Contacts of the helix formed by residues 277 - 287 (chain A) in PDB entry 1EG4
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 GLU 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A PHE* 3.5 7.1 - - - -
226A THR 5.0 1.9 - - - +
227A GLY 3.7 11.6 - - - +
228A PHE* 3.2 44.9 - - + -
276A ILE* 1.3 76.4 - - - +
278A ALA* 1.3 65.6 + - - +
279A ALA* 3.2 7.0 - - + +
280A LEU* 3.2 17.9 + - + +
281A PHE* 3.2 9.7 + - - +
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Residues in contact with ALA 278 (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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216A ARG* 4.2 27.8 - - + +
219A PHE* 3.3 33.6 - - + -
227A GLY 4.4 0.8 + - - -
277A GLU* 1.3 74.0 - - - +
279A ALA* 1.3 63.3 + - - +
281A PHE* 3.2 4.4 + - + +
282A LEU* 2.8 28.9 + - + +
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Residues in contact with ALA 279 (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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216A ARG* 5.2 3.9 - - - +
277A GLU* 3.2 5.2 - - + +
278A ALA* 1.3 79.4 - - - +
280A LEU* 1.3 57.6 + - - +
282A LEU* 3.2 12.5 + - - +
283A ASP* 3.0 37.2 + - - +
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Residues in contact with LEU 280 (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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266A CYS* 4.5 6.7 - - - -
269A PHE* 3.9 28.3 - - + +
270A ALA* 3.6 22.7 - - + -
276A ILE* 3.5 37.2 - - + -
277A GLU* 3.2 12.7 + - + +
279A ALA* 1.3 79.4 - - - +
281A PHE* 1.3 58.3 + - - +
283A ASP* 3.1 9.6 + - + +
284A TRP* 2.8 26.9 + - - +
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Residues in contact with PHE 281 (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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215A TYR* 3.9 29.8 - + + -
218A LEU* 5.9 0.2 - - + -
219A PHE* 3.5 43.5 - + + -
234A LEU* 3.9 26.0 - - + -
237A LEU* 3.8 20.0 - - + -
238A LEU* 5.0 4.5 - - + -
276A ILE* 4.4 7.6 - - + -
277A GLU 3.2 2.8 + - - +
278A ALA* 3.2 9.1 + - - +
280A LEU* 1.3 83.4 - - - +
282A LEU* 1.4 68.9 + - + +
284A TRP* 3.3 19.6 + + - +
285A MET* 2.9 58.1 + - + +
292A MET* 5.5 4.5 - - + -
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Residues in contact with LEU 282 (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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212A GLU* 4.0 21.3 - - + +
215A TYR* 3.4 40.7 - - + -
216A ARG* 3.3 48.9 - - + +
278A ALA* 2.8 20.1 + - + +
279A ALA* 3.2 10.5 + - - +
281A PHE* 1.4 79.1 - - + +
283A ASP* 1.3 62.4 - - - +
285A MET* 3.3 6.6 + - - +
286A ARG* 3.0 25.8 + - - +
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Residues in contact with ASP 283 (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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269A PHE* 4.0 16.4 - - + -
279A ALA* 3.0 22.7 + - - +
280A LEU* 3.1 11.7 + - + +
282A LEU* 1.3 77.2 - - - +
284A TRP* 1.3 65.1 + - - +
286A ARG* 3.0 22.7 + - - +
287A LEU* 3.6 5.0 + - - +
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Residues in contact with TRP 284 (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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234A LEU* 4.7 1.3 - - + -
238A LEU* 4.2 24.9 - - + -
262A SER* 3.5 33.7 - - - -
265A SER* 4.4 10.9 + - - -
266A CYS* 3.6 38.1 - - + +
269A PHE* 3.4 43.9 - + + +
280A LEU 2.8 16.9 + - - +
281A PHE* 3.7 18.6 - + - +
283A ASP* 1.3 72.5 - - - +
285A MET* 1.3 79.0 + - - +
287A LEU* 2.8 34.4 + - + +
289A PRO* 3.4 40.9 - - + +
291A SER* 4.6 3.1 - - - -
292A MET* 5.1 0.2 - - + -
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Residues in contact with MET 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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215A TYR* 3.6 55.5 + - + +
281A PHE* 2.9 47.7 + - + +
282A LEU 3.5 8.1 - - - +
284A TRP* 1.3 89.0 - - - +
286A ARG* 1.4 58.9 + - - +
288A GLU* 2.7 25.8 + - - +
289A PRO* 3.7 21.7 - - + +
292A MET* 3.6 34.5 - - + +
296A PRO* 5.3 1.6 - - + +
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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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282A LEU 3.0 12.1 + - - +
283A ASP* 3.0 18.1 + - - +
285A MET* 1.4 77.7 - - - +
287A LEU* 1.3 63.8 + - + +
288A GLU* 3.3 10.5 + - - +
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Residues in contact with LEU 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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269A PHE* 3.7 29.8 - - + -
283A ASP 4.3 7.0 - - - +
284A TRP* 2.8 19.6 + - + +
286A ARG* 1.3 80.7 - - + +
288A GLU* 1.3 71.2 + - - +
289A PRO* 3.5 2.5 - - + +
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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