Contacts of the strand formed by residues 273 - 280 (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 PRO 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B GLU* 3.6 31.4 - - + +
266B GLU 3.8 4.3 - - - +
267B LYS* 4.2 9.0 - - + -
271B GLY 3.4 6.7 - - - +
272B ARG* 1.3 93.1 - - + +
274B GLY* 1.3 58.1 + - - +
307B GLY* 3.6 34.2 + - - +
308B LEU 3.5 21.6 - - - +
309B GLY* 4.0 4.9 - - - +
307C GLY 5.5 3.6 - - - +
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Residues in contact with GLY 274 (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* 3.1 5.5 - - - -
266B GLU 2.8 36.7 + - - -
272B ARG 3.8 0.4 + - - -
273B PRO* 1.3 74.1 - - - +
275B GLN* 1.3 66.1 + - - -
276B PHE* 3.8 13.7 - - - -
296B ARG* 4.2 13.9 - - - -
305B VAL 6.0 1.1 - - - -
307B GLY 5.7 0.9 - - - -
308B LEU 5.0 0.2 - - - -
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Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.9 18.3 - - + +
264B ARG 3.6 1.5 - - - -
265B GLU* 2.9 37.3 + - - +
273B PRO* 4.2 0.6 - - - +
274B GLY* 1.3 81.9 + - - -
276B PHE* 1.3 62.3 + - - +
296B ARG* 3.8 6.4 - - - +
297B LEU* 3.0 37.0 + - + +
305B VAL 5.2 4.7 + - - +
308B LEU 3.2 21.0 + - - +
310B HIS* 3.0 39.2 + - - +
313B THR* 3.5 28.3 - - + +
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Residues in contact with PHE 276 (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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263B LEU* 3.3 6.6 - - - -
264B ARG* 2.7 46.2 + - - +
266B GLU* 3.6 35.0 - - + -
274B GLY* 3.8 20.4 - - - -
275B GLN* 1.3 75.1 - - - +
277B LEU* 1.3 61.8 + - - +
278B TRP* 3.0 23.4 + + + -
294B GLY* 4.4 10.5 - - - +
295B ASP 3.4 4.3 - - - +
296B ARG* 3.6 58.6 - - + -
1341B SO4 4.1 10.5 - - - -
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Residues in contact with LEU 277 (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* 3.9 19.7 - - + -
262B LEU 3.4 6.3 - - - +
263B LEU* 4.2 6.3 - - + +
276B PHE* 1.3 69.9 - - - +
278B TRP* 1.3 60.6 + - - +
279B GLU 3.3 1.6 - - - +
280B VAL* 4.1 21.1 - - + -
291B MET* 3.1 40.8 - - + -
292B GLN 4.1 3.8 - - - +
293B ALA* 3.5 0.9 - - - -
294B GLY* 2.7 33.3 + - - -
295B ASP* 2.7 35.9 + - + +
297B LEU* 3.9 28.7 - - + +
328B VAL* 4.3 6.5 - - + -
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Residues in contact with TRP 278 (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* 2.8 27.5 + - + +
264B ARG* 3.6 46.8 - - + +
266B GLU* 3.1 43.3 - - + -
276B PHE* 3.0 24.5 + + + -
277B LEU* 1.3 74.4 - - - +
279B GLU* 1.3 88.5 + - - +
293B ALA* 3.6 11.5 - - - +
294B GLY* 4.4 2.5 + - - +
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Residues in contact with GLU 279 (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* 3.3 6.9 - - - +
262B LEU* 2.9 49.6 + - + +
277B LEU 4.7 0.2 - - - -
278B TRP* 1.3 102.6 + - - +
280B VAL* 1.3 62.4 + - - +
281B ASP* 4.2 7.9 - - - +
293B ALA* 4.2 6.1 - - + -
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Residues in contact with VAL 280 (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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260B GLY 3.6 2.7 - - - -
261B PHE* 4.5 1.1 - - + -
277B LEU* 4.1 20.0 - - + -
279B GLU* 1.3 78.2 - - - +
281B ASP* 1.3 64.9 + - - +
282B PRO* 3.6 5.9 - - - +
286B ALA* 3.9 12.6 - - + -
287B LYS* 3.4 44.9 + - + +
291B MET 3.6 15.9 - - - +
292B GLN 3.6 8.5 - - - +
293B ALA* 3.4 33.0 - - + +
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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