Contacts of the helix formed by residues 13 - 36 (chain A) in PDB entry 1VGO
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 GLU 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG* 3.2 33.8 + - - +
12A PRO* 1.3 79.8 - - - +
14A THR* 1.3 57.0 + - + +
15A LEU 2.9 5.8 - - - -
16A TRP* 2.8 33.9 + - + +
17A LEU* 3.2 20.2 + - + +
84A TYR* 3.0 27.3 + - + +
206A LEU* 3.9 31.8 - - + +
207A GLY* 4.5 7.2 - - - -
210A THR* 3.8 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP* 4.2 0.7 - - - -
6A LEU* 3.2 29.0 + - - +
7A LEU* 3.5 22.3 - - + +
9A ASP* 4.3 1.3 - - - +
11A ARG* 3.0 58.0 + - + +
13A GLU* 1.3 79.6 - - + +
15A LEU* 1.3 58.9 + - - +
17A LEU* 3.7 11.7 - - + -
18A GLY* 2.9 25.3 + - - -
65A PHE* 3.4 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP 5.4 4.3 - - - +
6A LEU* 3.8 30.9 - - + +
12A PRO 3.1 14.3 + - - +
13A GLU 2.9 0.2 - - - -
14A THR* 1.3 82.4 + - - +
16A TRP* 1.3 99.5 + - + +
18A GLY* 3.9 0.5 + - - -
19A ILE* 3.1 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PRO 4.5 3.0 + - - -
13A GLU* 2.8 26.7 + - + +
15A LEU* 1.3 106.5 - - + +
17A LEU* 1.3 60.2 + - - +
18A GLY 3.3 0.4 - - - -
19A ILE* 3.8 18.3 - - + +
20A GLY 3.1 20.6 + - - -
207A GLY* 3.3 29.5 + - - -
208A ILE* 6.2 0.9 - - + +
210A THR* 3.8 14.4 - - + +
211A LEU* 3.8 45.7 - - + +
214A MET* 3.4 21.3 - - + +
308A BNG 3.2 32.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG* 4.4 1.6 - - - +
13A GLU* 3.2 19.3 + - + +
14A THR* 3.3 14.8 + - - +
16A TRP* 1.3 75.8 - - - +
18A GLY* 1.3 54.9 + - - +
21A THR* 2.5 35.7 + - - -
61A TYR* 3.5 29.9 - - + +
64A MET* 3.6 46.4 - - + +
65A PHE* 4.3 13.2 - - - +
84A TYR* 4.2 18.4 - - + +
87A ARG* 5.4 4.7 - - - +
210A THR* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 5.1 3.6 - - - -
14A THR 2.9 15.3 + - - -
15A LEU 4.4 1.1 - - - -
17A LEU* 1.3 76.6 - - - +
19A ILE* 1.3 63.2 + - - +
21A THR* 3.2 7.5 + - - -
22A LEU* 3.1 33.6 + - - +
65A PHE* 3.8 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.1 33.4 + - + +
16A TRP* 3.6 29.4 + - + +
18A GLY* 1.3 75.0 - - - +
20A GLY* 1.3 58.5 + - - +
22A LEU* 3.3 8.8 + - + +
23A LEU* 3.0 50.4 + - + +
214A MET* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP 3.1 12.9 + - - -
17A LEU 3.6 0.2 + - - -
18A GLY 3.2 0.2 - - - -
19A ILE* 1.3 74.1 - - - +
21A THR* 1.3 63.7 + - - +
23A LEU* 4.2 3.3 - - - +
24A MET* 3.0 32.4 + - - +
61A TYR* 3.8 15.2 - - - -
214A MET* 3.7 24.9 - - - -
218A VAL* 6.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 2.5 24.4 + - - -
18A GLY* 3.2 11.3 + - - -
20A GLY* 1.3 77.7 - - - +
22A LEU* 1.3 59.0 + - + +
24A MET* 3.6 3.2 - - - +
25A LEU* 2.9 50.2 + - + +
58A SER* 3.9 16.9 + - - +
61A TYR* 3.2 22.1 + - - -
62A LEU* 3.9 25.8 - - + +
65A PHE* 4.6 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY* 3.1 25.5 + - - +
19A ILE* 3.6 9.9 - - + +
20A GLY 3.3 0.2 - - - -
21A THR* 1.3 80.8 - - + +
23A LEU* 1.3 56.8 + - + +
25A LEU* 3.2 17.7 + - + +
26A ILE* 2.7 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.0 39.6 + - + +
20A GLY* 4.2 3.4 - - - +
22A LEU* 1.3 77.5 - - + +
24A MET* 1.3 58.4 + - - +
26A ILE* 3.8 16.6 - - + +
27A GLY* 2.9 25.8 + - - -
214A MET* 4.1 17.0 - - + -
218A VAL* 4.1 25.3 - - + +
222A VAL* 4.0 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLY* 3.0 20.5 + - - +
21A THR* 3.6 2.7 - - - +
23A LEU* 1.3 78.7 - - - +
25A LEU* 1.3 51.2 + - - +
28A THR* 2.5 37.2 + - - -
54A PRO* 3.3 23.6 - - - +
57A ALA* 3.3 29.4 - - + +
58A SER* 3.0 15.9 - - - +
61A TYR* 4.2 13.7 - - + -
214A MET 5.4 0.4 - - - +
217A ASP* 3.8 28.9 - - + +
218A VAL* 3.9 9.0 - - + +
221A LYS* 3.5 29.8 - - + -
222A VAL* 4.2 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 2.9 43.6 + - + +
22A LEU* 3.5 18.4 - - + +
24A MET* 1.3 75.4 - - - +
26A ILE* 1.3 65.1 + - + +
28A THR* 3.2 5.8 + - - +
29A PHE* 3.0 46.4 + - + -
58A SER* 3.0 24.1 + - - +
62A LEU* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 2.7 41.2 + - + +
23A LEU* 3.8 17.7 - - + +
25A LEU* 1.3 73.2 - - + +
27A GLY* 1.3 59.1 + - - +
29A PHE* 3.2 8.5 + - - +
30A TYR* 3.0 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 2.9 16.9 + - - -
24A MET 4.0 1.1 - - - -
26A ILE* 1.3 74.7 - - - +
28A THR* 1.3 65.3 + - - +
30A TYR* 3.8 6.4 - - - +
31A PHE* 3.1 35.5 + - - -
54A PRO* 4.5 2.5 - - - -
222A VAL* 4.1 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET 2.5 25.6 + - - -
25A LEU* 3.2 9.6 + - - -
27A GLY* 1.3 77.3 - - - +
29A PHE* 1.3 59.8 + - + +
31A PHE* 3.5 4.4 + - - +
32A ILE* 3.2 40.0 + - + +
51A ILE* 3.5 29.7 - - + +
54A PRO* 3.1 26.7 + - - +
55A GLY* 3.5 11.2 - - - -
58A SER* 3.7 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.0 43.1 + - + +
26A ILE* 3.7 6.7 - - - +
28A THR* 1.3 79.4 - - + +
30A TYR* 1.3 58.9 + - - +
31A PHE 3.2 0.2 - - - -
32A ILE* 3.4 20.6 + - + +
33A ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.0 19.9 + - + +
27A GLY* 3.4 6.0 + - - +
29A PHE* 1.3 77.1 - - - +
31A PHE* 1.3 79.9 + + - +
33A ALA* 3.5 6.8 + - + +
34A ARG* 2.9 68.0 + - + +
222A VAL* 6.1 1.1 - - + -
226A PHE* 3.8 34.4 - + - -
230A ARG* 4.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLY 3.1 20.4 + - - +
28A THR 3.7 4.9 - - - +
30A TYR* 1.3 101.4 - + - +
32A ILE* 1.3 64.6 + - - +
34A ARG* 4.6 4.3 - - - -
35A GLY* 3.0 17.5 + - - -
47A TYR* 3.4 14.6 - - - -
50A THR* 4.1 10.5 - - + -
51A ILE* 3.9 17.1 - - + +
54A PRO* 4.0 22.2 - - + -
221A LYS 4.0 15.5 - - - -
222A VAL* 3.5 34.5 - - + -
225A GLY* 3.7 7.2 - - - -
226A PHE* 3.6 21.8 - - + -
229A LEU* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.2 28.2 + - + +
29A PHE* 3.8 23.3 - - + +
30A TYR 3.3 0.2 - - - -
31A PHE* 1.3 74.9 - - - +
33A ALA* 1.3 56.1 + - - +
35A GLY 3.1 0.9 + - - -
36A TRP* 2.8 48.5 + - + +
51A ILE* 3.6 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE 2.9 18.2 + - - +
30A TYR* 3.7 8.3 - - + +
32A ILE* 1.3 80.3 - - - +
34A ARG* 1.3 59.1 + - - +
35A GLY 3.5 0.2 + - - -
36A TRP* 3.9 11.7 + - - +
37A GLY 4.7 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 2.9 55.9 + - + +
31A PHE* 4.1 3.8 - - - +
33A ALA* 1.3 76.1 - - - +
35A GLY* 1.3 58.9 + - - +
37A GLY 4.8 2.2 + - - -
38A VAL* 3.6 14.9 - - - +
47A TYR* 3.1 24.0 + - + +
226A PHE* 5.6 0.4 - - - -
229A LEU* 3.6 26.3 + - - -
230A ARG* 3.6 17.5 - - - +
238B THR 4.3 7.1 + - - -
239B GLU* 2.8 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE 3.0 9.8 + - - -
32A ILE* 3.1 2.4 + - - -
34A ARG* 1.3 78.5 - - - +
36A TRP* 1.3 65.5 + - - +
37A GLY 3.2 3.3 + - - -
38A VAL* 3.3 11.2 + - - +
44A ARG* 3.1 18.6 + - - +
47A TYR* 3.5 32.3 - - - +
51A ILE* 5.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 2.8 33.6 + - + +
33A ALA* 3.9 8.3 + - - +
34A ARG 3.6 0.8 - - - -
35A GLY* 1.3 72.8 - - - +
37A GLY* 1.3 62.4 + - - +
44A ARG* 3.3 29.7 + - - +
----------------------------------------------------------
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