Contacts of the helix formed by residues 313 - 333 (chain B) in PDB entry 3HYW
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 313 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B PRO* 4.3 18.2 - - + -
312B LYS* 1.3 74.6 - - - +
314B GLY* 1.3 65.4 + - - +
315B MET* 3.8 2.8 + - - +
316B MET* 3.2 25.9 + - - +
317B ILE* 3.0 24.3 + - - +
345B ALA* 3.3 22.7 - - + +
346B ILE 5.4 0.7 - - - -
347B CSS 3.5 25.6 - - - -
363B VAL* 5.7 0.9 - - + -
441B FAD 3.4 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 4.5 9.6 - - - +
43B PRO* 6.4 0.2 - - - -
313B THR* 1.3 69.7 - - - +
315B MET* 1.3 55.1 + - - +
317B ILE* 3.2 7.2 + - - +
318B GLU* 2.8 39.5 + - - +
441B FAD 2.7 34.8 + - - -
500B DCQ 4.2 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B THR* 3.3 2.7 + - - +
314B GLY* 1.3 71.0 - - - +
316B MET* 1.3 64.4 + - - +
318B GLU* 3.4 7.5 + - + +
319B GLN* 3.0 36.7 + - + +
344B SER* 3.4 30.1 - - - +
345B ALA* 3.7 3.8 - - - -
346B ILE* 3.5 55.2 - - + +
359B PHE* 4.8 2.5 - - - -
407B LEU* 3.7 28.3 - - + -
413B VAL* 4.8 4.9 - - + -
500B DCQ 3.4 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ILE* 4.9 6.1 - - + -
310B VAL* 5.0 5.2 - - + -
311B PRO 3.4 21.5 - - - +
312B LYS* 4.2 7.2 - - + -
313B THR* 3.2 36.9 + - - +
315B MET* 1.3 75.9 - - - +
317B ILE* 1.3 58.1 + - - +
319B GLN* 3.3 9.5 + - - +
320B MET* 2.9 40.3 + - + +
343B LEU* 3.6 33.3 - - + +
344B SER 3.3 18.1 + - - +
363B VAL* 3.9 28.9 - - + -
364B ILE* 5.2 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 4.0 7.0 - - + -
13B GLY* 3.6 35.0 - - - +
292B VAL* 3.8 1.5 - - + +
293B GLY* 3.7 25.4 - - - -
294B VAL* 4.2 0.2 - - + -
312B LYS* 3.4 32.5 - - + +
313B THR 3.0 16.7 + - - +
314B GLY* 3.5 7.9 - - - +
315B MET 3.2 0.2 - - - -
316B MET* 1.3 76.0 - - - +
318B GLU* 1.3 60.1 + - - +
320B MET* 3.3 9.5 + - - +
321B ALA* 2.9 27.7 + - - +
441B FAD 3.5 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 4.6 7.2 - - + -
16B ALA* 4.8 3.8 - - + -
20B ASN* 4.6 1.2 + - - -
314B GLY* 2.8 21.6 + - - +
315B MET* 3.7 5.8 - - + +
317B ILE* 1.3 74.4 - - - +
319B GLN* 1.3 56.9 + - - +
321B ALA* 3.4 8.3 + - - +
322B MET* 3.0 43.3 + - + +
385B PHE* 4.1 4.3 - - - -
389B PHE* 3.5 28.4 - - + -
392B LYS* 3.5 18.3 + - - -
398B ILE* 3.8 19.5 - - + +
403B GLU* 3.8 9.5 - - - +
500B DCQ 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B MET* 3.0 29.6 + - + +
316B MET 3.5 6.5 - - - +
318B GLU* 1.3 74.2 - - + +
320B MET* 1.3 65.2 + - - +
322B MET* 3.2 13.9 + - + +
323B ALA 2.9 19.2 + - - -
341B PRO* 3.5 13.9 - - + +
342B ARG* 4.3 1.7 - - - +
343B LEU* 2.8 31.6 + - - -
344B SER* 2.9 30.7 + - - +
413B VAL* 3.8 10.1 - - - +
415B PRO* 3.4 44.6 - - + +
416B ILE* 3.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 3.5 48.9 - - + -
292B VAL* 3.9 9.6 - - + -
293B GLY* 3.3 27.1 - - - +
296B THR* 4.1 0.9 - - - +
298B ILE* 4.0 15.5 - - + -
312B LYS* 4.1 18.2 - - + -
316B MET* 2.9 25.3 + - + +
317B ILE* 3.3 12.8 + - - +
319B GLN* 1.3 75.4 - - - +
321B ALA* 1.3 58.1 + - - +
323B ALA* 3.2 2.4 + - - +
324B VAL* 2.8 35.5 + - - +
341B PRO* 3.6 10.0 - - + +
343B LEU* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 3.5 29.6 - - + -
17B THR* 3.3 29.6 - - - +
20B ASN* 3.7 6.0 + - - +
292B VAL* 3.9 6.7 - - + +
317B ILE 2.9 15.4 + - - +
318B GLU 3.5 4.3 - - - +
319B GLN 3.2 0.2 - - - -
320B MET* 1.3 75.2 - - - +
322B MET* 1.3 57.1 + - - +
324B VAL* 3.9 0.9 - - - +
325B ALA* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASN* 3.6 17.7 - - - +
318B GLU* 3.0 38.7 + - + +
319B GLN* 3.2 14.3 + - + +
321B ALA* 1.3 76.2 - - - +
323B ALA* 1.3 62.4 + - - +
325B ALA* 3.5 1.4 + - - +
326B HIS* 3.1 36.3 + - + +
399B ALA* 4.5 20.4 - - + -
404B GLU* 4.9 6.5 - - - +
415B PRO* 3.6 39.7 - - + -
416B ILE* 3.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B CYS 5.0 2.0 - - - +
281B PHE* 5.9 0.2 - - + -
319B GLN 2.9 16.3 + - - +
320B MET 3.6 4.3 - - - +
322B MET* 1.3 76.1 - - - +
324B VAL* 1.3 58.4 + - + +
326B HIS* 3.3 2.4 + - - +
327B ASN* 2.9 37.3 + - - +
339B TYR* 3.7 27.6 - - - +
341B PRO* 3.7 24.0 - - + -
416B ILE* 3.7 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.9 15.9 - - + -
102B VAL* 4.1 3.4 - - + -
280B CYS 4.2 1.6 - - - +
281B PHE* 3.8 34.5 - - + +
290B PHE* 3.6 27.1 - - + -
292B VAL* 3.7 20.4 - - + -
320B MET 2.8 20.6 + - - +
321B ALA 3.9 2.7 - - - +
323B ALA* 1.3 75.1 - - - +
325B ALA* 1.3 57.5 + - - +
327B ASN* 3.1 7.9 + - - +
328B ILE* 2.9 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 4.3 2.2 - - + +
20B ASN* 3.6 26.0 - - + -
21B LEU* 3.7 25.2 - - + +
24B LEU* 3.9 12.1 - - + -
321B ALA 3.0 19.1 + - - +
322B MET* 3.7 3.6 - - - +
324B VAL* 1.3 78.5 - - - +
326B HIS* 1.3 61.6 + - - +
328B ILE 3.5 0.2 + - - -
329B VAL* 3.1 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.1 33.8 - - + +
322B MET* 3.1 32.6 + - + +
323B ALA 3.7 1.8 - - - +
325B ALA* 1.3 73.8 - - - +
327B ASN* 1.3 61.6 + - - +
329B VAL* 3.5 3.4 + - - +
330B ASN* 2.9 41.5 + - - +
339B TYR* 3.6 32.8 + + + -
416B ILE* 3.8 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B CYS* 3.1 24.3 - - - +
290B PHE* 3.8 20.4 - - + -
323B ALA 2.9 22.3 + - - +
324B VAL 3.1 4.7 + - - +
326B HIS* 1.3 75.5 - - - +
328B ILE* 1.3 62.1 + - - +
330B ASN* 4.6 0.4 - - - -
331B ASP* 3.2 8.0 + - - +
337B ASP 4.6 0.2 + - - -
338B LYS* 2.9 44.6 + - + +
339B TYR* 2.7 52.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.5 4.9 - - + -
21B LEU* 3.9 24.9 - - + -
28B LEU* 5.2 1.3 - - + -
100B TYR* 3.8 33.3 - - + -
102B VAL* 3.7 29.6 - - + -
290B PHE* 3.4 28.7 - - + -
324B VAL* 2.9 26.7 + - + +
325B ALA 3.8 4.7 - - - +
327B ASN* 1.3 75.3 - - - +
329B VAL* 1.3 63.0 + - - +
331B ASP* 3.1 9.3 + - - +
332B ILE* 3.1 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.2 13.9 - - + +
24B LEU* 4.0 26.9 - - + -
25B MET* 3.5 30.1 - - + -
28B LEU* 5.0 1.6 - - + -
325B ALA 3.1 20.2 + - - +
326B HIS* 3.9 6.1 - - - +
328B ILE* 1.3 75.7 - - + +
330B ASN* 1.3 64.6 + - - +
332B ILE* 3.2 6.6 + - - +
333B ARG* 3.0 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B HIS* 2.9 23.1 + - - +
329B VAL* 1.3 84.6 - - - +
331B ASP* 1.3 57.5 + - - +
333B ARG* 4.5 4.5 + - - +
334B ASN* 3.1 7.3 + - - -
335B ASN* 2.7 65.1 + - - +
337B ASP* 2.8 36.5 + - - +
338B LYS* 3.9 5.4 - - - +
339B TYR* 3.7 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B TYR* 2.4 36.5 + - + +
287B LYS 6.1 1.1 - - - -
290B PHE* 6.2 1.6 - - + -
327B ASN 3.2 12.5 + - - +
328B ILE 3.1 10.2 + - - +
330B ASN* 1.3 72.5 - - - +
332B ILE* 1.3 66.4 + - - +
334B ASN* 3.4 11.2 + - - +
338B LYS* 3.4 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 4.1 29.8 - - + +
25B MET* 4.0 32.5 - - + -
28B LEU* 4.2 10.1 - - + -
100B TYR* 3.4 34.1 - - + +
328B ILE* 3.1 24.7 + - + +
329B VAL* 3.2 7.2 + - - +
331B ASP* 1.3 78.4 - - - +
333B ARG* 1.3 60.2 + - + +
334B ASN* 3.3 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.2 26.1 + - - +
25B MET* 3.3 32.4 - - + +
26B PRO* 5.6 1.0 - - - +
329B VAL* 3.0 33.4 + - - +
330B ASN* 4.3 7.9 + - - +
332B ILE* 1.3 76.3 - - + +
334B ASN* 1.3 70.0 + - - +
335B ASN* 3.4 7.2 + - + +
----------------------------------------------------------
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