Contacts of the helix formed by residues 305 - 327 (chain D) in PDB entry 1HYH
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 THR 305 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304D THR* 1.3 73.4 - - - +
306D ASP* 1.3 74.9 + - - +
308D GLN* 3.4 16.0 + - - +
309D GLU* 3.0 22.4 + - - +
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Residues in contact with ASP 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D THR* 3.3 8.2 + - - +
305D THR* 1.3 85.1 + - - +
307D GLU* 1.3 58.5 + - + +
309D GLU* 3.2 7.4 + - - +
310D LYS* 2.8 47.4 + - - +
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Residues in contact with GLU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D PHE* 3.3 34.8 - - + -
204D VAL 4.6 1.0 - - - +
205D ALA* 4.2 3.1 - - - -
206D TRP* 3.5 10.7 + - - +
207D SER* 2.7 47.8 + - - -
303D LEU* 3.2 24.6 - - + +
304D THR* 2.8 37.3 + - - +
306D ASP* 1.3 77.8 - - + +
308D GLN* 1.3 57.0 + - - +
310D LYS* 3.4 3.0 + - + +
311D LEU* 3.0 25.5 + - - +
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Residues in contact with GLN 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D LEU* 2.9 42.4 + - + +
304D THR 2.9 18.0 + - - +
305D THR* 3.8 12.7 - - - +
307D GLU* 1.3 76.5 - - - +
309D GLU* 1.3 62.8 + - - +
311D LEU* 3.4 8.2 + - + +
312D LEU* 3.0 34.9 + - + +
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Residues in contact with GLU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D THR 3.0 13.9 + - - +
306D ASP* 3.2 11.2 + - - +
308D GLN* 1.3 77.0 - - - +
310D LYS* 1.3 64.5 + - + +
312D LEU* 3.1 8.7 + - - +
313D GLN* 2.9 28.4 + - - +
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Residues in contact with LYS 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D SER* 4.6 3.2 - - - +
203D PHE* 3.9 45.1 - - + +
204D VAL 5.7 1.0 + - - -
231D GLU* 5.8 2.2 + - - -
306D ASP* 2.8 35.3 + - - +
307D GLU* 3.9 2.0 - - - +
309D GLU* 1.3 73.8 - - + +
311D LEU* 1.3 56.2 + - - +
313D GLN* 3.6 19.3 - - - +
314D SER* 3.0 29.1 + - - -
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Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 4.0 14.6 - - + -
196D GLY* 4.0 27.8 - - - +
203D PHE* 3.7 6.9 - - + -
277D ARG* 6.2 0.2 - - - -
280D MET* 4.5 21.1 - - + -
284D LEU* 3.9 19.1 - - + +
286D TYR* 3.8 30.1 - - + -
303D LEU* 4.3 9.4 - - + -
307D GLU 3.0 17.3 + - - +
308D GLN* 3.6 8.7 - - + +
310D LYS* 1.3 75.8 - - - +
312D LEU* 1.3 60.4 + - + +
314D SER* 3.2 5.6 - - - -
315D ARG* 3.0 26.3 + - - +
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Residues in contact with LEU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ASP 5.8 0.2 - - - +
280D MET* 4.2 25.6 - - + -
308D GLN* 3.0 27.1 + - + +
309D GLU* 3.1 6.3 + - - +
311D LEU* 1.3 73.9 - - + +
313D GLN* 1.3 65.8 + - - +
315D ARG* 3.3 32.1 + - - +
316D ASP* 3.1 30.1 + - - +
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Residues in contact with GLN 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D SER* 5.4 5.0 - - - -
309D GLU* 2.9 19.2 + - - +
310D LYS* 3.6 21.0 - - - +
312D LEU* 1.3 77.0 - - - +
314D SER* 1.3 61.3 + - - +
316D ASP* 3.2 9.4 + - - +
317D TYR* 3.2 57.5 + - + +
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Residues in contact with SER 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D GLY* 3.6 11.1 - - - -
197D GLU 3.2 20.1 + - - -
201D SER* 3.0 43.3 + - - -
203D PHE* 5.1 0.2 - - - -
284D LEU* 4.7 2.2 - - - -
310D LYS 3.0 11.9 + - - -
311D LEU* 3.2 11.9 - - - -
313D GLN* 1.3 75.9 - - - +
315D ARG* 1.3 60.9 + - - -
317D TYR* 3.3 5.4 + - - +
318D ILE* 3.2 28.2 + - - +
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Residues in contact with ARG 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ASP 4.9 3.2 + - - -
280D MET* 3.0 52.9 + - - +
282D MET* 4.5 11.0 - - + +
283D TYR 5.6 0.2 - - - -
284D LEU* 3.5 23.1 - - + +
311D LEU 3.0 5.6 + - - +
312D LEU* 3.5 36.5 + - - +
313D GLN 3.3 0.2 - - - -
314D SER* 1.3 82.2 - - - +
316D ASP* 1.3 85.9 + - - +
318D ILE* 3.4 6.1 + - - +
319D GLN* 3.0 28.8 + - + +
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Residues in contact with ASP 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D LEU* 3.1 16.6 + - - +
313D GLN* 3.2 10.7 + - - +
315D ARG* 1.3 102.8 + - - +
317D TYR* 1.3 71.7 + - + +
319D GLN* 3.5 6.3 + - - +
320D GLN* 3.0 24.4 + - - +
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Residues in contact with TYR 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D GLU* 3.2 18.2 - - - +
200D ASN* 5.7 2.5 - - + -
201D SER* 3.4 31.4 - - - -
313D GLN* 3.2 37.5 + - + +
314D SER 3.5 3.8 - - - +
315D ARG 3.3 0.4 - - - -
316D ASP* 1.3 79.5 - - + +
318D ILE* 1.3 66.0 + - - +
320D GLN* 3.3 5.0 + - - +
321D ARG* 3.0 29.6 + - + +
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Residues in contact with ILE 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ASP* 3.7 23.1 - - + -
147D VAL* 4.1 13.2 - - + +
197D GLU* 3.5 37.7 - - + +
282D MET* 3.2 30.1 - - + -
283D TYR 3.3 22.2 - - - +
284D LEU* 3.7 17.5 - - + -
314D SER 3.2 15.9 + - - +
315D ARG* 3.8 4.9 - - - +
316D ASP 3.4 0.2 - - - -
317D TYR* 1.3 76.2 - - - +
319D GLN* 1.3 58.0 + - - +
321D ARG* 3.8 1.5 - - - +
322D PHE* 2.9 32.1 + - - +
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Residues in contact with GLN 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D GLY 4.4 6.2 - - - +
282D MET* 4.1 26.0 - - + +
315D ARG* 3.0 19.0 + - + +
316D ASP* 3.6 8.3 - - - +
318D ILE* 1.3 78.8 - - - +
320D GLN* 1.3 57.3 + - - +
322D PHE* 3.3 14.1 + - - +
323D ASP* 2.9 50.4 + - - +
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Residues in contact with GLN 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D ASP 3.0 17.9 + - - +
317D TYR* 3.9 5.6 - - - +
319D GLN* 1.3 76.4 - - - +
321D ARG* 1.3 62.6 + - + +
323D ASP* 3.1 10.8 + - - +
324D GLU* 3.1 22.2 + - - +
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Residues in contact with ARG 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ARG* 4.8 7.0 - - - +
115D LEU* 6.0 0.2 - - - +
144D PRO* 5.7 3.1 - - + -
147D VAL* 4.0 19.6 - - + +
197D GLU* 5.9 1.6 - - - +
317D TYR* 3.0 20.1 + - + +
318D ILE 4.0 2.5 - - - +
320D GLN* 1.3 76.1 - - + +
322D PHE* 1.3 61.0 + - - +
324D GLU* 3.5 20.7 - - - +
325D ILE* 3.2 23.6 + - - +
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Residues in contact with PHE 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D VAL* 4.0 16.6 - - + +
150D ALA* 3.7 24.9 - - + -
151D LEU* 3.7 33.0 - - + -
154D HIS* 4.5 14.1 - + + -
282D MET* 4.0 17.9 - - + -
318D ILE 2.9 18.7 + - - +
319D GLN* 3.4 17.9 - - - +
321D ARG* 1.3 75.4 - - - +
323D ASP* 1.3 67.2 + - - +
325D ILE* 3.3 9.3 + - + +
326D VAL* 2.9 51.5 + - + +
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Residues in contact with ASP 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D GLN* 2.9 38.4 + - - +
320D GLN* 3.1 12.4 + - - +
322D PHE* 1.3 86.1 - - - +
324D GLU* 1.3 61.8 + - - +
326D VAL* 3.2 22.3 - - - +
327D ASP* 3.2 17.7 + - - +
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Residues in contact with GLU 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ARG* 2.5 42.1 + - - -
115D LEU* 3.6 19.1 - - + +
320D GLN 3.1 9.2 + - - +
321D ARG* 3.5 20.2 - - - +
323D ASP* 1.3 79.0 - - - +
325D ILE* 1.4 59.4 + - - +
327D ASP* 3.2 23.2 + - - +
328D THR* 3.5 10.7 - - - +
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Residues in contact with ILE 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU* 4.0 32.1 - - + +
118D THR* 3.8 28.7 - - + -
119D SER* 3.9 16.2 - - - +
147D VAL* 3.7 20.9 - - + -
148D ILE* 4.5 6.5 - - + -
151D LEU* 3.8 23.3 - - + +
321D ARG 3.2 11.3 + - - +
322D PHE* 3.4 13.7 - - + +
324D GLU* 1.4 75.2 - - - +
326D VAL* 1.3 67.1 + - - +
327D ASP 3.1 2.0 - - - -
328D THR* 2.8 26.4 + - - +
329D LEU 3.7 2.6 + - - -
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Residues in contact with VAL 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU* 4.4 9.6 - - + -
154D HIS* 3.7 36.3 - - + +
322D PHE* 2.9 38.2 + - + +
323D ASP* 3.2 24.2 - - - +
325D ILE* 1.3 79.5 - - - +
327D ASP* 1.4 65.0 + - - +
329D LEU* 3.3 22.9 + - + +
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Residues in contact with ASP 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D ASP* 3.2 19.7 + - - +
324D GLU* 3.2 13.7 + - - +
325D ILE 3.1 1.0 - - - -
326D VAL* 1.4 82.3 - - - +
328D THR* 1.3 61.8 + - + +
329D LEU 3.5 5.9 + - - +
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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
------------------------------------------------------------
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