Contacts of the helix formed by residues 302 - 327 (chain Y) in PDB entry 3EXG
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 302 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1Y PHE* 3.9 17.9 - - - -
296Y VAL* 4.2 3.1 - - - -
301Y ALA* 1.3 74.3 - - - +
303Y VAL* 1.3 65.3 + - - +
304Y GLU* 3.0 18.7 + - - +
305Y GLU* 2.9 37.0 + - - +
306Y LEU* 3.4 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292Y LYS* 4.6 20.0 - - - -
296Y VAL* 3.9 21.2 - - + +
302Y SER* 1.3 71.7 - - - +
304Y GLU* 1.3 86.9 + - + +
306Y LEU* 3.7 5.2 + - - +
307Y LYS* 3.1 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302Y SER* 3.0 20.7 + - - +
303Y VAL* 1.3 93.0 - - + +
305Y GLU* 1.3 66.7 + - - +
307Y LYS* 3.0 9.2 + - - +
308Y GLU* 2.9 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 305 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1Y PHE* 3.5 9.8 - - + -
29Y ARG* 2.9 32.2 + - - -
33Y LEU* 4.3 10.4 - - - +
301Y ALA* 3.1 14.1 - - - -
302Y SER* 2.9 41.0 + - - +
304Y GLU* 1.3 76.2 - - - +
306Y LEU* 1.3 62.0 + - + +
308Y GLU* 3.0 26.9 + - - +
309Y ILE* 3.1 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Y LEU* 4.3 2.9 - - + -
36Y TYR* 3.7 38.5 - - + +
292Y LYS* 3.6 48.2 - - + +
295Y MET* 4.0 27.4 - - + -
296Y VAL* 4.6 7.9 - - + -
301Y ALA* 4.2 9.4 - - + -
302Y SER 3.4 9.3 + - - +
303Y VAL* 3.8 8.1 - - - +
304Y GLU 3.2 0.4 - - - -
305Y GLU* 1.3 81.1 - - + +
307Y LYS* 1.3 64.6 + - - +
309Y ILE* 3.1 24.4 + - + +
310Y ASP* 3.1 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 307 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303Y VAL* 3.1 18.0 + - + +
304Y GLU* 3.0 9.0 + - - +
306Y LEU* 1.3 81.0 - - - +
308Y GLU* 1.3 58.3 + - + +
310Y ASP* 3.4 21.2 - - - +
311Y VAL* 3.2 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304Y GLU* 2.9 30.7 + - + +
305Y GLU* 3.0 11.2 + - - +
307Y LYS* 1.3 75.4 - - - +
309Y ILE* 1.3 65.3 + - - +
311Y VAL* 3.6 12.1 + - + +
312Y GLU* 3.3 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Y LEU* 4.5 24.9 - - + +
36Y TYR* 4.2 21.5 - - + -
37Y ARG* 3.4 55.9 - - + +
40Y GLN* 5.8 0.9 - - + -
305Y GLU* 3.1 16.6 + - + +
306Y LEU* 3.1 16.7 + - + +
308Y GLU* 1.3 75.4 - - + +
310Y ASP* 1.3 67.6 + - - +
312Y GLU* 3.2 3.5 + - - +
313Y VAL* 2.8 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 310 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Y TYR* 3.3 15.6 + - - -
40Y GLN* 3.1 39.0 - - - +
44Y ARG* 5.7 0.2 - - - +
306Y LEU 3.1 13.0 + - - +
307Y LYS* 3.4 32.2 - - + +
309Y ILE* 1.3 77.3 - - - +
311Y VAL* 1.3 58.6 + - - +
313Y VAL* 3.2 5.0 + - - +
314Y ARG* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 311 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307Y LYS* 3.2 33.4 + - + +
308Y GLU* 3.7 11.7 - - + +
309Y ILE 3.1 0.6 - - - -
310Y ASP* 1.3 76.5 - - - +
312Y GLU* 1.3 65.2 + - + +
314Y ARG* 4.0 4.4 - - - +
315Y LYS* 3.1 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 312 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y ARG* 2.7 38.2 + - - +
308Y GLU* 3.3 17.1 + - - +
309Y ILE* 3.2 7.3 + - - +
311Y VAL* 1.3 78.5 - - + +
313Y VAL* 1.3 57.8 + - - +
315Y LYS* 3.1 7.8 + - - +
316Y GLU* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y ARG* 3.8 26.5 - - - +
40Y GLN* 3.6 29.6 - - + +
41Y THR* 3.5 27.8 - - - +
44Y ARG* 3.7 15.3 - - + -
309Y ILE* 2.8 28.1 + - + +
310Y ASP* 3.7 5.8 - - - +
312Y GLU* 1.3 72.9 - - - +
314Y ARG* 1.3 63.5 + - - +
316Y GLU* 3.0 10.5 - - + +
317Y ILE* 3.0 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 314 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Y ARG* 3.2 50.0 - - + +
310Y ASP 2.9 17.0 + - - +
311Y VAL* 4.0 4.7 - - - +
313Y VAL* 1.3 79.0 - - - +
315Y LYS* 1.3 61.9 + - - +
317Y ILE* 3.7 5.6 + - - +
318Y GLU* 3.2 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 315 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311Y VAL* 3.1 36.1 + - - +
312Y GLU* 3.4 10.5 - - - +
314Y ARG* 1.3 75.2 - - - +
316Y GLU* 1.3 65.9 + - - +
318Y GLU* 3.1 8.3 + - + +
319Y ASP* 2.9 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 316 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y ARG* 4.8 10.9 + - - +
41Y THR* 5.5 5.8 - - + +
102Y VAL* 5.5 9.3 - - + +
312Y GLU* 2.8 19.2 + - - +
313Y VAL* 3.0 18.8 - - + +
315Y LYS* 1.3 70.6 - - - +
317Y ILE* 1.3 68.5 + - + +
319Y ASP* 3.4 8.8 + - - +
320Y ALA* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Y THR* 4.1 21.1 - - + +
44Y ARG* 3.6 27.6 - - + +
45Y MET* 4.2 5.8 - - + -
48Y LYS* 3.6 36.1 - - + -
102Y VAL* 3.6 32.1 - - + -
106Y LEU* 4.7 4.9 - - + -
313Y VAL* 3.0 19.5 + - + +
314Y ARG* 4.1 5.2 - - - +
316Y GLU* 1.3 79.1 - - + +
318Y GLU* 1.3 62.6 + - - +
320Y ALA* 3.1 3.9 + - - +
321Y ALA* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Y LYS* 3.1 36.4 + - - -
314Y ARG* 3.2 27.0 + - + +
315Y LYS* 3.1 8.7 + - + +
317Y ILE* 1.3 81.5 - - - +
319Y ASP* 1.3 62.8 + - - +
321Y ALA* 3.6 4.3 + - - +
322Y GLN* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 319 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Y ARG* 5.1 4.3 + - - +
315Y LYS* 2.9 41.8 + - - +
316Y GLU* 3.8 8.9 + - - +
318Y GLU* 1.3 74.6 - - - +
320Y ALA* 1.3 61.6 + - - +
322Y GLN* 3.2 16.5 + - + +
323Y PHE* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Y VAL* 4.1 14.1 - - + -
103Y ARG* 4.2 27.0 - - + +
106Y LEU* 3.9 15.5 - - + -
316Y GLU 3.1 14.5 + - - +
317Y ILE* 3.2 12.3 - - - +
319Y ASP* 1.3 74.2 - - - +
321Y ALA* 1.3 59.9 + - - +
323Y PHE* 2.9 9.4 + - - +
324Y ALA* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Y LYS* 3.8 35.9 - - + +
52Y LEU* 4.4 8.5 - - + -
106Y LEU* 3.6 10.9 - - + +
317Y ILE 2.8 18.3 + - - +
318Y GLU* 4.0 5.2 - - - +
320Y ALA* 1.3 72.4 - - - +
322Y GLN* 1.3 59.4 + - - +
324Y ALA* 3.5 4.2 - - - -
325Y THR* 2.7 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 322 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Y ARG* 5.5 3.0 - - - +
318Y GLU 3.2 13.9 + - - +
319Y ASP* 3.2 24.3 + - + +
320Y ALA 3.2 0.8 - - - -
321Y ALA* 1.3 75.3 - - - +
323Y PHE* 1.3 81.4 + - - +
325Y THR* 3.6 8.1 + - - -
326Y ALA* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 323 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Y ARG* 3.3 78.3 - - + +
107Y ALA* 4.2 9.0 - - + -
114Y GLY* 4.4 13.0 - - - -
319Y ASP 3.1 13.6 + - - +
320Y ALA 2.9 8.5 + - - +
322Y GLN* 1.3 86.2 - - - +
324Y ALA* 1.3 60.0 + - - +
326Y ALA* 3.8 1.1 - - - -
327Y ASP* 2.9 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Y LEU* 5.3 1.6 - - + -
103Y ARG 4.7 1.1 - - - +
106Y LEU* 3.7 14.4 - - + -
107Y ALA* 3.7 27.1 - - + +
110Y THR* 2.9 34.9 + - + +
112Y ARG* 3.2 16.3 + - - +
320Y ALA 2.8 15.4 + - - +
321Y ALA* 3.6 8.7 - - - +
323Y PHE* 1.3 75.1 - - - +
325Y THR* 1.3 59.9 + - + +
327Y ASP* 4.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 325 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Y LEU* 3.8 28.5 - - + -
55Y GLN* 6.2 0.2 - - - +
57Y ILE* 4.1 18.2 - - + -
110Y THR* 4.6 1.3 - - + -
112Y ARG* 3.2 15.7 + - - +
321Y ALA* 2.7 26.0 + - + +
322Y GLN* 3.6 9.2 + - - -
324Y ALA* 1.3 76.8 - - - +
326Y ALA* 1.3 62.5 + - - +
327Y ASP 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322Y GLN* 3.1 24.6 + - - +
323Y PHE* 4.5 0.7 - - - +
325Y THR* 1.3 77.2 - - - +
327Y ASP* 1.3 65.6 + - - +
328Y PRO* 3.6 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 327 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107Y ALA* 4.7 0.9 - - + +
112Y ARG* 3.1 42.2 + - + +
113Y LYS* 3.7 4.0 + - - +
114Y GLY* 2.7 38.8 + - - -
323Y PHE* 2.9 41.0 + - + +
324Y ALA* 4.4 1.6 - - - +
325Y THR 3.5 0.4 - - - -
326Y ALA* 1.3 78.2 - - - +
328Y PRO* 1.3 77.9 - - - +
----------------------------------------------------------
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