Contacts of the helix formed by residues 305 - 325 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304B THR* 1.3 74.0 - - - +
306B ASP* 1.3 63.0 + - - +
308B GLN* 3.1 22.6 + - - +
309B GLU* 2.8 28.6 + - + +
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Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B THR* 3.8 11.9 + - - +
305B THR* 1.3 81.1 + - - +
307B GLU* 1.3 60.0 + - + +
309B GLU* 3.0 10.7 + - - +
310B LYS* 2.8 48.4 + - - +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PHE* 3.5 30.7 - - + -
204B VAL 4.4 1.0 - - - +
205B ALA* 3.8 9.2 - - + -
206B TRP* 3.2 26.0 + - - +
207B SER* 2.5 34.2 + - - -
303B LEU* 3.7 17.9 - - + +
304B THR* 3.0 32.6 + - - +
306B ASP* 1.3 81.1 - - + +
308B GLN* 1.3 61.8 + - - +
310B LYS* 3.3 7.5 + - - +
311B LEU* 3.1 20.4 + - - +
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B LEU* 2.8 42.1 + - + +
304B THR 2.7 21.7 + - - +
305B THR* 3.2 20.1 + - - +
307B GLU* 1.3 70.5 - - - +
309B GLU* 1.3 64.8 + - - +
311B LEU* 3.1 15.4 + - - +
312B LEU* 3.2 24.0 + - + +
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B THR* 2.8 13.0 + - + +
306B ASP* 3.2 13.2 - - - +
308B GLN* 1.3 75.2 - - - +
310B LYS* 1.3 63.2 + - + +
312B LEU* 3.1 12.5 + - - +
313B GLN* 3.0 23.3 + - - +
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Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B SER* 4.9 2.3 - - - +
203B PHE* 3.7 43.0 - - + +
204B VAL 5.5 2.2 + - - -
231B GLU* 5.9 0.8 + - - -
306B ASP* 2.8 38.6 + - - +
307B GLU* 3.8 7.7 - - - +
309B GLU* 1.3 73.0 - - + +
311B LEU* 1.3 57.2 + - - +
313B GLN* 3.3 19.9 - - - +
314B SER* 3.0 28.8 + - - -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 4.0 11.9 - - + -
196B GLY* 3.8 24.9 - - - +
203B PHE* 3.8 7.8 - - + -
280B MET* 4.2 22.0 - - + -
284B LEU* 3.6 30.4 - - + +
285B SER 4.3 0.9 - - - +
286B TYR* 3.8 29.2 - - + -
303B LEU* 4.2 11.9 - - + -
307B GLU 3.1 12.6 + - - +
308B GLN* 3.1 10.1 + - - +
310B LYS* 1.3 75.3 - - - +
312B LEU* 1.3 60.4 + - + +
314B SER* 3.1 6.6 + - - -
315B ARG* 3.0 25.5 + - - +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B ASP 5.8 1.1 - - - +
280B MET* 4.1 24.2 - - + -
308B GLN* 3.2 19.5 + - + +
309B GLU* 3.1 9.1 + - - +
311B LEU* 1.3 72.3 - - + +
313B GLN* 1.3 66.8 + - - +
315B ARG* 3.1 31.2 + - - +
316B ASP* 3.0 31.4 + - - +
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Residues in contact with GLN 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B SER* 5.1 3.9 - - - -
309B GLU 3.0 11.4 + - - +
310B LYS* 3.3 22.8 + - - +
311B LEU 3.2 0.2 - - - -
312B LEU* 1.3 77.5 - - - +
314B SER* 1.3 61.4 + - - +
316B ASP* 3.2 13.0 + - - +
317B TYR* 2.9 61.7 + - + +
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Residues in contact with SER 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLY* 3.4 27.1 - - - -
197B GLU* 3.8 4.0 - - - -
201B SER* 3.4 38.6 + - - -
203B PHE* 4.5 0.9 - - - -
284B LEU* 4.7 1.6 - - - -
310B LYS 3.0 15.8 + - - -
311B LEU 3.1 8.7 + - - -
313B GLN* 1.3 76.6 - - - +
315B ARG* 1.3 63.5 + - - +
317B TYR* 3.1 3.3 + - - +
318B ILE* 2.9 30.2 + - - +
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Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B ASP 5.5 1.8 + - - -
280B MET* 3.0 42.3 + - + +
282B MET* 4.0 15.5 - - + +
284B LEU* 3.9 18.8 - - + +
311B LEU 3.0 12.4 + - - +
312B LEU* 3.1 43.8 + - - +
314B SER* 1.3 76.3 - - - +
316B ASP* 1.3 78.6 + - - +
318B ILE* 3.3 5.9 + - - +
319B GLN* 2.7 46.8 + - - +
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Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 3.0 16.6 + - - +
313B GLN* 3.5 11.2 - - - +
315B ARG* 1.3 102.7 + - - +
317B TYR* 1.3 60.2 + - + +
319B GLN* 3.6 5.9 - - - +
320B GLN* 2.7 39.1 + - - +
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Residues in contact with TYR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 6.0 0.2 - - - -
197B GLU* 3.7 15.1 - - - +
200B ASN* 3.8 12.6 - - - +
201B SER* 3.4 29.2 - - - -
313B GLN* 2.9 55.9 + - + +
314B SER 3.1 3.7 + - - +
316B ASP* 1.3 80.0 - - + +
318B ILE* 1.3 64.2 + - - +
320B GLN* 4.0 4.2 - - - +
321B ARG* 3.0 27.2 + - - +
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ASP* 3.9 22.9 - - + -
147B VAL* 4.2 13.9 - - + +
197B GLU* 3.6 40.4 - - + +
282B MET* 3.4 22.7 - - + -
283B TYR 3.3 29.6 - - - +
284B LEU* 3.9 15.7 - - + -
314B SER 2.9 17.0 + - - +
315B ARG* 3.8 4.0 - - - +
317B TYR* 1.3 79.2 - - - +
319B GLN* 1.3 63.6 + - - +
321B ARG 3.9 0.2 - - - -
322B PHE* 3.0 26.0 + - - +
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Residues in contact with GLN 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B MET 5.5 0.5 - - - +
281B GLY 4.2 7.6 - - - +
282B MET* 3.9 25.7 - - + +
315B ARG* 2.7 33.7 + - - +
316B ASP* 3.6 8.1 - - - +
318B ILE* 1.3 74.7 - - - +
320B GLN* 1.3 62.2 + - - +
322B PHE* 3.3 10.4 - - - +
323B ASP* 2.7 56.8 + - - +
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Residues in contact with GLN 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B ASP 2.7 22.0 + - - +
317B TYR* 4.0 4.5 - - - +
319B GLN* 1.3 73.5 - - - +
321B ARG* 1.3 56.2 + - - +
323B ASP* 3.2 11.5 + - - +
324B GLU* 2.9 29.5 + - - +
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 4.5 20.0 - - + -
115B LEU* 5.0 6.6 - - + +
147B VAL* 4.4 14.6 - - + +
317B TYR 3.0 18.7 + - - +
318B ILE 4.2 1.1 - - - +
320B GLN* 1.3 76.7 - - - +
322B PHE* 1.3 61.9 + - - +
324B GLU* 3.5 12.9 - - - +
325B ILE* 3.1 24.9 + - - +
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 4.1 11.6 - - + +
150B ALA* 3.7 31.9 - - + -
151B LEU* 3.7 33.7 - - + -
154B HIS* 4.0 24.2 - + + -
282B MET* 4.2 22.2 - - + -
318B ILE 3.0 19.3 + - - +
319B GLN* 3.3 7.9 - - - +
321B ARG* 1.3 74.9 - - - +
323B ASP* 1.3 79.0 + - - +
325B ILE* 3.0 22.6 - - - +
326B VAL* 3.0 12.9 + - - -
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B GLN* 2.7 48.8 + - - +
320B GLN* 3.7 8.1 - - - +
322B PHE* 1.3 82.3 - - - +
324B GLU* 1.3 64.1 + - - +
325B ILE 3.2 0.5 + - - -
326B VAL* 3.3 15.3 + - - +
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Residues in contact with GLU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 5.1 6.6 - - - +
320B GLN 2.9 17.5 + - - +
321B ARG* 3.5 13.7 - - - +
323B ASP* 1.3 78.3 - - - +
325B ILE* 1.3 69.2 + - - +
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 4.5 18.2 - - + +
116B LYS* 5.4 4.0 - - - -
119B SER* 3.5 33.0 - - - +
147B VAL* 4.0 6.5 - - + -
151B LEU* 3.9 27.3 - - + +
321B ARG 3.1 13.6 + - - +
322B PHE* 3.0 27.3 + - - +
323B ASP 4.0 0.2 - - - -
324B GLU* 1.3 88.8 - - - +
326B VAL* 1.3 56.5 + - - +
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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
------------------------------------------------------------
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