83.8 - - - +
266B GLU* 1.3 75.9 + - - +
267B LYS* 3.7 25.7 - - + +
273B PRO* 3.6 20.0 - - + +
274B GLY 3.1 12.6 - - - +
275B GLN* 2.9 31.0 + - - +
309B GLY* 3.7 1.7 - - - -
310B HIS* 3.1 29.0 + - + +
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Residues in contact with GLU 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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264B ARG* 3.8 7.1 + - - -
265B GLU* 1.3 80.4 - - - +
267B LYS* 1.3 69.6 + - - +
268B GLY 3.9 0.5 + - - -
274B GLY* 2.8 32.3 + - - +
276B PHE* 3.6 17.6 - - + -
278B TRP* 3.1 42.7 - - + -
1341B SO4 4.6 6.7 + - - +
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Residues in contact with LYS 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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265B GLU* 3.7 26.2 - - + +
266B GLU* 1.3 80.9 + - - +
268B GLY* 1.3 72.2 + - - +
271B GLY* 3.4 27.6 + - - +
272B ARG 3.4 2.9 - - - -
273B PRO* 4.2 10.3 - - + -
1341B SO4 4.4 5.4 + - - -
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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