Contacts of the strand formed by residues 280 - 287 (chain A) in PDB entry 5HVO
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 LYS 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A GLY 4.2 0.6 + - - -
279A THR* 1.3 71.8 - - - +
281A LEU* 1.3 61.4 + - - +
282A MET* 5.6 0.9 - - + -
311A TRP* 3.8 25.3 - - + -
314A LYS 2.9 12.9 + - - +
315A VAL* 3.4 6.3 - - + +
316A VAL 3.0 25.5 + - - -
377A ASP* 3.6 34.3 - - + -
440A VAL* 3.0 47.3 + - + +
447A ARG* 4.3 14.4 - - - +
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Residues in contact with LEU 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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272A LEU* 5.1 3.6 - - + +
276A PHE* 3.8 48.9 - - + -
279A THR 3.5 4.2 + - - +
280A LYS* 1.3 73.4 - - - +
282A MET* 1.3 62.2 + - - +
316A VAL* 3.7 10.3 - - + +
318A VAL* 3.7 29.4 - - + -
372A LEU* 4.8 10.1 - - + -
375A ALA* 3.9 32.8 - - + +
376A SER* 3.7 11.8 - - - +
377A ASP* 2.9 37.2 + - - +
378A ALA 3.3 4.9 + - - -
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Residues in contact with MET 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 LYS* 4.9 1.3 - - + +
281A LEU* 1.3 76.8 - - - +
283A VAL* 1.3 57.7 + - - +
301A LEU* 5.6 5.4 - - - -
304A PHE* 5.9 0.4 - - - -
315A VAL* 4.1 24.2 - - + -
316A VAL 2.8 14.6 + - - +
317A LEU* 3.3 18.6 - - + +
318A VAL* 2.6 34.8 + - - +
376A SER* 4.5 0.7 - - - -
377A ASP* 6.2 0.2 - - + -
378A ALA* 3.5 28.9 - - + +
380A VAL* 3.5 22.2 - - + -
407A ILE* 3.9 7.9 - - + -
436A TYR* 3.5 42.6 - - + +
439A ALA* 4.6 2.7 - - + -
440A VAL* 4.4 12.3 - - + -
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Residues in contact with VAL 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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282A MET* 1.3 73.9 - - - +
284A SER* 1.3 66.0 + - - +
285A VAL* 4.1 16.8 - - + -
317A LEU* 4.3 1.1 - - - -
318A VAL* 3.4 6.1 - - - +
372A LEU* 3.7 34.1 - - + -
373A TYR* 4.3 10.8 - - + -
376A SER* 3.1 25.8 + - - +
378A ALA 2.9 18.6 + - - +
379A CYS* 3.4 16.8 - - + -
380A VAL* 3.0 25.8 + - - +
395A TYR* 4.2 9.2 - - + -
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Residues in contact with SER 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 VAL* 1.3 75.0 + - - +
285A VAL* 1.3 60.0 + - - +
286A ASP* 3.7 0.4 - - - -
297A LYS* 3.3 22.0 + - - +
317A LEU* 3.6 5.9 - - - +
318A VAL 2.7 13.0 + - - +
319A GLN* 3.1 28.3 - - - -
320A VAL* 2.7 31.9 + - - +
379A CYS* 5.3 1.8 - - - -
380A VAL* 3.0 26.2 + - - +
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Residues in contact with VAL 285 (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 VAL* 4.1 10.8 - - + -
284A SER* 1.3 78.8 - - - +
286A ASP* 1.3 67.5 + - - +
320A VAL* 3.6 22.0 - - + +
322A VAL* 4.5 3.4 - - + -
369A LEU* 3.8 12.6 - - + -
372A LEU* 5.0 1.6 - - + -
373A TYR* 3.7 34.1 - - + +
379A CYS* 5.8 0.2 - - - -
380A VAL 5.2 0.6 + - - -
391A VAL* 3.3 35.0 - - + +
501A UDP 3.7 36.8 - - + -
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Residues in contact with ASP 286 (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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284A SER* 3.7 0.3 - - - -
285A VAL* 1.3 83.4 + - - +
287A ARG* 1.3 71.2 + - - +
292A LYS* 3.7 37.7 - - + +
294A ILE* 4.5 4.4 - - + +
297A LYS* 2.9 24.6 + - - -
319A GLN* 2.8 25.3 + - - +
320A VAL 2.9 9.2 + - - +
321A ALA* 3.3 3.5 - - - -
322A VAL* 2.9 21.9 + - - -
380A VAL 4.9 0.8 - - - +
381A VAL* 5.1 8.0 - - - +
382A SER 5.1 0.5 + - - -
383A SER* 4.8 3.1 + - - -
389A ASN* 4.8 6.2 + - - -
391A VAL* 5.4 1.1 - - - -
501A UDP 6.4 1.1 - - - -
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Residues in contact with ARG 287 (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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105A TRP* 3.3 30.9 - - - -
286A ASP* 1.3 78.6 - - - +
288A LEU* 1.3 59.0 + - - +
289A ASP* 2.8 36.1 + - + +
292A LYS* 3.6 24.0 - - - +
294A ILE* 4.4 0.7 - - - +
322A VAL* 3.0 35.3 - - + +
324A SER* 3.3 28.5 + - - -
325A ARG* 4.2 8.8 - - - +
331A TYR* 4.4 0.4 + - - -
501A UDP 2.7 46.4 + - - +
502A VDM 3.8 23.4 - - - +
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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