Contacts of the helix formed by residues 6 - 24 (chain C) in PDB entry 6X0A
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 6 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 1.3 80.2 - - - +
7C PRO* 1.3 73.1 - - - +
8C ALA* 3.4 7.5 + - - +
9C ALA* 2.9 23.6 + - - +
10C GLU 3.1 10.0 + - - -
80C ILE 3.0 10.0 + - - -
81C VAL* 2.7 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 3.8 17.9 - - - +
6C SER* 1.3 86.5 - - - +
8C ALA* 1.3 61.1 + - - +
10C GLU* 3.4 9.1 - - + +
11C GLY* 3.3 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 3.1 7.2 + - - +
7C PRO* 1.3 79.1 - - - +
9C ALA* 1.3 64.8 + - - +
11C GLY* 3.0 4.7 + - - -
12C ASP* 3.0 24.9 + - - +
82C ARG* 3.6 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 4.4 3.8 - - + -
6C SER* 2.9 23.9 + - - +
8C ALA* 1.3 74.3 - - - +
10C GLU* 1.3 65.9 + - - +
12C ASP* 3.1 22.6 + - - +
13C LEU* 3.2 17.6 + - - +
80C ILE* 3.7 16.2 - - + +
81C VAL 3.3 12.7 + - - +
83C ILE* 3.7 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 2.7 50.1 + - - +
6C SER 3.1 7.1 + - - -
7C PRO* 3.4 12.2 - - - +
9C ALA* 1.3 76.3 - - - +
11C GLY* 1.3 69.3 + - - +
13C LEU* 3.0 13.6 + - + +
14C VAL* 3.0 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PRO 3.3 5.1 + - - -
8C ALA* 3.0 9.3 + - - -
10C GLU* 1.3 86.8 - - - +
12C ASP* 1.3 63.2 + - - +
14C VAL* 3.4 6.3 + - - +
15C ASP* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ALA 3.0 10.4 + - - +
9C ALA* 3.1 7.7 + - - +
11C GLY* 1.3 77.0 - - - +
13C LEU* 1.3 50.6 + - - +
15C ASP* 3.1 11.1 + - - +
16C ILE* 2.7 41.8 + - + +
82C ARG* 2.5 46.8 + - - -
83C ILE* 2.8 45.7 + - + +
84C VAL* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 6.4 3.1 - - + -
9C ALA 3.2 12.5 + - - +
10C GLU* 3.0 12.8 + - - +
12C ASP* 1.3 75.8 - - - +
14C VAL* 1.3 58.8 + - + +
16C ILE* 3.6 5.4 - - + +
17C TRP* 2.8 28.9 + - - +
32C LEU* 3.6 32.3 - - + +
35C ILE* 3.9 30.3 - - + -
39C ILE* 5.2 7.2 - - + -
80C ILE* 6.3 0.2 - - + -
83C ILE* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 3.0 25.1 + - + +
11C GLY* 3.9 6.1 - - - +
13C LEU* 1.3 74.8 - - + +
15C ASP* 1.3 62.4 + - - +
17C TRP* 3.1 6.5 + - + +
18C LEU* 2.8 50.7 + - + +
32C LEU* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLY* 2.9 20.8 + - - +
12C ASP* 3.4 12.0 - - - +
14C VAL* 1.3 78.9 - - - +
16C ILE* 1.3 64.4 + - + +
18C LEU* 3.4 9.9 + - - +
19C ALA* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP* 2.7 23.9 + - - +
13C LEU* 3.6 13.2 - - + +
15C ASP* 1.3 74.4 - - + +
17C TRP* 1.3 63.4 + - - +
19C ALA* 3.4 5.0 + - - +
20C ILE* 3.2 28.4 + - + +
31C PHE* 3.6 32.1 - - + -
32C LEU* 4.8 2.9 - - + -
35C ILE* 4.3 9.2 - - + -
67C TYR* 4.2 30.5 - - + +
83C ILE* 3.5 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU 2.8 18.1 + - - +
14C VAL* 3.1 8.3 + - + +
16C ILE* 1.3 79.0 - - - +
18C LEU* 1.3 74.4 + - + +
20C ILE* 3.2 1.9 + - - -
21C ALA* 2.6 55.9 + - + +
25C PRO* 3.9 25.6 - - + -
28C ALA* 3.2 33.2 - - + +
29C ASP* 3.0 25.4 + - - -
32C LEU* 3.1 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 2.8 41.2 + - + +
15C ASP* 4.0 9.0 - - - +
17C TRP* 1.3 97.7 - - + +
19C ALA* 1.3 63.1 + - - +
21C ALA* 3.1 3.5 + - + +
22C ASN* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP 3.1 18.5 + - - +
16C ILE* 3.5 6.7 - - - +
18C LEU* 1.3 78.2 - - - +
20C ILE* 1.3 63.7 - - + +
22C ASN* 3.2 20.4 + - - +
23C ASP* 4.1 1.4 + - - +
19F ALA* 6.0 3.4 - - - +
22F ASN* 5.9 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 3.2 21.7 + - + +
17C TRP* 3.9 2.7 - - - +
19C ALA* 1.3 77.4 - - + +
21C ALA* 1.3 62.3 + - - +
23C ASP* 3.2 11.7 + - + +
24C SER 3.0 19.0 + - - +
27C ALA* 3.9 14.6 - - + +
28C ALA* 3.6 25.8 - - + +
31C PHE* 3.5 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TRP* 2.6 56.5 + - + +
18C LEU* 3.1 7.4 + - + +
20C ILE* 1.3 71.1 - - - +
22C ASN* 1.4 65.9 + - - +
23C ASP 3.4 0.2 + - - -
24C SER 3.4 17.5 + - - -
25C PRO* 3.5 18.6 - - + +
28C ALA* 3.8 1.3 - - + +
88F ARG* 3.9 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 3.0 18.9 + - - +
19C ALA* 3.4 13.6 - - - +
20C ILE 3.1 0.6 - - - -
21C ALA* 1.4 74.8 - - - +
23C ASP* 1.3 59.0 + - - +
19F ALA* 6.1 4.5 - - + +
67F TYR* 3.9 9.8 + - - +
85F HIS* 3.0 24.1 + - - -
88F ARG* 3.1 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA 4.1 1.2 + - - +
20C ILE* 3.2 13.1 + - + +
21C ALA 3.8 0.2 - - - -
22C ASN* 1.3 78.8 - - - +
24C SER* 1.3 65.6 + - - +
25C PRO* 4.6 0.5 - - - +
27C ALA* 5.2 5.4 - - - +
66F ASN* 3.6 21.1 + - - +
67F TYR* 3.7 28.5 + - + +
85F HIS* 3.0 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE 3.0 12.0 + - - +
21C ALA* 3.6 3.5 - - - -
23C ASP* 1.3 89.3 - - - +
25C PRO* 1.3 69.0 - - - +
26C ARG* 3.2 18.9 + - - +
27C ALA* 3.3 26.0 + - - +
28C ALA 3.3 6.1 + - - -
66F ASN* 4.0 15.7 + - - -
----------------------------------------------------------
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