Contacts of the helix formed by residues 278 - 292 (chain A) in PDB entry 2HD1
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 SER 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A LYS 4.3 0.4 + - - -
277A PHE* 1.3 78.2 - - - +
279A GLN* 1.3 64.3 + - - +
280A THR* 3.3 11.7 + - - -
281A ASP* 3.1 31.6 + - - +
282A ILE* 3.1 21.6 + - - +
351A GLN* 5.7 0.2 + - - -
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Residues in contact with GLN 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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222A LEU 2.9 24.8 + - - +
223A GLY* 3.5 8.1 + - - -
224A LEU* 3.7 6.8 - - - +
226A ARG* 4.1 4.2 - - - +
227A ASP* 2.8 31.6 + - + +
228A PHE* 3.4 24.6 - - + -
274A GLN* 3.1 24.2 + - - +
277A PHE 5.1 0.7 - - - +
278A SER* 1.3 72.7 - - - +
280A THR* 1.3 59.9 + - - +
282A ILE* 3.3 12.3 + - - +
283A LEU 2.9 23.0 + - - -
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Residues in contact with THR 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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228A PHE* 3.6 20.1 - - + -
278A SER* 3.1 10.1 + - - -
279A GLN* 1.3 79.6 - - - +
281A ASP* 1.3 58.5 + - - +
283A LEU* 3.2 3.3 + - - +
284A ILE* 2.9 42.1 + - + +
348A GLY* 5.3 0.7 - - - +
351A GLN* 4.1 28.6 + - - +
352A ILE* 3.8 28.3 - - + -
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Residues in contact with ASP 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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277A PHE* 3.6 29.4 - - + -
278A SER* 3.1 28.4 + - - +
280A THR* 1.3 74.8 - - - +
282A ILE* 1.3 59.4 + - - +
284A ILE* 3.3 13.2 + - - +
285A LEU* 2.9 34.5 + - - +
351A GLN* 5.4 2.9 - - - +
390A MET* 5.2 4.7 - - - +
394A LYS* 2.7 37.9 + - + +
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Residues in contact with ILE 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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222A LEU* 4.2 30.5 - - + -
224A LEU* 4.1 13.5 - - + -
268A VAL* 4.4 12.1 - - + -
273A LEU* 4.2 20.0 - - + +
274A GLN* 4.3 14.8 - - + +
277A PHE* 3.9 20.9 - - + +
278A SER 3.1 14.9 + - - +
279A GLN* 3.6 22.9 - - - +
281A ASP* 1.3 75.4 - - - +
283A LEU* 1.3 64.0 + - - +
285A LEU* 3.1 11.7 + - + +
286A MET* 2.9 26.6 + - + +
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Residues in contact with LEU 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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219A TYR* 3.9 20.4 - - + -
224A LEU* 4.0 20.4 - - + +
228A PHE* 3.9 28.7 - - + -
230A ILE* 4.8 5.2 - - + -
279A GLN 2.9 14.5 + - - +
280A THR 3.4 8.1 - - - +
282A ILE* 1.3 76.5 - - - +
284A ILE* 1.3 56.5 + - - +
287A THR* 2.7 54.0 + - - +
341A PHE* 3.9 21.1 - - + -
344A ILE* 4.1 2.2 - - + -
352A ILE* 3.6 33.2 - - + -
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Residues in contact with ILE 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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280A THR* 2.9 28.2 + - + +
281A ASP* 3.5 20.4 - - - +
282A ILE 3.2 0.2 - - - -
283A LEU* 1.3 76.6 - - - +
285A LEU* 1.3 61.8 + - - +
288A ALA* 3.0 29.6 + - - +
351A GLN* 3.9 24.5 - - + +
352A ILE* 3.9 24.5 - - + +
355A GLY* 3.6 33.4 - - - -
356A MET* 3.7 10.0 - - - +
359A LEU* 3.7 15.9 - - + -
394A LYS* 4.8 9.6 - - + +
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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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264A MET* 3.8 40.5 - - + +
268A VAL* 5.8 0.7 - - + -
273A LEU* 4.8 4.0 - - + -
277A PHE* 4.5 9.4 - - + -
281A ASP 2.9 25.1 + - - +
282A ILE* 3.6 18.8 - - + +
284A ILE* 1.3 77.3 - - - +
286A MET* 1.3 57.0 + - + +
288A ALA* 4.0 1.6 - - - +
289A ALA* 3.1 29.1 + - - +
359A LEU* 3.8 21.5 - - + -
394A LYS* 3.9 37.0 - - + +
397A LEU* 4.2 15.7 - - + -
398A ILE* 4.8 0.9 - - - +
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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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218A MET* 3.6 40.8 - - + -
219A TYR* 3.6 22.9 - - + +
222A LEU* 3.6 27.6 - - + -
224A LEU* 4.5 4.3 - - + -
261A ALA* 3.8 15.3 - - + +
264A MET* 3.6 28.3 - - + -
265A TYR* 4.0 9.4 - - + -
268A VAL* 5.1 2.5 - - + -
282A ILE* 2.9 21.7 + - + +
283A LEU 4.1 1.6 - - - +
285A LEU* 1.3 77.1 - - + +
287A THR* 1.3 65.2 + - - +
289A ALA* 3.2 4.0 + - - +
290A ILE* 3.0 28.8 + - + +
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Residues in contact with THR 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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219A TYR* 2.8 15.8 + - - -
238A TRP* 3.7 26.7 - - + -
283A LEU* 2.7 35.9 + - - +
286A MET* 1.3 75.2 - - - +
288A ALA* 1.3 58.3 + - - +
290A ILE* 3.4 3.0 + - - +
291A CYS* 3.0 30.3 + - - +
333A LEU* 5.2 2.0 - - + -
340A ILE* 4.5 1.1 - - + -
341A PHE* 4.1 13.3 - - + -
356A MET* 3.6 31.4 - - + -
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Residues in contact with ALA 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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284A ILE 3.0 20.0 + - - +
285A LEU 4.0 1.1 - - - +
287A THR* 1.3 78.0 - - - +
289A ALA* 1.3 55.0 + - - +
291A CYS 3.5 0.3 - - - -
292A HIS* 2.7 39.0 + - - +
356A MET* 4.4 12.7 - - - +
359A LEU* 4.0 17.0 - - + -
360A ILE* 4.0 18.4 - - + +
398A ILE* 3.8 19.3 - - + -
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Residues in contact with ALA 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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257A CYS 4.1 4.5 - - - +
260A VAL* 3.9 26.9 - - + +
261A ALA* 3.9 17.9 - - - -
264A MET* 4.5 11.4 - - + -
285A LEU 3.1 20.1 + - - +
286A MET* 3.2 6.9 + - - +
288A ALA* 1.3 77.2 - - - +
290A ILE* 1.3 58.6 + - - +
292A HIS* 2.9 27.2 + - - -
398A ILE* 4.0 7.5 - - + +
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Residues in contact with ILE 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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215A LEU* 4.1 19.5 - - + -
219A TYR* 3.7 35.7 - - + +
238A TRP* 4.0 19.3 - - + -
239A LEU* 4.1 16.4 - - + -
242A VAL* 3.7 23.8 - - + -
246A TYR* 2.7 30.3 + - - -
257A CYS* 3.4 16.9 - - - +
261A ALA* 3.7 19.1 - - + -
286A MET* 3.0 16.7 + - + +
287A THR 3.8 3.6 - - - +
289A ALA* 1.3 76.3 - - - +
291A CYS* 1.3 54.4 + - - +
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Residues in contact with CYS 291 (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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238A TRP* 3.8 28.9 - - - -
242A VAL* 4.7 4.7 - - - -
246A TYR* 3.6 2.0 - - - -
287A THR* 3.0 26.0 + - - +
288A ALA 3.5 1.6 - - - +
290A ILE* 1.3 79.7 - - - +
292A HIS* 1.3 61.4 + - - +
293A ASP 3.2 4.6 + - - -
294A LEU* 3.4 37.6 + - + +
325A HIS* 4.0 7.3 - - - +
329A ALA* 3.8 20.9 - - + -
332A ILE* 6.3 0.2 - - - -
333A LEU* 5.8 0.9 - - - -
356A MET* 4.5 2.7 - - + -
360A ILE* 4.2 10.2 - - + +
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Residues in contact with HIS 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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101A ZN 2.1 36.2 - - - -
102A MG 4.0 4.2 - - - -
246A TYR* 4.3 1.0 + - - -
256A HIS* 3.3 8.1 - + - -
257A CYS* 4.3 6.5 - - - -
260A VAL* 3.2 33.9 - - + +
288A ALA 2.7 20.6 + - - +
289A ALA 2.9 19.1 + - - +
290A ILE 3.5 2.0 - - - -
291A CYS* 1.3 73.2 - - - +
293A ASP* 1.3 75.1 + - + +
294A LEU 3.6 0.2 - - - -
325A HIS* 3.0 22.7 - - - +
360A ILE* 4.0 17.0 - - + +
363A THR* 4.5 12.9 + - + -
398A ILE* 4.5 11.7 - - + -
402A ASP* 2.9 12.0 + - + -
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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