Contacts of the helix formed by residues 306 - 320 (chain C) in PDB entry 1AX4
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 306 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLY* 4.4 1.6 - - - -
69C ASP 3.3 24.9 - - - -
70C GLU* 2.8 14.4 + - - +
77C ASN* 3.6 13.0 - - - +
301C TYR* 5.7 0.2 - - - +
304C LEU 3.8 1.2 + - - -
305C ALA* 1.3 70.9 - - - +
307C ARG* 1.3 62.3 + - - +
309C MET* 3.2 19.7 + - - +
310C ALA* 3.0 18.2 + - - +
500D K 4.4 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C MET* 3.4 58.2 - - + +
68C GLY* 4.3 6.4 - - - -
70C GLU* 2.9 16.7 + - - +
305C ALA* 3.7 15.4 - - + +
306C GLY* 1.3 76.8 - - - +
308C ASP* 1.3 67.7 + - - +
310C ALA* 3.3 3.2 + - - +
311C ALA 3.0 22.7 + - - -
57D MET* 3.7 13.7 - - - +
62D TRP* 4.7 9.7 - - - -
65D MET* 3.8 30.2 - - - +
270D LEU* 6.1 0.6 - - - +
271D ASN* 3.0 40.0 + - - +
272D ILE* 4.3 2.6 - - - +
307D ARG* 4.7 4.4 - - - +
308D ASP* 2.7 29.9 + - - -
311D ALA* 5.7 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 308 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C MET* 4.1 4.0 - - - +
270C LEU* 4.5 3.4 - - + +
272C ILE* 3.6 25.5 - - + +
304C LEU* 4.2 23.0 - - + +
305C ALA* 3.0 27.9 + - - +
307C ARG* 1.3 79.4 + - - +
309C MET* 1.3 65.6 + - - +
311C ALA* 3.8 6.4 - - - +
312C MET* 2.9 24.6 + - - +
272D ILE* 5.0 1.4 - - - +
307D ARG* 2.7 30.0 + - - -
308D ASP* 4.2 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C SER* 3.9 18.6 - - - +
77C ASN* 3.8 13.7 - - + +
78C TYR* 4.0 15.7 - - - +
81C LEU* 4.4 11.7 - - + +
96C PRO* 4.1 12.6 - - - -
300C THR 3.3 27.4 - - - +
301C TYR* 3.8 22.2 - - + -
304C LEU* 4.1 20.6 - - + -
305C ALA 3.3 6.2 + - - +
306C GLY* 3.2 24.5 + - - +
308C ASP* 1.3 75.7 - - - +
310C ALA* 1.3 62.9 + - - +
312C MET* 3.2 8.2 + - - +
313C VAL* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 3.2 41.2 - - + +
68C GLY* 4.3 2.0 - - - -
77C ASN* 3.5 28.4 - - - +
306C GLY 3.0 11.2 + - - +
307C ARG 3.5 7.0 - - - +
309C MET* 1.3 77.8 - - - +
311C ALA* 1.3 63.2 + - - +
313C VAL* 3.2 15.8 + - - +
314C GLN* 3.3 8.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
57C MET* 4.2 13.2 - - - -
61C GLN* 3.7 15.0 + - + +
64C ALA* 4.4 2.2 - - - +
65C MET* 3.8 18.8 - - + -
270C LEU* 3.6 18.1 - - + +
307C ARG 3.0 16.2 + - - +
308C ASP* 3.8 8.7 - - - +
310C ALA* 1.3 76.2 - - - +
312C MET* 1.3 51.9 + - - +
314C GLN* 3.3 2.4 + - - +
315C GLY* 2.7 35.0 + - - -
307D ARG* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 3.7 31.6 - - + -
262C MET* 5.8 0.9 - - - +
264C ALA* 3.8 17.3 - - + -
268C PRO* 5.0 0.9 - - + -
270C LEU* 3.5 19.5 - - + +
273C GLY* 3.9 4.7 - - - -
274C GLY 3.5 33.2 - - - +
275C LEU* 4.6 10.1 - - - -
304C LEU* 3.7 24.2 - - + -
308C ASP 2.9 15.4 + - - +
309C MET* 3.5 6.7 - - - +
311C ALA* 1.3 78.1 - - - +
313C VAL* 1.3 63.0 + - - +
316C LEU* 2.9 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ASN* 4.2 2.5 - - - +
80C ASP* 3.9 23.8 - - + +
81C LEU* 3.6 41.7 - - + +
84C LYS* 4.0 20.3 + - + -
309C MET 3.1 15.9 + - - +
310C ALA* 3.6 9.6 - - - +
312C MET* 1.3 79.2 - - - +
314C GLN* 1.3 62.0 + - - +
316C LEU* 3.8 6.7 + - - +
317C GLU* 3.6 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C HIS* 3.8 19.7 + - - +
61C GLN* 3.5 25.4 - - + +
64C ALA* 4.7 6.3 - - + -
310C ALA 3.3 9.0 + - - +
311C ALA 3.3 7.0 + - - +
313C VAL* 1.3 78.6 - - - +
315C GLY* 1.3 65.3 + - - +
317C GLU* 3.2 15.0 + - - +
318C GLU* 2.9 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLN* 3.3 17.0 - - - +
268C PRO* 3.1 31.6 - - - +
269C LEU* 4.8 0.4 - - - -
311C ALA 2.7 17.5 + - - -
312C MET 3.8 0.9 - - - -
314C GLN* 1.3 70.4 - - - +
316C LEU* 1.3 58.2 + - - +
318C GLU* 4.0 4.2 - - - +
319C GLY* 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 3.9 26.0 - - + -
84C LYS* 4.1 18.2 - - + -
85C ALA* 5.5 2.5 - - - +
88C LEU* 3.9 17.8 - - + +
89C PHE* 4.8 3.8 - - + -
227C PHE* 4.0 21.5 - - + -
228C CYS* 5.2 1.4 - - - -
262C MET* 4.1 13.0 - - + -
268C PRO* 3.8 26.6 - - + +
275C LEU* 4.9 8.7 - - + -
312C MET* 2.9 29.9 + - + +
313C VAL 3.9 4.5 - - - +
314C GLN 3.3 0.2 - - - -
315C GLY* 1.3 75.0 - - - +
317C GLU* 1.3 61.5 + - - +
319C GLY* 3.7 2.3 + - - -
320C THR* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LYS* 2.7 33.0 + - - +
247C LYS* 2.7 39.7 + - - -
313C VAL 3.6 5.7 + - - +
314C GLN* 3.2 20.6 + - - +
316C LEU* 1.3 79.1 - - - +
318C GLU* 1.3 60.9 + - - +
320C THR* 2.7 26.0 + - - -
321C GLU* 3.9 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C SER* 2.4 29.0 + - - -
60C HIS* 4.1 2.1 - - - +
61C GLN* 3.5 5.0 - - - +
269C LEU* 3.8 13.0 - - + -
314C GLN* 2.9 46.1 + - - +
315C GLY* 3.3 2.0 + - - +
317C GLU* 1.3 75.1 - - + +
319C GLY* 1.3 61.6 + - - +
321C GLU* 3.1 39.7 + - - +
324C TYR* 3.8 10.4 - - - +
420C ARG* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C CYS* 3.3 27.2 - - - +
267C ASP 3.6 20.1 - - - +
268C PRO* 5.1 0.2 - - - -
269C LEU* 3.6 7.6 - - - +
315C GLY 2.8 17.0 + - - -
316C LEU* 4.3 1.3 - - - -
317C GLU 3.2 0.4 - - - -
318C GLU* 1.3 76.5 - - - +
320C THR* 1.3 56.5 + - - +
321C GLU 3.3 0.2 - - - -
324C TYR* 4.0 5.3 - - - -
325C LEU* 3.4 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 4.2 19.3 - - + -
227C PHE* 5.0 0.2 - - + -
228C CYS* 4.0 10.1 - - - -
246C ILE* 3.3 32.6 - - - +
247C LYS* 3.6 23.2 - - + +
250C ILE* 3.8 20.9 - - + -
316C LEU 3.1 19.7 - - - +
317C GLU* 2.7 16.3 + - - -
319C GLY* 1.3 78.5 - - - +
321C GLU* 1.3 64.3 + - - +
322C GLU 3.4 0.7 + - - -
325C LEU* 3.9 2.2 - - - -
----------------------------------------------------------
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