Contacts of the helix formed by residues 299 - 320 (chain C) in PDB entry 1Y8Q
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 MET 299 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C VAL* 4.5 4.0 - - - +
160C GLY* 3.7 22.8 + - - +
161C TYR* 3.5 47.1 - - + +
296C PHE 4.9 3.8 - - - +
297C SER* 3.9 3.5 + - - +
298C GLU* 1.3 75.7 - - - +
300C ALA* 1.3 66.0 + - - +
301C PRO* 4.2 7.4 - - + -
302C VAL* 2.8 28.7 + - + +
303C CYS* 3.0 13.5 + - - -
7D LEU* 3.7 36.6 - - + -
39D THR* 5.9 0.7 - - + -
400D LEU* 4.9 4.9 - - + -
403D LEU* 4.5 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU* 5.3 1.0 - - - +
78C ALA 5.9 0.4 - - - +
298C GLU 4.0 1.8 + - - -
299C MET* 1.3 70.5 - - - +
301C PRO* 1.3 72.8 - - + +
303C CYS* 3.2 10.9 + - - +
304C ALA* 3.0 23.4 + - - +
35D ASN* 4.1 9.9 - - - +
38D LEU* 3.7 41.9 + - + +
39D THR* 4.0 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C MET* 3.4 11.4 - - + -
300C ALA* 1.3 89.2 - - + +
302C VAL* 1.3 56.0 + - - +
304C ALA* 3.6 1.4 + - + -
305C VAL* 3.2 32.2 + - - +
35D ASN* 4.8 3.8 - - + +
39D THR* 3.2 31.9 - - + +
396D GLY* 3.6 29.1 - - - +
399D VAL* 3.5 20.9 - - + -
400D LEU* 3.8 22.9 - - + -
403D LEU* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C VAL* 3.3 22.7 - - + -
160C GLY 3.4 20.2 - - - +
161C TYR* 3.9 16.4 - - - +
162C HIS 3.6 21.5 - - - +
299C MET* 2.8 21.8 + - + +
301C PRO* 1.3 72.8 - - - +
303C CYS* 1.3 63.1 + - - +
304C ALA 3.1 1.3 - - - -
305C VAL* 3.2 4.1 + - - -
306C VAL* 2.8 31.7 + - + +
331C PHE* 4.2 16.2 - - + -
400D LEU* 4.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLY* 3.5 43.5 - - - +
47C LEU* 3.5 9.7 - - - +
50C GLU* 3.7 8.1 - - + +
158C VAL* 4.1 24.7 - - - -
298C GLU* 4.5 7.9 - - - -
299C MET 3.0 21.0 + - - -
300C ALA* 3.6 10.1 - - - +
302C VAL* 1.3 75.1 - - - +
304C ALA* 1.3 55.0 + - - +
307C GLY* 2.6 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU* 3.6 20.9 - - - +
300C ALA 3.0 16.3 + - - +
301C PRO 3.6 5.4 - - - +
303C CYS* 1.3 78.4 - - - +
305C VAL* 1.3 57.1 + - - +
308C GLY* 2.9 25.5 + - - -
34D LYS* 4.5 1.1 - - - +
35D ASN* 3.7 24.2 - - - +
392D ALA* 3.8 28.0 - - + +
396D GLY* 4.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C PRO 3.2 18.1 + - - +
302C VAL 3.2 3.5 + - - +
304C ALA* 1.3 77.6 - - - +
306C VAL* 1.3 62.9 + - + +
308C GLY 3.3 0.9 + - - -
309C ILE* 3.1 33.0 + - + +
329C PHE* 5.2 0.7 - - + -
331C PHE* 3.9 42.4 - - + -
393D VAL* 3.6 40.4 - - + +
396D GLY* 4.0 1.6 - - - -
397D LEU* 3.9 22.7 - - + +
400D LEU* 4.8 0.7 - - + -
429D LEU* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.8 18.6 - - + -
157C ASP 4.1 7.9 - - - +
158C VAL* 4.2 5.4 - - + -
163C GLY* 3.7 28.0 - - - -
164C TYR 3.6 24.9 - - - +
165C THR* 4.9 5.8 - - - +
302C VAL* 2.8 23.8 + - + +
305C VAL* 1.3 71.2 - - + +
307C GLY* 1.3 65.6 + - - +
309C ILE* 3.4 5.7 + - - +
310C LEU* 3.0 24.0 + - + +
329C PHE* 4.9 5.4 - - + -
331C PHE* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.2 16.4 - - - +
50C GLU* 4.2 6.3 - - - -
51C ILE* 3.9 13.8 - - - +
54C ASN* 3.2 15.9 + - - -
303C CYS 2.6 24.7 + - - -
304C ALA 3.9 0.4 - - - -
306C VAL* 1.3 73.6 - - - +
308C GLY* 1.3 59.1 + - - +
311C ALA* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASN* 3.7 12.3 - - - +
304C ALA 2.9 18.8 + - - -
305C VAL 3.7 1.3 - - - -
306C VAL 3.2 0.2 - - - -
307C GLY* 1.3 75.8 - - - +
309C ILE* 1.3 58.7 + - - +
312C GLN* 3.1 29.7 + - - +
389D THR* 3.3 15.6 - - - +
392D ALA* 4.7 1.6 - - - -
393D VAL* 3.9 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C THR* 4.7 5.2 - - + -
305C VAL* 3.1 20.5 + - + +
306C VAL 3.9 4.0 - - - +
308C GLY* 1.3 74.8 - - - +
310C LEU* 1.3 66.3 + - - +
312C GLN* 3.2 16.3 + - - +
313C GLU* 3.0 29.8 + - + +
325C HIS* 4.8 3.6 - - + +
329C PHE* 3.8 49.6 - - + -
393D VAL* 3.9 17.9 - - + -
418D LEU* 4.4 14.8 - - + -
428D LEU* 4.4 22.0 - - + -
429D LEU* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 4.8 3.1 - - + -
51C ILE* 3.8 24.2 - - + -
130C CYS* 3.8 17.5 - - - -
131C LEU 5.3 0.4 - - - +
154C PHE* 3.8 35.4 - - + -
155C THR 4.1 2.7 - - - +
156C GLY* 4.0 21.5 - - - -
164C TYR 5.3 0.2 - - - +
165C THR* 3.0 28.2 + - + +
166C PHE 4.9 0.4 - - - +
306C VAL* 3.0 19.4 + - + +
307C GLY 4.2 1.8 - - - +
309C ILE* 1.3 74.6 - - - +
311C ALA* 1.3 67.4 + - - +
313C GLU* 2.9 16.3 + - + +
314C ILE* 2.9 15.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 4.4 10.0 - - - +
54C ASN* 3.4 31.2 - - + +
55C LEU* 3.9 15.9 - - + +
307C GLY 3.1 19.1 + - - +
310C LEU* 1.3 78.1 - - - +
312C GLN* 1.3 57.4 + - - +
314C ILE* 3.3 6.8 + - - +
315C VAL* 2.9 35.4 + - + +
389D THR* 3.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 6.5 0.2 - - + -
308C GLY 3.1 19.1 + - - +
309C ILE* 3.3 20.4 - - - +
310C LEU 3.0 0.8 - - - -
311C ALA* 1.3 78.9 - - - +
313C GLU* 1.3 61.4 - - - +
315C VAL* 3.6 5.0 + - - +
316C LYS* 3.1 37.2 + - + +
325C HIS* 5.4 4.3 - - - -
144D TYR* 3.7 36.9 + - + +
387D ILE* 4.7 0.7 - - + -
389D THR* 2.9 32.3 + - - +
390D THR* 3.3 24.4 + - - +
393D VAL* 5.7 1.2 - - - +
418D LEU* 5.6 5.4 - - - +
428D LEU* 5.9 0.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
154C PHE* 4.1 17.8 - - + -
165C THR* 5.3 7.6 - - + -
167C ALA* 5.6 1.6 - - + -
309C ILE* 3.0 21.2 + - + +
310C LEU* 2.9 11.2 + - + +
312C GLN* 1.3 77.9 - - - +
314C ILE* 1.3 68.4 + - - +
316C LYS* 3.2 23.8 + - - +
317C ALA* 2.9 25.3 + - - +
324C PRO* 3.3 13.6 - - + +
325C HIS* 2.8 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 4.4 8.1 - - + -
51C ILE* 4.4 5.4 - - + -
55C LEU* 3.9 31.4 - - + -
128C ALA* 4.5 8.3 - - + -
130C CYS* 3.9 36.6 - - + -
154C PHE* 3.6 31.2 - - + -
310C LEU* 2.9 22.3 + - + +
311C ALA* 3.6 6.5 - - - +
313C GLU* 1.3 75.8 - - - +
315C VAL* 1.3 64.1 + - - +
317C ALA* 3.1 2.8 + - - +
318C LEU* 3.0 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 3.8 29.2 - - + -
34C LEU* 3.7 34.5 - - + +
54C ASN 5.3 0.9 - - - +
55C LEU* 3.7 19.5 - - + -
58C ALA* 4.0 18.8 - - + -
60C VAL* 5.6 0.2 - - + -
311C ALA* 2.9 22.5 + - + +
312C GLN* 3.8 7.2 - - + +
314C ILE* 1.3 76.9 - - - +
316C LYS* 1.3 59.0 + - + +
318C LEU 3.4 0.3 + - - -
319C SER* 3.1 28.9 + - - +
389D THR* 5.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C HIS* 4.4 1.7 + - - -
312C GLN* 3.1 24.3 + - + +
313C GLU* 3.2 45.4 + - - +
315C VAL* 1.3 76.3 - - - +
317C ALA* 1.3 59.8 + - - +
319C SER* 3.6 7.0 - - - -
320C GLN* 3.0 21.8 + - - -
321C ARG 3.3 20.5 + - - +
322C ASP* 3.8 25.5 - - - +
323C PRO 3.8 18.4 + - - -
324C PRO* 4.5 9.2 - - + -
325C HIS* 4.4 6.7 + - - -
144D TYR* 5.0 20.5 - - + +
420D LYS* 4.5 7.7 + - - +
421D GLN* 4.3 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LYS* 3.1 28.8 - - + -
154C PHE* 3.9 14.4 - - + -
169C LEU* 3.8 26.0 - - + -
172C HIS* 3.2 19.4 - - - -
313C GLU 2.9 17.9 + - - +
314C ILE 3.5 3.4 - - - +
316C LYS* 1.3 78.8 - - - +
318C LEU* 1.3 63.3 + - - +
320C GLN* 3.3 8.1 + - - +
324C PRO* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG* 3.9 13.1 - - - +
34C LEU* 3.8 20.2 - - + -
37C SER* 3.6 38.3 + - - +
39C VAL* 3.8 22.4 - - + -
60C VAL* 4.3 5.2 - - + -
127C ASP* 3.9 22.4 - - + +
128C ALA* 4.0 14.6 - - + -
152C LYS* 4.3 10.4 - - + +
154C PHE* 6.4 0.2 - - + -
314C ILE* 3.0 29.7 + - + +
315C VAL* 3.8 4.5 - - - +
317C ALA* 1.3 78.6 - - - +
319C SER* 1.3 60.2 + - - +
320C GLN* 3.6 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 5.7 4.4 - - - +
30C ALA* 3.6 32.2 - - - +
33C ARG* 3.1 33.5 + - - -
34C LEU* 4.8 5.8 - - - +
315C VAL* 3.1 19.5 + - - +
316C LYS* 3.5 6.6 + - - -
318C LEU* 1.3 75.4 - - - +
320C GLN* 1.3 71.1 + - - +
321C ARG* 3.2 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG* 4.3 19.1 + - - +
152C LYS* 4.8 8.9 + - - -
172C HIS* 4.3 6.0 - - + -
173C GLU* 3.6 26.2 + - - +
174C PHE* 3.7 12.5 - - - +
175C VAL* 3.1 28.2 + - - +
316C LYS 3.0 9.6 + - - -
317C ALA 3.3 14.5 + - - +
318C LEU 4.3 4.5 - - - +
319C SER* 1.3 81.4 - - - +
321C ARG* 1.3 57.8 + - - +
----------------------------------------------------------
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