Contacts of the helix formed by residues 286 - 294 (chain B) in PDB entry 5DVX
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 ASN 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B GLU 3.5 1.8 + - - -
285B GLU* 1.3 69.4 - - - +
287B SER* 1.3 63.9 + - - +
288B ALA* 3.1 11.6 + - - +
289B TYR* 3.0 41.9 + - + -
290B GLU* 3.0 8.8 + - - +
315B ALA 4.7 4.3 + - - +
349B VAL* 4.8 4.2 - - - +
350B SER 3.1 32.4 + - - +
351B LEU* 4.2 3.0 - - + +
355B GLN* 2.8 37.7 + - - +
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU* 3.5 8.2 + - - -
286B ASN* 1.3 72.8 + - - +
288B ALA* 1.3 65.4 + - - +
290B GLU* 3.4 18.6 + - - +
291B GLN* 3.6 12.4 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASN* 3.1 9.3 + - - +
287B SER* 1.3 82.2 + - - +
289B TYR* 1.3 61.8 - - - +
291B GLN* 3.3 31.6 + - - +
292B LEU* 4.2 0.9 + - - +
311B LEU* 4.1 2.9 - - + +
312B ASP 5.2 1.1 - - - +
315B ALA* 3.5 42.2 - - + +
316B LEU* 3.8 14.5 - - + +
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Residues in contact with TYR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU* 4.3 17.7 - - + -
250B ILE* 3.3 16.1 - - + +
279B LEU* 3.6 34.5 - - + +
286B ASN* 3.0 36.5 + - + +
288B ALA* 1.3 75.5 - - + +
290B GLU* 1.3 61.3 + - - +
292B LEU* 2.9 13.6 + - + +
293B LEU* 2.9 45.3 + - + +
315B ALA 4.6 0.7 - - - -
316B LEU* 2.7 56.4 + - + -
349B VAL* 4.0 13.4 - - + +
351B LEU* 3.9 17.3 - - + -
355B GLN* 4.4 0.4 - - - +
359B LEU* 6.5 0.2 - - + -
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Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU* 3.7 26.1 - - - +
286B ASN 3.0 12.8 + - - +
287B SER* 3.5 13.9 - - - +
288B ALA 3.2 0.2 - - - -
289B TYR* 1.3 78.0 - - - +
291B GLN* 1.3 58.6 + - - +
293B LEU* 3.9 7.1 - - - +
294B SER* 2.8 52.7 + - - -
354B LYS* 6.2 0.2 - - - -
355B GLN* 3.1 27.3 + - - +
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B SER 3.7 8.5 - - - +
288B ALA* 3.4 21.3 - - - +
289B TYR 3.1 0.4 - - - -
290B GLU* 1.3 78.3 - - - +
292B LEU* 1.3 61.3 + - + +
294B SER* 3.5 11.2 + - - -
295B ARG* 3.6 14.2 + - - +
308B VAL* 5.1 2.8 - - - +
309B PRO* 5.1 8.3 + - - +
310B GLY 4.5 5.1 + - - -
311B LEU* 3.6 43.2 - - + +
312B ASP 5.0 1.2 + - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 4.2 24.9 - - + +
204B LEU* 4.3 20.9 - - + -
225B LEU* 4.5 9.4 - - + -
227B LEU* 5.9 8.3 - - + -
288B ALA 4.9 1.8 - - - +
289B TYR* 2.9 13.8 + - + +
291B GLN* 1.3 80.8 - - + +
293B LEU* 1.3 68.6 + - + +
294B SER 3.2 2.2 - - - -
295B ARG* 3.0 15.7 + - - +
296B LEU* 3.5 16.0 + - + +
308B VAL* 4.3 22.9 - - + -
311B LEU* 4.5 16.4 - - + -
316B LEU* 4.0 29.6 - - + -
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU* 5.3 5.2 - - + -
289B TYR* 2.9 24.9 + - + +
290B GLU* 4.3 9.6 - - - +
292B LEU* 1.3 78.0 - - + +
294B SER* 1.3 61.8 + - - +
295B ARG 3.1 1.6 + - - -
296B LEU* 3.2 40.5 + - + +
297B GLU 4.7 0.9 + - - -
351B LEU* 4.1 12.8 - - + -
355B GLN* 3.5 50.0 - - + +
358B THR* 3.8 18.8 - - + +
359B LEU* 4.0 28.5 - - + +
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLU* 2.8 39.6 + - - -
291B GLN* 3.5 11.3 + - - -
293B LEU* 1.3 76.1 - - - +
295B ARG* 1.3 67.4 + - - +
296B LEU 3.5 0.2 - - - -
297B GLU* 4.8 7.3 + - - +
298B GLU* 4.6 2.3 - - - +
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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