Contacts of the helix formed by residues 284 - 292 (chain A) in PDB entry 5EMV
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A PHE* 5.3 1.1 - - - -
279A PRO* 2.8 30.7 - - - -
280A GLU 4.9 1.6 - - - -
281A LYS 4.8 3.4 - - - -
282A LYS* 2.9 5.6 - - - +
283A GLY* 1.3 83.4 - - - +
285A LEU* 1.3 67.1 + - - -
286A ARG* 3.2 3.1 - - - -
287A GLU* 3.5 6.3 + - - +
288A LEU* 3.3 20.2 + - - +
409A LEU* 5.5 0.2 - - - -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A VAL* 3.7 27.8 - - + +
274A ILE* 3.8 32.8 - - + +
275A TYR* 4.3 10.7 + - + +
278A PHE* 4.0 30.2 - - + +
279A PRO 4.0 3.2 + - - -
284A GLY* 1.3 72.2 - - - -
286A ARG* 1.3 62.7 + - - +
288A LEU* 3.4 4.8 + - + -
289A TYR* 3.0 24.4 + - - +
297A PHE* 4.2 24.5 - - + -
409A LEU* 4.3 12.3 - - + +
423A CYS* 4.2 14.6 - - - -
425A ALA* 5.0 1.3 - - + -
444A LEU* 4.7 6.3 - - + -
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TYR* 3.8 45.9 - - + +
280A GLU* 4.8 16.1 + - - +
281A LYS 4.8 8.9 + - - -
284A GLY* 3.2 1.5 - - - -
285A LEU* 1.3 80.0 - - - +
287A GLU* 1.3 76.9 - - - +
289A TYR* 3.4 2.9 + - - +
290A ASP* 3.0 51.2 + - - +
446A ARG* 4.1 3.0 + - - +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LYS 3.8 9.7 - - - +
282A LYS* 3.5 12.5 - - - +
283A GLY 3.4 20.2 + - - +
284A GLY* 3.5 9.8 + - - +
285A LEU 3.4 0.4 - - - -
286A ARG* 1.3 92.4 - - - +
288A LEU* 1.3 61.8 + - - +
290A ASP* 3.2 12.6 + - + +
291A ARG* 2.4 56.8 + - - +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A GLY* 4.0 19.5 - - - +
284A GLY 3.3 18.0 + - - +
285A LEU* 3.8 6.3 - - - +
286A ARG 3.3 0.2 - - - -
287A GLU* 1.3 77.1 - - - +
289A TYR* 1.3 64.3 + - - +
291A ARG* 3.3 31.9 + - + +
292A GLY 3.1 19.1 + - - +
297A PHE* 3.3 18.6 - - + -
346A LYS* 5.7 1.3 - - - +
409A LEU* 4.3 9.4 - - + -
411A VAL* 4.0 35.9 - - + -
420A LEU* 4.9 9.3 - - + +
423A CYS* 4.5 7.0 - - - -
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Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A VAL* 4.1 20.6 - - + -
275A TYR* 5.3 0.2 - - - +
285A LEU 3.0 18.1 + - - +
286A ARG* 3.9 4.3 - - - +
288A LEU* 1.3 76.7 - - - +
290A ASP* 1.3 63.5 + - - +
292A GLY* 3.4 11.1 + - - -
294A PRO* 3.6 31.1 - - + +
297A PHE* 3.5 41.1 - + + -
444A LEU 3.2 30.1 + - - -
445A VAL* 3.3 12.8 - - - +
446A ARG* 3.4 53.1 + - + +
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ARG* 3.0 47.0 + - - +
287A GLU* 3.4 12.5 - - + +
288A LEU 3.1 0.4 - - - -
289A TYR* 1.3 79.1 - - - +
291A ARG* 1.3 62.5 + - + +
292A GLY* 4.4 0.3 - - - -
446A ARG* 2.8 32.4 + - - +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLY* 5.1 4.9 - - - +
287A GLU* 2.4 63.5 + - - +
288A LEU* 3.3 30.7 + - - +
290A ASP* 1.3 79.7 - - + +
292A GLY* 1.3 66.1 + - - +
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A LEU 3.1 11.2 + - - +
289A TYR 3.4 10.7 + - - -
290A ASP 3.2 3.0 - - - -
291A ARG* 1.3 85.1 - - - +
293A PRO* 1.3 75.6 - - - +
294A PRO* 3.9 4.0 - - - -
297A PHE* 4.2 1.6 - - - -
420A LEU* 3.6 22.5 - - - +
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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