Contacts of the strand formed by residues 275 - 281 (chain F) in PDB entry 3NVQ
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 275 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223F LEU* 3.9 23.6 - - + -
265F ALA* 4.7 0.7 - - + -
266F ARG 3.7 3.6 - - - -
267F ILE* 3.4 23.2 - - + +
273F VAL* 3.9 4.8 + - - +
274F LEU* 1.3 81.0 - - - +
276F GLN* 1.3 62.0 + - - +
277F GLY* 3.1 39.9 - - - -
278F GLN* 4.0 6.7 - - + -
342F ARG* 3.2 32.8 + - + -
343F VAL 3.6 22.0 - - - -
347F PHE* 3.9 33.2 - + + -
348F LYS 5.2 1.1 - - - +
349F THR* 4.1 21.8 - - + -
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Residues in contact with GLN 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F GLY 5.5 0.4 + - - -
243F SER* 2.7 24.0 + - - -
266F ARG* 2.9 60.3 + - - +
267F ILE 3.3 2.8 - - - -
268F ALA* 3.2 32.3 + - + +
274F LEU* 3.3 18.6 - - + +
275F PHE* 1.3 74.8 - - - +
277F GLY* 1.3 59.1 + - - +
340F ALA 3.3 12.3 - - - +
341F LYS* 4.7 0.2 - - - -
342F ARG* 3.8 37.3 + - - +
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Residues in contact with GLY 277 (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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265F ALA* 3.6 0.7 - - - -
266F ARG* 3.0 25.1 + - - -
275F PHE* 3.1 22.0 - - - -
276F GLN* 1.3 81.1 - - - +
278F GLN* 1.3 60.4 + - - -
340F ALA* 3.6 12.1 - - - -
341F LYS 3.2 20.0 - - - -
342F ARG 3.9 0.2 - - - -
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Residues in contact with GLN 278 (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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248F TYR* 3.3 15.7 + - - +
263F SER* 4.3 10.3 + - - -
264F MET 3.5 9.2 - - - +
275F PHE* 4.0 11.0 - - + -
277F GLY* 1.3 75.4 - - - +
279F ALA* 1.3 65.8 + - - +
280F SER* 5.3 0.6 + - - -
339F ARG 4.0 2.1 - - - +
340F ALA* 3.3 11.5 - - - +
341F LYS 3.2 12.8 + - - +
343F VAL* 4.5 8.2 - - + +
345F TRP* 3.5 11.7 + - - +
346F ASP* 2.6 50.0 + - - +
347F PHE* 4.2 8.0 - - + -
360F PRO* 3.4 36.8 - - - +
361F GLU 4.8 0.3 + - - -
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Residues in contact with ALA 279 (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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263F SER* 3.0 6.6 - - - -
264F MET* 3.0 34.0 + - + +
278F GLN* 1.3 78.9 - - - +
280F SER* 1.3 61.7 + - - +
281F LEU* 4.2 3.9 - - + +
336F ILE* 4.5 7.6 - - + +
339F ARG 3.8 7.2 - - - +
340F ALA* 3.7 23.1 - - + +
360F PRO* 4.7 2.5 - - - -
361F GLU 3.7 8.7 - - - +
363F VAL* 4.1 16.4 - - + -
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Residues in contact with SER 280 (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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261F TRP* 3.3 43.2 - - - +
262F PRO 3.5 6.1 - - - -
263F SER* 3.7 7.8 + - - -
278F GLN* 5.3 0.9 + - - -
279F ALA* 1.3 75.4 - - - +
281F LEU* 1.3 57.0 + - - +
360F PRO* 4.0 17.1 + - - +
361F GLU 3.0 12.0 + - - -
362F ARG* 3.9 7.6 - - - -
363F VAL* 2.8 34.9 + - - +
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Residues in contact with LEU 281 (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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261F TRP* 5.0 3.4 - - - +
262F PRO* 2.8 33.0 + - + +
263F SER* 3.8 25.6 - - - +
264F MET* 4.2 13.9 - - + -
279F ALA* 4.2 6.7 - - + +
280F SER* 1.3 81.0 - - - +
282F ASP* 1.3 62.1 + - - +
283F CYS 3.7 2.3 + - - -
291F ARG 5.3 0.5 - - - +
294F LEU* 5.5 2.7 - - + -
306F TRP* 4.1 22.9 - - + -
310F PHE* 4.2 14.1 - - + -
331F PHE* 3.8 33.2 - - + -
336F ILE* 4.0 20.4 - - + -
362F ARG* 5.8 0.2 - - - -
363F VAL* 3.9 9.6 - - + -
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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