Contacts of the helix formed by residues 275 - 288 (chain A) in PDB entry 7ENL
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A GLY 5.1 2.4 + - - -
258A TYR* 4.3 13.2 - - - -
274A THR* 1.3 71.8 - - - +
276A PRO* 1.3 65.8 - - - +
278A LEU* 3.3 0.9 + - - +
279A ALA* 3.0 22.6 + - - +
298A PHE* 3.3 15.6 - - - -
302A ASP* 4.9 1.1 + - - -
305A ALA* 3.7 26.7 - - - -
308A HIS* 5.6 1.3 - - - -
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Residues in contact with PRO 276 (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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274A THR* 3.3 13.9 - - - +
275A GLY* 1.3 90.9 - - - +
277A GLN* 1.3 59.5 + - + +
279A ALA* 3.3 10.6 - - + +
280A ASP* 3.2 24.4 + - - +
305A ALA* 5.4 1.6 - - + -
308A HIS* 4.6 22.4 - - + +
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Residues in contact with GLN 277 (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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257A LYS* 5.4 0.7 + - - -
272A TRP 3.9 4.7 + - - +
273A LEU* 3.3 27.3 - - + +
274A THR* 2.7 49.0 + - - +
276A PRO* 1.3 74.3 - - + +
278A LEU* 1.3 65.2 + - - +
280A ASP* 3.3 11.6 + - - +
281A LEU* 3.2 18.2 + - - +
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Residues in contact with LEU 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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252A PHE* 4.9 2.7 - - + -
258A TYR* 3.5 37.5 - - + -
260A LEU* 4.1 20.0 - - + -
273A LEU* 4.0 25.1 - - + +
274A THR 3.1 8.5 + - - +
275A GLY 3.5 8.7 - - - +
277A GLN* 1.3 74.1 - - - +
279A ALA* 1.3 54.4 + - - +
280A ASP 3.0 1.6 - - - -
281A LEU* 2.9 10.9 + - + +
282A TYR* 2.8 73.8 + - + +
297A PRO 3.6 11.4 - - - +
298A PHE* 4.1 6.1 - - + -
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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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275A GLY 3.0 13.6 + - - +
276A PRO* 3.3 16.2 - - + +
278A LEU* 1.3 76.8 - - - +
280A ASP* 1.3 61.7 - - - +
282A TYR* 3.4 4.6 + - - +
283A HIS* 3.0 36.2 + - + -
298A PHE* 4.2 10.0 - - + -
308A HIS* 4.6 13.2 - - + +
309A PHE* 3.9 26.4 - - + -
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Residues in contact with ASP 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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276A PRO 3.2 13.1 + - - +
277A GLN* 3.4 13.9 - - - +
278A LEU 3.0 0.6 - - - -
279A ALA* 1.3 81.6 - - - +
281A LEU* 1.3 62.9 + - - +
283A HIS* 3.5 11.4 + - - +
284A SER* 3.2 20.3 + - - -
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 4.0 21.8 - - - +
260A LEU* 3.0 39.5 - - + -
273A LEU* 4.3 4.7 - - + -
277A GLN 3.2 10.4 + - - +
278A LEU* 2.9 15.6 + - + +
280A ASP* 1.3 72.3 - - - +
282A TYR* 1.3 65.6 + - + +
284A SER* 2.9 30.1 - - - -
285A LEU* 3.1 20.7 + - + +
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Residues in contact with TYR 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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166A LEU* 4.9 12.1 - - + +
245A LEU* 5.4 2.0 - - + -
247A CYS* 3.5 30.3 - - - +
249A SER* 4.6 1.7 - - - -
252A PHE* 4.9 1.2 - - - -
260A LEU* 5.9 0.9 - - + -
278A LEU* 2.8 46.7 + - + +
279A ALA 3.5 4.9 - - - +
281A LEU* 1.3 77.3 - - + +
283A HIS* 1.3 66.1 + - - +
285A LEU* 3.1 16.6 + - + +
286A MET* 2.9 40.1 + - + +
294A ILE* 4.5 14.2 - - + +
297A PRO* 2.6 44.7 + - + -
298A PHE* 3.8 17.0 - + - -
309A PHE* 3.8 14.1 - + + -
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Residues in contact with HIS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ALA* 3.0 27.8 + - + +
280A ASP* 4.0 12.8 - - - +
281A LEU 3.3 0.4 - - - -
282A TYR* 1.3 73.4 - - - +
284A SER* 1.3 60.6 + - - +
286A MET* 3.0 31.3 + - + +
287A LYS* 3.1 30.7 - - - +
309A PHE* 3.7 13.2 - + - -
312A THR* 2.6 52.3 + - - -
313A ALA* 3.9 12.7 + - - -
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLU* 5.4 2.0 + - - -
280A ASP 3.2 13.7 + - - -
281A LEU* 2.9 23.8 - - - -
283A HIS* 1.3 72.0 - - - +
285A LEU* 1.3 70.7 + - - +
287A LYS* 3.4 9.4 + - - +
288A ARG* 3.2 22.9 + - - +
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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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166A LEU* 5.1 3.6 - - + -
221A ALA* 4.1 20.9 - - + -
222A GLU* 3.3 33.0 - - + +
225A LEU* 3.8 12.6 - - + -
245A LEU* 5.0 11.7 - - + -
281A LEU* 3.1 26.0 + - + +
282A TYR* 3.1 17.1 + - + +
284A SER* 1.3 80.9 - - - +
286A MET* 1.3 55.8 + - - +
288A ARG* 3.1 2.4 + - + -
289A TYR* 2.9 56.3 + - + +
291A ILE* 3.8 16.0 - - + +
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Residues in contact with MET 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 TYR* 2.9 48.6 + - + +
283A HIS* 3.0 35.8 + - - +
285A LEU* 1.3 75.1 - - - +
287A LYS* 1.3 60.6 + - + +
289A TYR 3.0 18.2 - - - +
291A ILE* 4.2 19.5 + - + +
294A ILE* 4.6 4.0 - - + -
309A PHE* 3.5 23.3 - - + -
313A ALA 4.1 13.9 - - - +
315A ILE* 3.8 35.0 - - + -
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Residues in contact with LYS 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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283A HIS* 3.1 28.9 + - + +
284A SER* 3.7 8.1 - - - +
285A LEU 3.3 0.2 - - - -
286A MET* 1.3 77.5 - - + +
288A ARG* 1.3 64.2 + - + +
289A TYR 3.5 0.8 - - - +
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Residues in contact with ARG 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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222A GLU* 4.3 15.3 - - - +
226A ASP* 3.1 25.3 + - - -
284A SER 3.2 15.9 + - - +
285A LEU* 3.1 3.9 + - - +
287A LYS* 1.3 82.0 - - + +
289A TYR* 1.3 94.4 + - + +
290A PRO* 4.6 1.2 - - - +
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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