Contacts of the helix formed by residues 305 - 327 (chain B) in PDB entry 1W98
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 GLN 305 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B MET* 5.2 0.2 - - - -
299B GLN* 3.6 22.4 + - - +
303B GLY 5.0 3.4 - - - +
304B TYR* 1.3 79.7 - - - +
306B TRP* 1.3 66.5 + - - +
307B CYS* 3.2 22.2 + - - -
308B ASP* 3.0 29.1 + - - +
309B ILE* 3.9 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B TYR* 3.7 36.0 - + - -
295B SER* 3.5 28.8 + - - +
298B MET* 5.2 3.8 - - - -
299B GLN* 4.8 4.2 - - - +
304B TYR 4.0 0.2 + - - -
305B GLN* 1.3 74.2 - - - +
307B CYS* 1.3 58.9 + - + +
309B ILE* 3.2 21.6 + - + +
310B GLU* 2.9 67.0 + - + +
313B VAL* 4.2 13.6 - - + +
314B LYS* 5.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLN* 4.1 25.1 - - - -
306B TRP* 1.3 75.6 - - + +
308B ASP* 1.3 74.1 + - - +
309B ILE 3.1 1.5 + - - -
310B GLU* 3.8 23.5 + - - +
311B ASN* 4.9 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PHE* 6.2 0.2 - - - -
283B ILE* 3.2 27.6 - - + +
303B GLY 4.7 0.7 - - - +
304B TYR* 3.5 29.5 - - + +
305B GLN* 3.0 38.8 + - - +
307B CYS* 1.3 83.1 - - - +
309B ILE* 1.3 59.6 + - + +
311B ASN* 5.1 4.0 + - - +
312B CYS 5.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 3.6 31.2 - - + -
286B ALA* 3.6 22.7 - - + -
287B SER* 3.8 10.3 - - - +
290B TYR* 4.8 3.1 - - + -
298B MET* 3.6 26.9 - - - -
304B TYR* 4.0 9.9 - - + -
305B GLN 4.0 8.3 - - - +
306B TRP* 3.5 22.0 - - + +
307B CYS 3.1 0.2 - - - -
308B ASP* 1.3 78.3 - - - +
310B GLU* 1.3 56.6 + - - +
311B ASN 3.4 1.6 - - - -
312B CYS* 3.1 6.5 + - - +
313B VAL* 2.7 59.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B TRP* 2.9 57.8 + - + +
307B CYS* 3.8 17.5 + - - +
308B ASP 3.6 0.2 - - - -
309B ILE* 1.3 76.6 - - - +
311B ASN* 1.3 63.9 + - - +
313B VAL* 3.3 3.8 + - - +
314B LYS* 2.9 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLU* 5.2 4.4 + - - -
279B PHE* 3.8 18.5 - - + -
307B CYS 4.9 3.7 + - - +
308B ASP 5.4 3.8 - - - +
309B ILE 3.4 0.6 - - - -
310B GLU* 1.3 84.0 - - - +
312B CYS* 1.3 63.0 + - - +
314B LYS* 3.1 10.4 + - - +
315B TRP* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PHE* 3.5 31.7 - - + -
283B ILE* 3.4 25.6 - - + -
284B LEU* 3.8 22.9 - - - -
287B SER* 3.1 30.5 - - - +
308B ASP 5.3 0.6 + - - +
309B ILE 3.1 5.7 + - - +
311B ASN* 1.3 75.7 - - - +
313B VAL* 1.3 57.0 + - - +
315B TRP* 3.0 4.0 + - - +
316B MET* 2.7 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B SER* 3.9 9.6 + - - -
290B TYR* 3.6 33.2 - - + -
291B HIS* 3.4 22.3 - - + +
306B TRP* 4.2 13.0 - - + +
309B ILE* 2.7 47.6 + - + +
310B GLU* 3.5 7.9 - - - +
312B CYS* 1.3 70.8 - - - +
314B LYS* 1.3 62.2 + - + +
316B MET* 3.4 1.3 + - - -
317B VAL* 3.0 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B TRP* 5.9 3.1 - - + -
310B GLU* 2.9 38.5 + - + +
311B ASN* 3.4 11.2 - - - +
312B CYS 3.1 0.2 - - - -
313B VAL* 1.3 76.6 - - + +
315B TRP* 1.3 65.0 + - - +
317B VAL* 3.2 25.0 - - + +
318B PRO* 3.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B CYS* 3.5 23.8 - - + -
273B ASP* 4.1 10.0 + - + -
275B ASP* 4.2 15.8 + - + +
276B CYS* 3.5 35.2 - - + -
278B GLU* 5.8 1.6 - - - -
279B PHE* 3.7 36.8 - + + -
284B LEU* 3.6 24.5 - - + -
311B ASN 3.0 6.7 + - - +
312B CYS 3.5 5.4 - - - +
314B LYS* 1.3 77.9 - - - +
316B MET* 1.3 86.7 + - + +
318B PRO* 3.2 13.9 - - - +
319B PHE* 3.5 35.8 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
266B LEU* 3.1 48.2 - - + -
267B LEU* 5.2 1.1 - - - -
270B CYS* 3.9 9.2 - - - -
284B LEU* 4.0 6.1 - - + +
287B SER* 3.6 12.3 - - - -
288B ALA* 3.3 29.4 - - - -
291B HIS* 3.3 28.0 - - + +
312B CYS* 2.7 21.0 + - - +
313B VAL* 4.3 0.2 - - - -
315B TRP* 1.3 96.0 - - + +
317B VAL* 1.3 66.1 + - - +
318B PRO 3.4 0.2 - - - -
319B PHE* 2.8 21.1 + - - +
320B ALA* 3.1 11.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B HIS* 4.0 13.7 + - - +
313B VAL* 3.0 31.8 + - + +
314B LYS* 3.2 17.5 - - + +
316B MET* 1.3 73.8 - - - +
318B PRO* 1.3 75.1 - - + +
320B ALA* 3.3 3.1 + - - +
321B MET* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LYS 3.8 4.0 - - - +
315B TRP* 3.2 18.2 - - - +
316B MET 3.4 0.7 - - - -
317B VAL* 1.3 100.1 - - + +
319B PHE* 1.3 65.3 + - + +
321B MET* 3.2 6.0 + - + +
322B VAL* 2.9 34.6 + - - +
357B LYS 4.3 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 3.7 6.5 - - + -
269B LEU* 3.8 30.3 - - + +
270B CYS* 3.7 28.5 - - - -
273B ASP* 3.8 19.3 - - + -
315B TRP* 3.5 52.9 - + - -
316B MET* 2.8 17.0 + - - +
318B PRO* 1.3 81.2 - - + +
320B ALA* 1.3 61.5 + - - +
322B VAL* 3.3 4.7 + - - +
323B ILE* 3.0 27.0 + - - +
354B LEU 5.9 0.2 - - - -
355B LEU* 3.6 29.6 - - + -
357B LYS 5.9 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 3.6 17.3 - - + +
291B HIS* 3.5 41.5 - - + +
292B PHE* 6.2 0.4 - - + -
316B MET* 3.1 8.6 + - + +
317B VAL 3.5 7.2 - - - +
319B PHE* 1.3 76.5 - - - +
321B MET* 1.3 58.2 + - + +
323B ILE* 3.3 5.1 + - - +
324B ARG* 2.7 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B HIS* 6.1 2.0 - - + -
317B VAL* 3.0 23.0 + - + +
318B PRO* 3.2 6.9 + - + +
320B ALA* 1.3 80.6 - - + +
322B VAL* 1.3 60.2 + - + +
324B ARG* 3.5 34.7 - - + +
325B GLU* 2.8 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU* 4.3 5.8 - - + -
318B PRO 2.9 15.8 + - - +
319B PHE* 3.8 4.7 - - - +
321B MET* 1.3 76.5 - - + +
323B ILE* 1.3 64.6 + - - +
325B GLU* 3.4 18.9 + - - +
326B THR* 3.2 24.1 + - - -
354B LEU* 3.7 46.4 - - + +
357B LYS* 3.5 43.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLN 5.3 0.2 - - - +
265B GLU* 3.8 39.0 - - + +
266B LEU* 4.3 14.6 - - + -
269B LEU* 4.1 12.8 - - + -
292B PHE* 4.1 28.7 - - + -
319B PHE 3.0 15.9 + - - +
320B ALA* 3.5 8.7 - - - +
322B VAL* 1.3 76.5 - - - +
324B ARG* 1.3 66.6 + - + +
326B THR* 3.1 8.0 + - - -
327B GLY* 3.0 24.7 + - - +
328B SER* 4.2 11.0 - - - +
349B ARG* 5.4 3.4 - - - +
354B LEU* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B HIS 3.2 25.0 + - - -
292B PHE* 3.5 49.8 + - + +
320B ALA* 2.7 26.5 + - + +
321B MET* 3.5 30.9 - - + +
323B ILE* 1.3 72.0 - - + +
325B GLU* 1.3 63.1 + - - +
327B GLY* 3.3 13.4 + - - -
328B SER* 5.2 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B MET* 2.8 38.5 + - + +
322B VAL* 3.4 23.6 - - - +
323B ILE 3.2 0.2 - - - -
324B ARG* 1.3 75.3 - - - +
326B THR* 1.3 58.4 + - - +
357B LYS* 5.3 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 3.2 14.2 + - - +
323B ILE* 3.1 7.5 + - + -
325B GLU* 1.3 77.9 - - - +
327B GLY* 1.3 62.6 + - - +
349B ARG* 3.3 33.7 + - - +
354B LEU* 3.7 24.8 - - + +
357B LYS* 5.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLU* 4.7 0.3 - - - +
323B ILE* 3.0 17.1 + - - +
324B ARG* 3.3 12.2 + - - -
325B GLU 3.4 0.2 - - - -
326B THR* 1.3 90.9 - - - +
328B SER* 1.3 65.7 + - - -
349B ARG* 3.7 8.0 + - - -
----------------------------------------------------------
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