Contacts of the strand formed by residues 310 - 315 (chain O) in PDB entry 1VYH
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 310 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284O TRP* 3.5 6.8 - - - +
285O ALA* 2.6 55.3 + - + +
289O SER* 4.8 22.2 - - - -
291O SER* 5.1 9.6 - - - +
292O SER* 5.2 13.5 - - - -
308O GLY* 3.1 33.4 - - - -
309O PRO* 1.3 72.4 - - - +
311O LEU* 1.3 56.7 + - - +
312O LEU* 5.6 0.7 - - - -
322O MET* 4.1 13.9 - - + -
323O TRP 3.0 4.3 - - - +
324O ASP* 2.8 35.9 - - + -
326O SER* 5.1 0.2 - - - -
331O LEU* 3.4 29.8 - - + -
346O PHE* 5.9 0.2 - - + -
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Residues in contact with LEU 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250O ALA* 3.4 32.5 - - + -
258O VAL* 4.5 6.5 - - + -
260O VAL* 4.5 7.6 - - + -
272O LEU* 3.6 31.6 - - + -
282O ILE* 4.1 17.7 - - + -
283O SER 3.3 13.0 - - - +
284O TRP* 3.8 26.9 - - + +
285O ALA 4.6 0.4 - - - +
309O PRO 4.3 0.4 + - - -
310O PHE* 1.3 74.5 - - - +
312O LEU* 1.3 65.4 + - - +
323O TRP* 2.7 56.8 + - + +
325O VAL* 4.9 6.1 - - + -
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Residues in contact with LEU 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282O ILE* 3.1 30.9 - - - +
283O SER 3.0 8.8 + - - +
311O LEU* 1.3 77.4 - - - +
313O SER* 1.3 61.4 + - - +
314O GLY 4.3 0.2 - - - -
320O ILE* 4.4 7.2 - - + -
321O LYS 2.8 8.7 - - - +
322O MET* 3.3 41.5 - - + -
334O LEU* 5.9 0.9 - - + -
344O VAL* 3.5 30.1 - - + -
345O LEU 4.2 0.9 - - - +
346O PHE* 3.5 33.9 - - + -
353O ILE* 3.6 35.9 - - + -
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Residues in contact with SER 313 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258O VAL* 3.8 27.8 - - - -
275O HIS* 3.3 18.9 + - - -
279O VAL* 4.0 5.4 - - - -
281O CYS 3.5 5.8 - - - -
282O ILE* 4.2 2.5 - - - -
311O LEU* 5.8 0.2 - - - -
312O LEU* 1.3 75.7 - - - +
314O GLY* 1.3 60.1 + - - +
320O ILE* 3.3 6.0 - - - -
321O LYS 2.7 34.1 + - - -
323O TRP* 2.4 37.7 + - - -
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Residues in contact with GLY 314 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279O VAL* 3.1 5.7 - - - +
280O GLU* 2.7 31.7 + - - -
281O CYS* 3.1 25.8 + - - +
313O SER* 1.3 72.8 - - - +
315O SER* 1.3 53.8 + - - -
319O THR 3.7 8.1 - - - -
320O ILE* 3.7 14.0 - - - +
341O VAL* 4.5 7.4 - - - -
344O VAL* 4.1 3.1 - - - +
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Residues in contact with SER 315 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275O HIS* 3.0 26.4 + - - -
277O HIS 3.8 9.2 - - - -
278O VAL 3.2 15.3 - - - -
279O VAL* 3.8 3.8 - - - +
280O GLU* 4.2 2.2 - - - +
314O GLY* 1.3 73.7 - - - -
316O ARG* 1.3 65.4 + - - +
317O ASP* 3.1 6.8 + - - -
318O LYS 4.5 0.2 + - - -
319O THR* 3.0 31.9 + - - -
340O TRP* 4.3 0.2 - - - -
341O VAL* 3.4 30.9 + - - +
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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