Contacts of the helix formed by residues 309 - 336 (chain C) in PDB entry 4WLU
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 SER 309 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C SER* 4.1 10.3 + - - -
308C VAL* 1.3 78.8 - - - +
310C SER* 1.3 54.6 + - - +
311C PHE* 3.5 10.8 + - - +
312C GLU* 3.0 36.7 + - - +
313C GLU* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C SER* 1.3 72.2 - - - +
311C PHE* 1.3 59.8 + - - +
313C GLU* 3.8 9.9 - - - +
314C LYS* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C GLN* 3.9 25.8 - - - +
223C LEU* 3.7 30.3 - - + -
224C THR* 4.2 20.9 - - + -
227C THR* 3.7 24.0 - - + -
309C SER* 3.5 10.7 + - - +
310C SER* 1.3 80.2 - - - +
312C GLU* 1.3 64.4 + - + +
314C LYS* 3.4 5.7 + - + +
315C MET* 3.1 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ILE* 4.4 0.7 - - - +
207C PRO 4.1 2.6 - - - +
208C LEU* 3.9 22.7 - - + +
209C ILE* 3.1 11.1 + - - +
210C SER* 2.6 48.7 + - - -
223C LEU* 6.1 1.0 - - - +
308C VAL* 3.3 16.7 - - + +
309C SER* 3.0 31.3 + - - +
311C PHE* 1.3 75.8 - - + +
313C GLU* 1.3 66.2 + - - +
315C MET* 3.0 23.8 + - + +
316C ILE* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C VAL* 4.0 21.6 - - + +
309C SER 2.8 22.6 + - - +
310C SER* 3.8 9.7 - - - +
312C GLU* 1.3 71.3 - - - +
314C LYS* 1.3 61.9 + - - +
316C ILE* 3.3 10.0 + - + +
317C SER* 3.1 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C SER 2.9 18.4 + - - +
311C PHE* 3.5 8.1 - - + +
312C GLU 3.2 0.2 - - - -
313C GLU* 1.3 77.6 - - - +
315C MET* 1.3 62.0 + - + +
317C SER* 3.3 10.5 + - - -
318C ASP* 2.8 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LYS* 4.6 4.4 - - - +
206C ILE* 3.8 28.1 - - + +
207C PRO* 4.4 8.1 - - + +
227C THR* 3.6 28.0 - - + +
231C GLN* 4.0 13.5 - - - +
311C PHE* 3.1 46.9 + - + +
312C GLU* 3.0 28.8 + - + +
314C LYS* 1.3 76.1 - - + +
316C ILE* 1.3 62.8 + - - +
318C ASP* 3.4 7.0 + - - +
319C ALA* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ILE* 3.9 24.7 - - + -
206C ILE* 3.7 20.9 - - + -
208C LEU* 5.2 1.1 - - + -
283C THR* 4.8 7.4 - - + -
288C PHE* 4.4 17.4 - - + -
305C ILE* 4.0 22.0 - - + -
308C VAL* 4.4 9.4 - - + -
312C GLU 2.9 20.3 + - - +
313C GLU* 3.5 15.7 - - + +
314C LYS 3.3 0.2 - - - -
315C MET* 1.3 75.3 - - - +
317C SER* 1.3 62.4 + - - +
319C ALA* 3.1 11.8 + - - +
320C ILE* 3.3 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C GLU* 3.1 10.8 + - - -
314C LYS* 3.3 14.4 + - - -
316C ILE* 1.3 80.1 - - - +
318C ASP* 1.3 67.1 + - - +
319C ALA 3.4 0.7 + - - -
320C ILE* 3.6 13.0 + - - +
321C PRO* 3.5 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LYS* 3.5 28.2 + - + +
314C LYS* 2.8 57.8 + - - +
315C MET* 3.4 6.9 + - - +
317C SER* 1.3 80.6 + - - +
319C ALA* 1.3 60.3 + - - +
320C ILE 3.5 0.2 - - - -
321C PRO* 3.7 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LYS* 3.8 26.9 - - - +
204C THR* 3.9 11.6 - - + +
206C ILE* 3.9 14.1 - - + -
288C PHE* 6.0 0.7 - - + -
315C MET 3.0 16.6 + - - +
316C ILE 3.1 5.4 + - - +
318C ASP* 1.3 78.7 - - - +
320C ILE* 1.3 64.7 + - - +
321C PRO 3.4 0.4 - - - -
322C GLU* 3.2 7.3 + - - +
323C LEU* 3.1 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C THR* 4.6 12.8 - - + -
284C GLU* 3.7 44.0 - - + +
285C CYS* 3.8 19.5 - - - -
288C PHE* 5.1 4.5 - - + -
316C ILE* 3.3 29.8 + - + +
317C SER* 3.9 11.7 - - - +
318C ASP 3.5 0.2 - - - -
319C ALA* 1.3 76.1 - - - +
321C PRO* 1.3 66.9 - - + +
323C LEU* 3.3 2.0 + - - +
324C LYS* 2.9 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C SER 3.5 13.2 - - - +
318C ASP* 3.7 10.3 - - - +
319C ALA 3.6 3.1 - - - -
320C ILE* 1.3 95.9 - - + +
322C GLU* 1.3 60.9 + - - +
324C LYS* 3.9 6.3 - - + +
325C ALA* 3.1 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ASN* 5.3 0.9 - - - +
201C ALA* 4.0 24.5 - - - +
202C GLY* 5.3 0.7 - - - -
203C LYS* 3.1 36.2 + - - +
204C THR* 3.6 17.5 - - + -
318C ASP 5.0 1.0 + - - -
319C ALA 3.2 8.8 + - - +
321C PRO* 1.3 75.8 - - - +
323C LEU* 1.3 59.3 + - - +
325C ALA* 3.2 7.4 + - - +
326C SER* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ASN* 3.6 33.7 - - + +
198C GLY* 4.1 10.5 - - - +
199C GLY* 3.9 9.6 - - - +
204C THR* 3.8 14.8 - - + -
277C PHE* 4.2 10.8 - - + -
285C CYS* 3.9 13.5 - - - -
287C TYR 4.8 1.6 - - - +
288C PHE* 3.7 36.6 - - + -
319C ALA* 3.1 23.5 + - + +
320C ILE* 3.7 6.7 - - - +
322C GLU* 1.3 76.6 - - - +
324C LYS* 1.3 56.7 + - - +
326C SER* 3.2 5.2 + - - -
327C ILE* 2.8 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 324 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLU* 3.0 36.2 + - + +
285C CYS* 4.1 19.3 - - - -
320C ILE* 2.9 34.0 + - + +
321C PRO* 3.9 6.1 - - + +
323C LEU* 1.3 72.8 - - - +
325C ALA* 1.3 57.7 + - - +
327C ILE* 3.7 8.4 - - + +
328C LYS* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C PRO 3.1 18.7 + - - +
322C GLU* 3.6 7.0 - - - +
324C LYS* 1.3 77.1 - - - +
326C SER* 1.3 57.1 + - - +
328C LYS* 3.5 7.5 + - - +
329C LYS* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASP* 5.1 6.5 + - - +
143C PRO* 6.1 0.6 - - - +
145C ASN* 3.6 31.3 + - - +
146C SER* 2.9 28.7 + - - -
322C GLU* 2.9 27.6 + - - +
323C LEU* 3.6 4.7 - - - -
325C ALA* 1.3 72.1 - - - +
327C ILE* 1.3 65.3 + - - +
329C LYS* 3.4 6.2 + - - +
330C GLY 3.2 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ASN 4.0 9.9 - - - +
149C PRO* 3.8 9.5 - - + +
277C PHE* 4.5 3.8 - - + -
285C CYS* 4.1 11.0 - - + -
286C THR* 3.6 16.4 - - - +
287C TYR* 3.6 53.2 - - + +
323C LEU* 2.8 33.5 + - + +
324C LYS* 3.7 8.1 - - + +
326C SER* 1.3 72.4 - - - +
328C LYS* 1.3 63.7 + - - +
330C GLY* 3.2 3.8 + - - -
331C GLU* 3.0 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C LYS 2.9 18.9 + - - +
325C ALA* 3.8 6.3 - - - +
327C ILE* 1.3 76.4 - - - +
329C LYS* 1.3 53.3 + - - +
331C GLU* 3.2 14.3 + - - +
332C ASP* 2.8 72.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASP* 3.0 41.1 + - - +
114C PHE* 3.6 42.7 - - + +
146C SER* 4.4 2.5 - - - +
325C ALA 3.0 18.4 + - - +
326C SER* 3.5 9.0 - - - +
327C ILE 3.2 0.2 - - - -
328C LYS* 1.3 76.7 - - - +
330C GLY* 1.3 61.5 + - - +
332C ASP* 3.9 6.6 - - - +
333C PHE* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 4.2 1.3 - - - -
146C SER* 3.7 15.4 - - - -
149C PRO* 4.5 0.2 - - - -
150C ILE* 3.4 37.9 - - - +
326C SER 3.2 5.3 + - - -
327C ILE 3.2 6.9 + - - -
329C LYS* 1.3 76.9 - - - +
331C GLU* 1.3 63.4 + - - +
333C PHE* 3.2 9.2 + - - +
334C VAL* 3.3 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C PRO* 4.3 9.1 - - + +
153C GLU* 4.2 32.3 - - + +
286C THR* 4.1 6.2 + - - +
287C TYR* 4.1 9.8 + - + -
327C ILE* 3.0 34.4 + - - +
328C LYS* 3.6 18.0 - - - +
330C GLY* 1.3 74.8 - - - +
332C ASP* 1.3 67.2 + - - +
334C VAL* 3.2 6.1 + - - +
335C LYS* 3.1 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C LYS* 2.8 59.5 + - - +
329C LYS* 3.9 6.3 - - - +
331C GLU* 1.3 76.9 - - - +
333C PHE* 1.3 61.2 + - - +
335C LYS* 3.4 15.9 + - - +
336C THR* 3.3 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 333 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 3.7 17.9 - + + -
115C ASN* 5.8 2.2 - - - -
118C ALA* 3.5 36.3 - - + -
119C THR* 3.5 33.4 - - + -
122C ALA* 3.9 4.9 - - + -
150C ILE* 4.0 9.0 - - + -
329C LYS 3.1 14.9 + - - +
330C GLY* 3.5 8.1 - - - +
331C GLU 3.2 0.4 - - - -
332C ASP* 1.3 77.6 - - - +
334C VAL* 1.3 68.4 + - + +
336C THR* 2.7 28.9 + - - -
337C LEU* 3.6 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ILE* 3.7 40.4 - - + +
153C GLU* 3.8 33.2 - - + +
154C VAL* 4.2 12.6 - - + -
157C LYS* 5.7 4.9 - - + -
330C GLY 3.3 13.4 + - - +
331C GLU 3.2 7.4 + - - +
333C PHE* 1.3 75.3 - - + +
335C LYS* 1.3 67.5 + - - +
337C LEU* 3.1 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C GLU* 3.2 31.9 + - - +
331C GLU* 3.1 24.8 + - - +
332C ASP* 3.5 15.3 - - - +
333C PHE 3.2 0.4 - - - -
334C VAL* 1.3 76.8 - - - +
336C THR* 1.3 58.6 + - + +
337C LEU 3.2 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ASP 3.3 15.0 - - - +
333C PHE* 2.7 24.9 + - - -
334C VAL 3.1 0.2 - - - -
335C LYS* 1.3 78.9 - - + +
337C LEU* 1.3 66.8 + - - +
----------------------------------------------------------
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