Contacts of the helix formed by residues 286 - 292 (chain B) in PDB entry 5M64
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 ARG 286 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B ASP* 1.3 74.1 - - - +
287B GLU* 1.3 53.0 + - - +
288B ILE 3.1 1.2 + - - -
289B PHE* 3.2 39.4 + - - +
290B ASP* 2.6 39.6 + - - +
2I SER* 4.7 13.3 - - - +
4I VAL* 4.8 6.9 - - - +
9I PHE* 3.4 61.3 - - + +
10I CYS 5.7 2.0 - - - +
14I GLY* 4.7 3.6 + - - -
15I ASP* 5.4 2.9 - - - +
27M PHE* 3.5 38.4 - - + +
28M LYS* 3.3 43.5 + - - +
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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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283B THR* 3.6 26.9 - - + +
285B ASP* 3.0 27.3 + - - +
286B ARG* 1.3 77.2 - - - +
288B ILE* 1.3 58.1 + - + +
290B ASP* 4.0 13.8 - - - +
291B GLY* 2.8 24.1 + - - -
375B LEU* 5.8 0.2 - - - +
577B PHE* 5.8 8.4 - - + -
25M SER 5.1 0.3 - - - +
26M PHE 3.7 15.2 - - - +
27M PHE* 4.5 1.9 - - + +
97M VAL* 4.8 5.0 - - - +
98M SER 3.4 11.8 - - - +
99M LYS* 3.3 31.6 + - - +
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Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 6.2 2.9 - - + -
277B LEU* 4.1 26.0 - - + -
278B LYS* 5.1 9.0 - - + -
283B THR* 4.3 21.1 - - - +
284B SER* 5.0 4.7 - - - -
285B ASP* 3.9 14.8 - - - +
286B ARG 3.1 0.8 - - - -
287B GLU* 1.3 75.6 - - + +
289B PHE* 1.3 66.0 + - - +
291B GLY* 3.1 3.7 + - - -
292B ILE* 3.1 28.2 + - + +
306B LEU* 5.4 5.2 - - + -
310B LEU* 6.0 6.1 - - + -
375B LEU* 4.5 18.1 - - + +
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Residues in contact with PHE 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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285B ASP 4.6 0.2 + - - -
286B ARG* 3.2 51.5 + - - +
288B ILE* 1.3 79.8 - - - +
290B ASP* 1.3 61.0 + - - +
292B ILE* 3.3 23.6 - - - +
293B ILE 5.1 3.1 - - - +
294B GLY* 5.7 4.1 - - - -
297B VAL* 5.0 15.9 - - + -
302B LEU* 3.7 26.7 - - + -
303B THR* 5.9 3.6 - - - -
306B LEU* 3.6 35.2 - - + -
4I VAL* 4.2 26.5 - - + -
9I PHE* 4.2 13.0 - + + -
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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* 2.6 25.7 + - - +
287B GLU* 4.0 11.4 - - - +
289B PHE* 1.3 73.4 - - - +
291B GLY* 1.3 60.5 + - - +
292B ILE 2.9 15.4 - - - +
294B GLY* 5.2 1.8 + - - -
577B PHE* 3.0 61.2 - - - +
27M PHE* 5.3 2.4 - - + -
28M LYS* 3.2 39.1 - - + +
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Residues in contact with GLY 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 2.8 19.9 + - - -
288B ILE 3.1 2.4 + - - -
290B ASP* 1.3 75.1 + - - +
292B ILE* 1.3 63.4 + - - +
293B ILE 3.8 0.5 + - - -
375B LEU* 3.3 24.2 - - - +
577B PHE* 5.7 4.0 - - - -
578B ALA 4.0 14.0 - - - +
579B ALA* 4.2 3.5 - - - +
595B TRP* 5.4 3.1 - - - -
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Residues in contact with ILE 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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288B ILE* 3.1 16.1 + - + +
289B PHE 3.3 13.5 - - - +
290B ASP 2.9 16.8 - - - +
291B GLY* 1.3 76.3 - - - +
293B ILE* 1.3 70.5 + - - +
294B GLY* 3.1 3.8 + - - -
302B LEU* 3.6 29.2 - - + -
306B LEU* 3.7 20.4 - - + -
375B LEU* 3.6 32.8 - - + -
378B ILE* 5.7 1.3 - - + -
379B ARG* 3.3 40.8 - - - +
382B TYR* 5.8 0.4 - - + -
578B ALA* 5.0 1.9 - - - -
579B ALA* 4.4 0.4 - - - +
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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