Contacts of the helix formed by residues 288 - 296 (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 SER 288 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285O ALA* 5.1 5.2 - - - +
286O PRO* 3.0 26.0 + - - +
287O GLU* 1.3 75.1 - - - +
289O SER* 1.3 59.4 + - - +
290O TYR* 2.8 20.5 + - - +
291O SER* 3.1 22.3 + - - -
346O PHE* 4.5 8.0 - - - -
349O GLY 3.9 3.7 + - - -
350O GLY* 2.9 37.3 - - - -
367O TYR* 5.1 0.7 - - - -
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Residues in contact with SER 289 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285O ALA* 5.6 4.8 + - - +
286O PRO 3.8 11.7 + - - -
288O SER* 1.3 72.7 - - - +
290O TYR* 1.3 61.8 + - - +
291O SER* 3.1 6.3 + - - -
292O SER* 3.7 16.2 + - - -
308O GLY 4.5 14.5 + - - -
310O PHE* 4.8 15.7 - - - -
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Residues in contact with TYR 290 (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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288O SER* 2.8 20.4 - - - -
289O SER* 1.3 74.5 - - - +
291O SER* 1.3 75.0 + - - +
292O SER* 2.7 19.2 + - - -
293O ILE* 3.0 43.7 + - + +
350O GLY* 3.0 34.1 + - - -
351O LYS* 5.1 2.4 + - - -
367O TYR* 4.9 4.4 - + - -
368O LYS* 5.6 4.9 + - - +
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Residues in contact with SER 291 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288O SER 3.4 13.1 + - - -
289O SER* 4.3 4.3 - - - -
290O TYR* 1.3 89.9 - - - +
292O SER* 1.3 66.7 + - - +
293O ILE* 3.1 2.6 + - - +
294O SER* 2.9 24.1 + - - -
295O GLU 4.4 0.3 + - - -
310O PHE* 5.1 9.7 - - - +
322O MET* 4.5 18.1 - - - +
346O PHE* 5.8 2.8 - - - -
367O TYR* 4.2 28.0 - - - -
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Residues in contact with SER 292 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289O SER 3.7 13.0 + - - -
290O TYR* 2.7 8.0 + - - -
291O SER* 1.3 74.3 + - - +
293O ILE* 1.3 52.7 + - - -
295O GLU 2.6 45.2 + - - -
296O ALA* 3.6 19.5 - - - +
310O PHE* 5.2 13.2 - - - -
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Residues in contact with ILE 293 (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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290O TYR* 3.0 40.9 + - + +
291O SER 4.4 1.3 - - - +
292O SER* 1.3 74.3 - - - +
294O SER* 1.3 63.3 + - - +
295O GLU 3.4 0.5 + - - -
296O ALA* 4.0 13.4 + - - +
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Residues in contact with SER 294 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291O SER* 2.9 17.9 + - - -
292O SER 2.7 4.9 + - - -
293O ILE* 1.3 78.1 - - - +
295O GLU* 1.3 66.2 + - - +
332O MET* 5.0 12.9 - - - +
367O TYR* 4.0 25.8 + - - +
369O ASN* 5.4 3.8 - - - -
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Residues in contact with GLU 295 (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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291O SER 4.4 0.2 + - - -
292O SER* 2.6 18.5 + - - +
293O ILE 4.2 0.2 - - - -
294O SER* 1.3 79.8 + - - +
296O ALA* 1.3 57.3 + - - +
297O THR 3.7 4.1 - - - +
331O LEU* 3.5 36.3 - - + +
332O MET* 5.2 4.7 - - - +
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Residues in contact with ALA 296 (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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292O SER* 3.2 33.8 + - - +
293O ILE* 4.0 11.6 + - - +
295O GLU* 1.3 72.3 - - - +
297O THR* 1.3 66.8 + - - +
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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
------------------------------------------------------------
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