Contacts of the helix formed by residues 15 - 36 (chain C) in PDB entry 1USI
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 ILE 15 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA* 3.9 4.5 - - + +
12C SER 5.6 0.2 - - - +
13C GLY 3.3 0.2 - - - -
14C PRO* 1.3 90.8 - - + +
16C ALA* 1.3 65.7 + - - +
17C GLN 3.0 4.8 + - - -
18C TRP* 3.0 29.9 + - + +
19C GLY 3.6 2.6 + - - -
53C CYS* 3.9 35.4 - - + -
77C LEU* 4.6 0.2 - - + -
78C CYS* 4.0 8.1 - - - -
148C GLN* 6.3 0.2 - - - +
202C TYR* 3.8 42.4 - - + -
203C TYR* 3.6 11.4 - - + -
204C PRO* 4.0 13.2 - - + -
205C GLU* 5.8 0.2 - - - +
1346C PHE* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ARG* 3.6 28.9 - - - +
10C ALA* 3.7 11.4 - - - +
11C MET 3.9 1.3 - - - -
12C SER 3.7 24.1 + - - +
13C GLY 3.3 15.2 + - - +
14C PRO 3.4 1.4 - - - -
15C ILE* 1.3 78.2 - - - +
17C GLN* 1.3 58.5 + - - +
19C GLY* 2.9 4.7 + - - -
20C ASP* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ARG* 4.4 1.4 + - - -
235A ASN* 2.9 34.8 + - + +
236A ILE* 4.4 12.1 - - - +
13C GLY 4.6 0.9 - - - +
14C PRO* 3.5 10.9 + - - +
15C ILE 3.0 0.8 + - - -
16C ALA* 1.3 83.1 + - - +
18C TRP* 1.3 60.6 + - - +
20C ASP* 3.2 24.0 + - - +
21C MET* 3.6 12.3 + - - +
203C TYR* 2.8 31.2 + - - +
230C ASN* 3.8 18.2 - - - +
232C SER* 3.0 26.7 + - - +
236C ILE* 5.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 3.0 26.4 + - + +
17C GLN* 1.3 77.1 - - - +
19C GLY* 1.3 63.5 + - - +
21C MET* 3.3 48.4 + - + +
22C GLU* 3.3 11.4 + - - +
77C LEU* 3.8 17.5 - - + +
202C TYR* 4.5 3.5 - + - -
203C TYR* 3.5 19.0 - + - -
226C GLU* 3.3 24.0 - - + -
227C GLY* 3.1 23.5 + - - -
229C GLY 3.4 22.7 - - - -
230C ASN* 3.6 25.4 - - + -
248C MET* 6.2 0.4 - - + -
275C PRO* 4.7 7.4 - - + -
276C TYR* 4.4 9.7 - + - +
1346C PHE* 3.1 42.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA 3.3 20.9 - - - -
15C ILE 3.6 0.6 + - - -
16C ALA 2.9 5.4 + - - -
18C TRP* 1.3 81.5 - - - +
20C ASP* 1.3 61.7 + - - +
22C GLU* 3.1 8.6 + - - +
23C PHE* 2.9 32.4 + - - -
77C LEU* 3.4 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ARG* 2.9 43.1 + - - -
235A ASN* 4.2 2.8 - - - +
238A GLY* 3.3 18.7 - - - -
239A ASP* 4.8 7.7 + - - +
11C MET* 5.6 1.7 - - - -
16C ALA 2.9 13.1 + - - +
17C GLN* 3.5 15.7 - - - +
18C TRP 3.2 0.4 - - - -
19C GLY* 1.3 75.3 - - - +
21C MET* 1.3 59.5 + - + +
23C PHE* 4.0 3.8 - - - +
24C ASN* 3.0 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLN 4.1 7.9 - - - +
18C TRP* 3.3 44.8 + - + +
19C GLY 3.2 0.2 - - - -
20C ASP* 1.3 74.4 - - + +
22C GLU* 1.3 65.0 + - - +
24C ASN* 3.4 2.4 + - - +
25C GLY 3.0 18.9 + - - -
230C ASN* 4.1 14.4 - - - +
231C ALA* 5.7 2.0 - - + +
271C ASP* 5.7 4.9 - - - +
274C GLY* 3.7 32.1 - - - -
275C PRO* 4.2 0.7 - - + -
276C TYR* 4.1 10.3 - - + -
277C VAL* 3.5 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 4.2 6.5 - - + +
8C VAL 2.8 26.2 + - - +
9C GLY* 3.4 21.4 - - - -
18C TRP 3.3 8.1 + - - +
19C GLY* 3.1 7.0 + - - +
21C MET* 1.3 80.3 - - - +
23C PHE* 1.3 68.1 + - - +
25C GLY 3.2 0.3 + - - -
26C ALA* 2.9 24.6 + - - +
74C ILE 3.9 8.1 - - - +
75C GLY* 4.3 0.9 - - - -
76C HIS 4.7 0.3 - - - -
77C LEU* 3.6 26.7 - - + +
99C PRO* 3.7 15.0 - - + +
276C TYR* 4.3 2.8 + - + +
280C THR* 3.2 37.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 3.4 42.8 - - + -
8C VAL 4.1 0.7 - - - -
9C GLY 3.7 26.2 - - - -
10C ALA 4.2 1.8 - - - -
11C MET* 3.4 35.2 - - + -
19C GLY 2.9 29.3 + - - +
20C ASP* 4.3 3.8 - - - +
22C GLU* 1.3 84.5 - - - +
24C ASN* 1.3 58.2 + - - +
26C ALA* 3.8 3.7 - - + +
27C ARG* 2.9 59.5 + - - +
48C GLU* 3.7 32.5 - - + -
49C TYR 3.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP* 2.7 39.6 + - - +
20C ASP* 3.0 27.5 + - - +
21C MET* 4.0 5.9 - - - +
23C PHE* 1.3 76.7 - - - +
25C GLY* 1.3 60.4 + - - +
27C ARG* 3.6 8.5 + - - +
28C GLN* 3.2 24.3 + - - +
265C LEU* 4.5 10.9 - - + +
270C LYS* 3.6 36.3 + - + +
271C ASP 5.4 5.2 + - - +
277C VAL* 4.7 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C MET 3.0 11.9 + - - -
22C GLU 3.7 2.5 - - - -
24C ASN* 1.3 78.1 - - - +
26C ALA* 1.3 55.0 + - - +
28C GLN* 3.4 1.6 + - - -
29C ALA* 2.9 30.5 + - - +
277C VAL* 3.4 33.5 - - - +
281C TYR* 3.5 16.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 3.8 36.8 - - + -
22C GLU 2.9 16.8 + - - +
23C PHE* 3.9 4.5 - - + +
25C GLY* 1.3 75.0 - - - +
27C ARG* 1.3 63.2 + - + +
29C ALA* 3.3 1.9 + - - +
30C ILE* 3.0 31.9 + - + +
48C GLU* 6.1 0.2 - - - +
74C ILE* 5.4 0.2 - - + -
280C THR* 3.8 10.8 - - + +
284C VAL* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP* 3.0 29.1 + - - +
11C MET* 3.8 16.6 - - - +
23C PHE* 2.9 35.6 + - - +
24C ASN* 3.7 10.1 + - - +
26C ALA* 1.3 76.8 - - + +
28C GLN* 1.3 56.9 + - - +
30C ILE* 3.8 7.5 - - + +
31C LYS* 3.0 30.4 + - - +
48C GLU* 2.7 42.5 + - - +
270C LYS* 5.0 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASN 3.2 15.7 + - - +
25C GLY* 3.9 3.1 - - - +
27C ARG* 1.3 76.9 - - - +
29C ALA* 1.3 59.8 + - - +
31C LYS* 3.4 23.0 + - - +
32C ASP* 2.8 67.7 + - - +
261C ILE* 4.3 13.5 - - + -
264C ALA* 3.7 30.9 - - + +
265C LEU* 4.4 14.2 - - + +
268C ASP* 4.2 13.9 - - - +
270C LYS* 5.8 0.5 + - - -
281C TYR* 3.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLY 2.9 18.5 + - - +
26C ALA 3.6 2.2 - - - +
28C GLN* 1.3 75.9 - - - +
30C ILE* 1.3 62.7 + - - +
32C ASP* 3.2 1.2 + - - +
33C ILE* 3.0 32.8 + - + +
281C TYR* 3.4 35.5 - - + +
284C VAL* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 5.3 7.2 - - + -
7C VAL* 4.6 13.0 - - + -
26C ALA* 3.0 25.5 + - + +
27C ARG* 3.8 6.7 - - + +
29C ALA* 1.3 71.4 - - - +
31C LYS* 1.3 67.2 + - - +
33C ILE* 3.9 0.9 - - - +
34C ASN* 3.0 31.1 + - - +
44C LEU* 3.5 42.6 - - + +
45C VAL 4.7 1.1 - - - -
46C GLY* 3.6 31.6 - - - +
284C VAL* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ARG 3.0 18.8 + - - +
28C GLN* 3.6 26.1 + - - +
29C ALA 3.3 0.2 - - - -
30C ILE* 1.3 77.7 - - - +
32C ASP* 1.3 60.1 + - - +
34C ASN* 3.3 5.9 + - - +
35C ALA* 3.0 30.6 + - + +
268C ASP* 5.0 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLN* 2.8 46.5 + - - +
29C ALA 3.2 2.6 + - - +
31C LYS* 1.3 75.9 - - - +
33C ILE* 1.3 65.5 - - + +
35C ALA* 3.6 5.6 + - - +
36C LYS* 3.3 31.6 + - + +
261C ILE* 4.0 9.7 - - - +
264C ALA* 5.5 0.2 - - - +
281C TYR* 2.6 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ALA* 3.0 24.4 + - + +
30C ILE 4.0 2.7 - - - +
32C ASP* 1.3 77.1 - - + +
34C ASN* 1.3 63.6 + - - +
36C LYS* 3.1 15.6 + - + +
37C GLY 3.4 1.0 + - - -
38C GLY* 2.9 36.3 + - - +
39C ILE* 4.2 10.5 - - + -
44C LEU* 3.8 20.2 - - + -
281C TYR* 5.8 1.6 - - + +
284C VAL* 3.7 30.3 - - + +
285C GLN* 4.5 10.8 - - + -
288C ALA* 4.0 20.0 - - + -
292C GLU* 4.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ILE* 3.0 25.5 + - - +
31C LYS* 3.6 5.9 - - - +
33C ILE* 1.3 78.4 - - - +
35C ALA* 1.3 60.5 + - - +
37C GLY* 3.3 11.1 + - - -
38C GLY* 3.7 11.5 + - - +
43C LYS* 3.5 23.8 - - + +
44C LEU* 2.7 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LYS* 3.0 19.6 + - + +
32C ASP* 4.1 6.3 - - - +
33C ILE 3.3 0.2 - - - -
34C ASN* 1.3 76.5 - - - +
36C LYS* 1.3 59.4 + - + +
37C GLY 3.3 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ASP* 3.3 19.6 + - + +
33C ILE* 3.1 11.1 + - + +
35C ALA* 1.3 79.0 - - + +
37C GLY* 1.3 55.4 + - - +
38C GLY 5.1 0.9 - - - +
----------------------------------------------------------
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