Contacts of the helix formed by residues 284 - 292 (chain B) in PDB entry 5DQ8
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 GLY 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B PRO* 3.1 32.4 + - - -
280B GLU* 5.4 1.1 - - - -
281B LYS 2.7 18.0 + - - -
282B LYS 3.2 1.4 + - - -
283B GLY* 1.3 75.3 - - - -
285B LEU* 1.3 64.7 + - - -
286B ARG 3.3 2.7 - - - -
287B GLU* 3.3 5.3 + - - +
288B LEU* 3.1 21.7 + - - +
409B LEU* 5.2 0.4 - - - -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B VAL* 3.8 15.5 - - + -
274B ILE* 3.7 39.0 - - + +
275B TYR* 4.0 17.1 + - + -
278B PHE* 3.7 28.8 - - + +
279B PRO 4.3 2.6 + - - -
284B GLY* 1.3 69.7 - - - -
286B ARG* 1.3 67.3 + - - +
288B LEU* 3.7 3.7 - - + +
289B TYR* 2.8 27.2 + - - +
297B PHE* 4.0 29.4 - - + -
409B LEU* 4.3 21.5 - - + +
423B CYS* 4.5 1.8 - - - -
425B ALA* 5.0 1.8 - - + -
444B LEU* 4.8 6.7 - - + -
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Residues in contact with ARG 286 (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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275B TYR* 3.4 57.0 - - + +
280B GLU* 5.8 9.0 - - - +
284B GLY 3.3 0.8 - - - -
285B LEU* 1.3 77.8 - - - +
287B GLU* 1.3 61.7 + - - +
289B TYR* 3.8 1.0 - - - +
290B ASP* 2.7 45.1 + - - +
446B ARG* 4.7 0.9 - - - +
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Residues in contact with GLU 287 (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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281B LYS 4.0 14.8 + - - +
282B LYS* 3.3 38.4 - - - +
283B GLY 3.9 8.8 + - - -
284B GLY 3.3 6.7 + - - +
285B LEU 3.2 0.4 - - - -
286B ARG* 1.3 76.9 - - - +
288B LEU* 1.3 76.8 + - - +
290B ASP* 3.2 9.7 + - + +
291B ARG* 3.1 27.1 + - + +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLY* 3.9 24.7 - - - +
284B GLY 3.1 19.7 + - - +
285B LEU* 3.7 5.6 - - - +
287B GLU* 1.3 84.2 - - - +
289B TYR* 1.3 62.5 + - - +
291B ARG* 3.2 35.3 + - - +
292B GLY 2.9 19.2 + - - +
297B PHE* 3.5 18.0 - - + -
409B LEU* 4.2 9.4 - - + -
411B VAL* 4.0 32.1 - - + -
420B LEU* 4.8 6.6 - - + +
423B CYS* 4.3 8.3 - - - -
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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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271B VAL* 4.2 22.0 - - + -
275B TYR* 5.0 1.3 - - - +
285B LEU 2.8 22.1 + - - +
286B ARG* 3.8 3.8 - - - +
288B LEU* 1.3 72.5 - - - +
290B ASP* 1.3 62.6 + - - +
292B GLY* 3.2 13.5 + - - -
294B PRO* 3.6 36.0 + - + +
297B PHE* 3.7 37.6 - + + -
444B LEU 3.2 30.7 + - - -
445B VAL* 3.4 11.3 - - - -
446B ARG* 3.4 51.7 + - + +
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Residues in contact with ASP 290 (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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286B ARG* 2.7 33.2 + - - +
287B GLU* 3.5 11.9 - - + +
288B LEU 3.2 0.2 - - - -
289B TYR* 1.3 74.0 - - - +
291B ARG* 1.3 64.8 + - - +
292B GLY* 4.5 0.2 - - - -
446B ARG* 2.9 30.0 + - - +
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Residues in contact with ARG 291 (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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287B GLU* 3.1 21.1 + - - +
288B LEU* 3.2 34.4 + - - +
290B ASP* 1.3 77.2 - - - +
292B GLY* 1.3 67.3 + - - +
411B VAL* 5.0 1.8 - - - +
413B THR* 4.5 11.7 - - - +
418B GLN* 2.8 30.1 + - - +
419B GLU 4.4 0.2 - - - -
420B LEU* 3.9 22.7 - - - +
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Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU 2.9 11.1 + - - +
289B TYR 3.2 12.5 + - - -
290B ASP 4.4 0.2 - - - -
291B ARG* 1.3 91.7 - - - +
293B PRO* 1.3 76.2 - - - +
294B PRO* 3.7 4.0 - - - -
297B PHE* 4.5 1.3 - - - -
420B LEU* 3.6 21.8 + - - +
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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
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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