Contacts of the helix formed by residues 318 - 335 (chain B) in PDB entry 3HU1
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 318 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B THR 3.7 0.9 - - - +
317B HIS* 1.3 80.2 - - - +
319B GLU* 1.3 64.6 + - - -
320B VAL 3.4 2.0 - - - -
321B GLU* 3.4 10.8 + - - +
322B ARG* 3.2 25.6 + - - +
317C HIS 5.9 0.4 - - - -
319C GLU* 3.3 25.6 - - - -
322C ARG* 3.6 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLY* 3.4 21.4 - - - -
319A GLU* 3.6 1.9 + - - +
320A VAL* 3.3 48.7 + - - +
321A GLU* 3.7 22.0 + - - +
317B HIS 3.9 2.4 + - - +
318B GLY* 1.3 69.0 - - - -
320B VAL* 1.3 62.4 + - + +
321B GLU 3.2 0.2 - - - -
322B ARG* 3.3 4.7 + - - +
323B ARG* 2.9 41.1 + - - +
319C GLU* 3.3 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ALA* 3.8 36.3 - - + -
282B SER* 4.7 1.3 - - - +
283B GLU* 3.9 11.4 - - - +
319B GLU* 1.3 76.3 - - + +
321B GLU* 1.3 56.3 + - + +
323B ARG* 3.3 24.0 + - - +
324B ILE* 3.0 53.2 + - + +
319C GLU* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B MET* 3.7 29.7 - - + +
309B ILE 4.5 2.1 - - - +
311B PRO* 5.2 3.6 - - + +
316B THR* 3.4 20.9 + - - +
318B GLY* 3.4 12.0 + - - +
319B GLU 3.2 0.6 - - - -
320B VAL* 1.3 80.1 - - + +
322B ARG* 1.3 60.1 + - - +
324B ILE* 3.6 4.2 + - - +
325B VAL* 3.4 23.8 + - - +
319C GLU* 3.7 22.2 - - - +
322C ARG* 2.7 56.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A MET* 5.3 0.4 - - - -
316A THR* 5.3 1.9 - - - +
317A HIS* 3.4 49.9 - - - +
318A GLY* 3.7 1.8 - - - +
321A GLU* 2.9 47.3 + - - +
313B ARG* 3.3 33.6 + - + +
314B GLU* 4.1 10.7 + - - +
316B THR* 3.1 39.4 + - + +
317B HIS 4.5 4.2 + - - -
318B GLY 3.2 10.3 + - - +
319B GLU* 3.3 7.5 + - - +
321B GLU* 1.3 75.4 - - - +
323B ARG* 1.3 64.0 + - - +
325B VAL* 3.1 20.2 + - - +
326B SER* 3.2 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A MET 3.2 25.6 - - - +
276A SER* 3.5 13.1 - - - +
277A LYS 3.4 22.8 + - - +
278A LEU* 4.3 21.8 - - - +
279A ALA* 4.8 9.3 - - - +
279B ALA* 5.1 2.2 - - - +
280B GLY* 4.7 6.5 - - - +
283B GLU* 2.9 33.6 + - - +
319B GLU* 2.9 23.9 + - - +
320B VAL* 3.3 36.6 + - - +
322B ARG* 1.3 76.0 - - - +
324B ILE* 1.3 57.4 + - - +
326B SER* 3.5 3.3 + - - -
327B GLN* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE* 5.1 2.7 - - + -
275B MET* 4.4 18.4 - - + -
282B SER* 3.5 19.7 - - - +
283B GLU* 3.4 34.1 - - + +
286B LEU* 4.5 14.3 - - + +
309B ILE* 3.5 35.2 - - + +
320B VAL* 3.0 35.8 + - + +
321B GLU* 3.8 6.5 - - + +
322B ARG 3.2 0.2 - - - -
323B ARG* 1.3 73.0 - - - +
325B VAL* 1.3 66.5 + - - +
327B GLN* 3.0 8.1 + - - +
328B LEU* 2.9 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ILE 3.5 18.8 - - - +
310B ALA* 4.3 5.2 - - + +
311B PRO* 3.9 19.5 - - + +
313B ARG* 4.0 26.9 - - + +
316B THR* 5.7 1.3 - - + -
321B GLU 3.4 17.5 - - - +
322B ARG* 3.1 6.2 + - - +
324B ILE* 1.3 73.4 - - - +
326B SER* 1.3 62.1 + - - +
328B LEU* 3.3 7.7 + - - +
329B LEU* 3.1 26.7 + - + +
354B ASP* 4.3 10.5 - - + -
357B LEU* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PRO* 3.3 29.4 + - - +
275A MET* 3.5 19.0 + - - +
276A SER* 3.6 15.9 - - - -
313B ARG* 4.3 14.7 + - - -
322B ARG 3.2 11.4 + - - -
323B ARG 3.6 5.8 - - - -
325B VAL* 1.3 76.9 - - - +
327B GLN* 1.3 60.1 + - - +
329B LEU* 3.5 4.0 + - - +
330B THR* 2.9 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 3.5 20.7 + - - -
283B GLU* 3.4 34.8 - - + +
286B LEU* 4.0 18.6 - - + -
287B ARG* 3.5 39.7 - - - +
323B ARG 2.9 14.7 + - - +
324B ILE* 3.0 12.8 + - - +
326B SER* 1.3 75.3 - - - +
328B LEU* 1.3 62.3 + - - +
330B THR* 3.6 5.3 + - - +
331B LEU* 3.3 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 4.4 15.3 - - + -
290B PHE* 4.2 19.5 - - + -
303B ILE* 3.8 24.0 - - + -
306B LEU* 3.9 14.1 - - + -
309B ILE* 3.8 23.3 - - + -
310B ALA* 4.1 9.9 - - + -
324B ILE* 2.9 12.4 + - + +
325B VAL* 3.6 9.2 - - - +
327B GLN* 1.3 74.3 - - - +
329B LEU* 1.3 64.5 + - - +
331B LEU* 3.2 7.5 + - - +
332B MET* 3.0 34.4 + - + +
357B LEU* 3.8 27.4 - - + -
363B PHE* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PRO* 4.0 23.3 - - + -
305A GLU* 5.7 0.2 - - - +
313B ARG* 3.8 35.4 - - - +
325B VAL* 3.1 24.8 + - + +
326B SER* 3.8 4.5 - - - +
328B LEU* 1.3 76.0 - - - +
330B THR* 1.3 62.3 + - - +
332B MET* 3.4 7.7 + - - +
333B ASP* 3.2 29.1 + - - -
356B ALA* 3.9 10.8 - - + -
357B LEU* 3.9 27.4 - - + -
362B ARG* 3.7 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN* 6.1 0.9 - - - +
272A PRO* 3.5 2.8 + - - +
273A GLU* 3.3 52.5 + - + +
276A SER* 4.1 4.0 + - - +
326B SER 2.9 17.8 + - - -
327B GLN* 3.7 9.0 - - - +
329B LEU* 1.3 78.1 - - - +
331B LEU* 1.3 54.0 + - + +
333B ASP* 3.4 6.9 + - - +
334B GLY* 2.8 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.8 24.7 - - + +
287B ARG* 4.2 15.3 - - + +
290B PHE* 3.7 52.3 - - + -
291B GLU* 6.3 1.6 - - + -
327B GLN* 3.3 34.7 + - + +
328B LEU* 3.2 10.2 + - - +
330B THR* 1.3 77.6 - - + +
332B MET* 1.3 60.1 + - - +
334B GLY* 3.0 17.0 + - - +
335B LEU* 3.3 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ARG* 3.1 27.0 + - + +
240B GLY* 4.8 2.2 - - - -
290B PHE* 4.2 11.7 - - - -
328B LEU* 3.0 30.4 + - + +
329B LEU* 3.4 10.8 - - - +
331B LEU* 1.3 76.6 - - - +
333B ASP* 1.3 63.2 + - - +
335B LEU* 4.1 9.4 + - + +
343B VAL* 4.0 27.8 - - + -
357B LEU* 4.9 3.4 - - + -
361B GLY 4.5 4.6 - - - +
362B ARG* 3.7 39.3 - - + +
363B PHE* 3.7 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN* 5.5 10.2 + - - +
272A PRO* 5.9 0.5 - - - +
305A GLU* 5.1 0.2 - - - +
239B ARG* 3.9 9.5 + - - +
329B LEU 3.2 15.9 + - - +
330B THR* 3.9 5.0 - - - +
332B MET* 1.3 77.2 - - - +
334B GLY* 1.3 63.5 + - - +
335B LEU 3.2 10.3 + - - +
336B LYS* 5.4 1.6 - - - +
361B GLY 5.1 1.4 - - - +
362B ARG* 2.7 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLU* 4.0 9.5 - - - +
330B THR 2.8 15.7 + - - -
331B LEU* 3.0 8.4 + - - -
333B ASP* 1.3 75.5 - - - +
335B LEU* 1.3 62.2 + - - +
336B LYS* 3.3 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ARG* 2.6 45.4 + - + +
290B PHE* 4.0 22.7 - - + +
294B GLU* 3.6 38.1 - - + +
301B ILE* 5.7 0.2 - - + -
331B LEU 3.3 10.9 + - - +
332B MET* 4.3 7.9 - - - +
333B ASP 3.2 4.6 - - - +
334B GLY* 1.3 73.8 - - - +
336B LYS* 1.3 62.3 + - - +
339B ALA* 4.5 4.3 - - + -
341B VAL* 3.8 42.8 - - + +
343B VAL* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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