Contacts of the strand formed by residues 277 - 284 (chain A) in PDB entry 2DVI
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 ALA 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A THR* 1.3 71.6 - - - +
278A VAL* 1.3 59.8 + - - +
279A PHE* 4.1 5.3 + - + -
331A PHE 3.5 1.6 - - - +
332A GLU* 3.0 5.9 - - - -
333A CYS* 2.7 47.3 + - + +
335A ILE 3.9 13.2 - - - +
336A LYS* 3.8 22.0 - - + +
385A PRO* 4.1 11.9 - - + -
386A GLU* 4.9 9.6 - - - +
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A VAL* 3.6 37.7 - - + +
276A THR* 3.8 14.1 + - - +
277A ALA* 1.3 75.3 - - - +
279A PHE* 1.3 66.1 + - - +
331A PHE 3.3 9.9 - - - +
332A GLU* 4.0 13.7 - - + +
386A GLU* 5.1 1.2 + - - +
416A SER* 3.8 13.7 + - - -
417A GLY 4.3 2.6 + - - -
420A LEU* 3.7 24.1 - - + +
421A PHE* 5.7 2.7 - - + -
429A LEU* 4.1 24.2 - - + -
432A MET* 4.8 4.5 - - + -
433A MET* 4.7 3.6 - - - -
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Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ALA 4.3 7.9 - - - -
278A VAL* 1.3 79.0 - - - +
280A ALA* 1.3 69.4 + - - +
281A VAL* 4.7 1.1 - - + -
308A LEU* 4.0 9.0 - - + -
330A LEU* 3.8 2.4 - - - +
331A PHE* 3.0 65.0 + + + +
333A CYS* 4.3 8.3 - - - -
385A PRO* 3.5 27.1 - - + -
386A GLU* 3.8 30.1 - - + +
389A VAL* 3.7 35.9 - - + -
414A ILE* 4.2 13.7 - - + -
415A ILE 3.5 12.3 - - - +
416A SER* 4.4 3.1 - - - -
420A LEU* 4.1 5.6 - - - -
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A PHE* 1.3 77.3 - - - +
281A VAL* 1.3 68.0 + - - +
282A LYS 3.8 0.8 + - - +
328A TYR* 4.7 11.0 - - + -
329A LEU 3.2 6.1 - - - +
330A LEU* 3.5 27.4 - - + -
413A GLU 3.5 0.7 - - - +
414A ILE* 3.3 7.3 - - - +
415A ILE* 2.9 35.6 + - + +
420A LEU* 3.7 17.9 - - + -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A PHE* 4.7 3.1 - - + -
280A ALA* 1.3 74.8 - - - +
282A LYS* 1.3 60.8 + - - +
283A PHE* 3.9 13.1 - - + -
304A ILE* 4.4 5.8 - - + -
327A CYS 3.7 0.9 - - - +
328A TYR* 3.5 5.5 - - - -
329A LEU* 2.9 37.2 + - + +
331A PHE* 4.0 21.3 - - + -
389A VAL* 3.8 26.9 - - + -
393A ALA* 5.0 6.7 - - + -
408A ILE* 4.9 7.0 - - + -
412A PHE* 3.9 32.3 - - + -
413A GLU 3.5 2.9 - - - -
414A ILE* 4.8 3.1 - - + +
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Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ALA 3.8 0.6 - - - +
281A VAL* 1.3 74.1 - - - +
283A PHE* 1.3 63.8 + - - +
326A PHE* 3.6 43.0 - - + -
327A CYS 3.6 5.8 - - - +
328A TYR* 3.6 28.1 + - + -
411A TYR* 4.1 15.2 - - - +
412A PHE* 3.1 7.8 - - - +
413A GLU* 2.9 49.4 + - + +
415A ILE* 4.3 19.4 - - + +
423A GLU* 2.9 28.0 + - - +
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Residues in contact with PHE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 3.9 9.6 - - + -
282A LYS* 1.3 80.3 - - - +
284A ARG* 1.3 83.7 + - - +
286A PRO* 4.6 1.3 - - + -
297A LEU* 3.6 11.0 - - + -
326A PHE* 3.3 9.6 - - - +
327A CYS* 3.0 59.1 + - + -
329A LEU* 3.7 24.7 - - + -
404A VAL* 3.5 37.9 - - + -
407A SER* 3.8 8.3 - - - +
408A ILE* 3.6 27.1 - - + -
411A TYR* 3.4 24.9 - - - +
412A PHE* 4.2 0.9 - - + -
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A PHE* 1.3 81.2 - - - +
285A LYS* 1.3 66.2 + - - +
286A PRO* 3.5 1.2 - - - +
325A GLU* 4.0 8.2 + - - +
326A PHE* 3.6 38.9 - - + -
407A SER* 2.6 29.8 + - - +
410A GLU* 5.7 7.2 - - - +
411A TYR* 4.0 21.2 - - + -
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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