Contacts of the helix formed by residues 17 - 32 (chain W) in PDB entry 6XAV
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 PHE 17 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281I TYR 5.3 0.7 - - - -
1282I GLY* 3.6 31.0 - - - -
483J LEU* 4.1 11.2 - - + -
910J ASN* 5.2 2.5 - - + -
911J LYS 4.2 18.6 - - - -
912J GLY 4.8 0.7 - - - -
913J GLU* 3.2 34.8 - - - -
1359J ALA 4.0 15.0 - - - -
1360J GLY* 4.0 17.9 - - - +
1361J THR* 3.9 20.5 - - + +
1363J TYR* 6.1 0.2 - - + -
15W ASN* 2.9 20.4 + - - +
16W ARG* 1.3 92.1 - - + +
18W ASP* 1.3 69.7 + - - +
19W LEU 3.2 2.1 + - - -
20W VAL* 3.4 13.0 + - - +
21W LEU* 3.5 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1364J ALA* 5.3 5.9 - - - +
13W ILE* 5.4 5.3 - - + +
15W ASN* 3.1 33.0 + - + +
17W PHE* 1.3 77.5 - - - +
19W LEU* 1.3 62.1 + - + +
21W LEU* 3.1 19.5 + - + +
22W VAL* 2.8 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482J ALA* 6.0 3.6 - - + -
9W ALA* 4.9 11.2 - - + +
10W VAL* 5.3 7.6 - - + -
13W ILE* 3.4 64.2 - - + +
15W ASN* 4.4 1.3 - - + -
16W ARG* 3.4 28.9 - - - +
17W PHE 3.2 0.8 - - - -
18W ASP* 1.3 77.9 - - - +
20W VAL* 1.3 60.0 + - + +
22W VAL* 3.3 10.1 - - + +
23W ALA* 2.9 33.2 + - - +
51W LEU* 5.0 6.4 - - + +
54W ILE* 4.5 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285I TYR* 5.9 0.4 - - + -
475J GLU* 4.1 12.1 - - + +
478J LEU* 3.7 26.6 - - + +
479J GLU* 3.8 21.5 - - + +
482J ALA* 4.2 23.1 - - + -
483J LEU* 4.6 13.2 - - + -
1361J THR* 4.2 9.9 - - + -
16W ARG 4.0 18.8 - - - +
17W PHE 3.4 7.1 + - - +
18W ASP 3.3 0.2 - - - -
19W LEU* 1.3 77.0 - - + +
21W LEU* 1.3 58.9 + - + +
23W ALA* 4.6 3.6 - - - -
24W ALA* 3.0 28.8 + - - +
51W LEU* 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1285I TYR* 3.9 34.8 - - + +
475J GLU* 5.7 2.5 - - + -
1361J THR* 4.2 21.8 - - + +
1364J ALA* 4.5 15.9 - - + -
17W PHE* 3.5 15.5 - - + +
18W ASP* 3.1 22.8 + - + +
20W VAL* 1.3 80.3 - - + +
22W VAL* 1.3 64.0 + - + +
24W ALA* 3.3 5.1 + - + +
25W ARG* 3.2 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W ASP* 2.8 31.1 + - + +
19W LEU* 3.3 22.9 - - + +
21W LEU* 1.3 75.6 - - + +
23W ALA* 1.3 61.7 + - + +
25W ARG* 3.7 8.7 + - - +
26W ARG* 3.1 28.2 + - - +
54W ILE* 5.0 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478J LEU* 3.7 17.7 - - + -
19W LEU 2.9 18.9 + - - +
20W VAL* 4.6 0.4 - - - -
22W VAL* 1.3 78.9 - - + +
24W ALA* 1.3 60.1 + - - +
26W ARG* 4.4 4.5 - - - -
27W ALA* 2.9 34.1 + - - +
50W ALA* 3.8 13.2 - - + +
51W LEU* 3.8 23.1 - - + -
54W ILE* 5.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474J LEU* 3.9 9.9 - - + +
475J GLU* 3.4 39.5 - - + +
478J LEU* 3.5 11.9 - - + +
20W VAL 3.0 19.2 + - - +
21W LEU* 3.3 6.3 + - + +
23W ALA* 1.3 77.2 - - - +
25W ARG* 1.3 62.6 + - + +
28W ARG* 3.1 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W LEU* 3.2 18.4 + - - +
22W VAL* 4.1 7.4 - - - +
24W ALA* 1.3 78.7 - - + +
26W ARG* 1.3 62.2 + - - +
28W ARG* 3.4 7.5 + - - +
29W GLN* 3.2 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22W VAL 3.1 19.3 + - - +
23W ALA* 3.9 5.6 - - - +
25W ARG* 1.3 78.1 - - - +
27W ALA* 1.3 61.4 + - - +
29W GLN* 3.2 25.2 + - - +
30W MET* 3.3 38.5 + - + +
35W LYS* 2.8 36.3 - - - +
36W ASP 5.6 0.4 + - - -
37W PRO* 5.7 0.6 - - - +
38W LEU* 3.7 23.6 - - - +
50W ALA* 4.7 6.5 - - + -
53W GLU* 3.2 31.0 + - - +
54W ILE* 5.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474J LEU* 3.7 18.4 - - + -
478J LEU* 5.5 1.6 - - + -
23W ALA 2.9 19.0 + - - +
24W ALA* 4.8 0.4 - - - -
26W ARG* 1.3 76.9 - - - +
28W ARG* 1.3 62.8 + - - +
30W MET* 3.2 8.7 + - - +
31W GLN* 3.1 23.9 + - - +
46W THR* 3.4 34.7 - - - +
47W THR* 4.4 4.5 - - + +
50W ALA* 3.8 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1312I ASN* 2.9 28.1 + - - -
1313I HIS 3.3 22.0 + - - -
1314I GLN* 3.3 35.6 + - - +
474J LEU* 3.5 29.5 - - + +
475J GLU* 4.3 16.4 + - - -
24W ALA 3.1 19.9 + - - +
25W ARG* 3.7 8.1 - - - +
26W ARG 3.2 0.2 - - - -
27W ALA* 1.3 78.5 - - - +
29W GLN* 1.3 57.2 + - + +
31W GLN* 4.5 4.3 - - - +
32W VAL* 2.8 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W ARG* 3.2 32.9 + - - +
26W ARG* 3.2 29.7 + - - +
28W ARG* 1.3 77.4 - - + +
30W MET* 1.3 57.9 + - - +
32W VAL* 5.0 2.2 - - - -
33W GLY* 3.1 21.2 + - - +
35W LYS* 4.1 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 30 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W ARG* 3.3 46.4 - - + +
27W ALA* 3.5 12.3 - - - +
28W ARG 3.1 0.8 - - - -
29W GLN* 1.3 79.4 - - - +
31W GLN* 1.3 60.6 + - - +
33W GLY 3.0 15.1 - - - +
34W GLY* 4.4 1.6 - - - -
35W LYS* 4.3 19.4 + - + +
36W ASP 6.5 0.2 - - - -
37W PRO* 4.8 11.9 - - + -
46W THR* 4.3 13.2 - - + +
49W ILE* 3.8 32.1 - - + -
50W ALA* 4.4 10.5 - - - -
53W GLU* 3.2 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1311I GLY* 2.9 32.4 + - - +
1312I ASN* 4.7 3.0 + - - +
1313I HIS* 4.1 23.1 + - - +
474J LEU* 3.7 29.9 - - - +
27W ALA 3.1 12.7 + - - +
28W ARG* 4.2 3.9 - - - +
30W MET* 1.3 79.5 - - - +
32W VAL* 1.3 70.0 + - - +
33W GLY 3.3 3.8 + - - -
34W GLY* 4.5 1.2 + - - -
46W THR* 3.7 26.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1311I GLY 5.6 1.6 - - - -
1312I ASN* 4.1 25.8 - - + +
1314I GLN* 5.5 0.7 - - - +
28W ARG* 2.8 56.1 + - + +
29W GLN* 5.0 1.3 - - - -
31W GLN* 1.3 75.7 - - + +
33W GLY* 1.3 56.8 - - - +
34W GLY 4.3 0.7 + - - -
----------------------------------------------------------
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