Contacts of the strand formed by residues 261 - 267 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337D THR 3.9 0.2 - - - +
338D SER* 3.5 5.3 + - - -
339D VAL* 2.9 55.2 + - + +
252F LEU* 4.5 0.9 - - + -
259F PHE* 3.7 14.6 - + + -
260F GLY* 1.3 80.3 - - - +
262F LEU* 1.3 60.1 + - - +
263F LEU* 4.1 19.7 - - + -
277F LEU* 3.3 42.2 - - + -
279F GLU 3.4 13.7 - - - +
280F VAL* 4.4 3.6 - - + +
281F ASP* 3.8 4.1 + - - -
286F ALA* 3.7 18.6 - - + -
291F MET* 5.1 0.2 - - - -
297F LEU* 5.1 2.5 - - + -
317F ILE* 4.3 17.0 - - + -
326F LEU* 3.7 32.3 - - + -
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Residues in contact with LEU 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B PRO* 3.7 25.6 - - + +
283B GLY* 3.6 32.1 - - - +
336D GLU* 3.5 23.1 - - + +
337D THR 3.6 18.4 - - - +
338D SER* 3.8 5.2 - - - +
261F PHE* 1.3 73.8 - - - +
263F LEU* 1.3 57.6 + - - +
277F LEU* 3.5 4.7 - - - -
278F TRP* 2.8 55.4 + - + +
279F GLU* 3.0 26.2 + - + +
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Residues in contact with LEU 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D GLU* 3.1 3.2 - - - +
337D THR* 2.8 38.2 + - - +
339D VAL* 5.4 2.5 - - + -
261F PHE* 3.9 11.2 - - + -
262F LEU* 1.3 71.4 - - - +
264F ARG* 1.3 59.3 + - - +
275F GLN* 3.7 33.2 - - + +
276F PHE 3.3 15.3 - - - +
277F LEU* 3.7 21.3 - - + -
297F LEU* 4.2 9.2 - - + -
310F HIS* 3.2 14.9 - - + +
313F THR* 4.0 25.6 - - + -
314F VAL* 4.4 9.0 - - + -
317F ILE* 4.2 15.0 - - + -
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Residues in contact with ARG 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B PRO* 5.7 0.2 - - - +
293D ALA* 4.0 25.0 + - - +
294D GLY* 4.0 1.7 - - - -
331D PRO* 4.0 27.1 - - - +
332D GLU 4.9 6.9 + - - -
333D ALA* 5.2 3.8 - - - +
335D ARG 3.3 10.7 + - - +
336D GLU* 2.7 43.1 + - + +
263F LEU* 1.3 76.8 - - - +
265F GLU* 1.3 68.9 + - - +
266F GLU* 3.7 8.2 + - - -
275F GLN* 4.1 3.4 - - - -
276F PHE* 3.0 32.6 + - - +
278F TRP* 3.4 59.3 - - + +
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Residues in contact with GLU 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D PRO* 5.1 5.5 - - - +
332D GLU* 4.9 0.2 - - - +
335D ARG* 2.7 59.4 + - + +
264F ARG* 1.3 78.5 - - - +
266F GLU* 1.3 77.7 + - - +
267F LYS* 4.4 10.2 - - + +
273F PRO* 3.5 26.2 - - + +
274F GLY 3.2 5.6 - - - +
275F GLN* 3.0 21.1 + - - +
309F GLY* 3.7 2.9 - - - -
310F HIS* 2.9 32.5 + - + +
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Residues in contact with GLU 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D PHE* 3.4 34.5 - - + -
294D GLY* 2.5 42.4 - - - +
296D ARG* 5.0 2.3 - - - +
331D PRO* 4.2 8.8 - - - +
264F ARG* 3.7 6.3 + - - -
265F GLU* 1.3 80.9 - - - +
267F LYS* 1.3 65.8 + - - +
268F GLY 3.7 0.5 + - - -
274F GLY* 2.9 30.6 + - - +
276F PHE* 3.7 16.5 - - + -
278F TRP* 3.5 31.0 - - + -
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Residues in contact with LYS 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D PHE* 4.0 15.1 - - - -
296D ARG* 3.8 11.6 + - - +
332D GLU* 4.7 8.5 - - - +
335D ARG* 4.4 11.0 - - - +
265F GLU* 4.4 14.8 - - - +
266F GLU* 1.3 77.7 + - - +
268F GLY* 1.3 69.1 + - - +
271F GLY* 3.9 25.5 + - - +
272F ARG 3.5 4.7 - - - -
273F PRO* 3.9 14.3 - - + +
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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