Contacts of the helix formed by residues 8 - 23 (chain D) in PDB entry 1GT0
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 ASN 8 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A T 3.1 15.6 + - - -
7A G 3.0 45.1 + - - +
8A T 4.2 24.0 - - - +
44B A 3.9 7.3 + - - -
6D PRO 3.7 3.2 + - - +
7D MET* 1.3 76.4 - - - +
9D ALA* 1.3 66.5 + - - +
10D PHE* 2.9 7.1 + - - +
11D MET* 2.7 36.3 + - - +
12D VAL* 3.1 11.4 + - - +
56D ALA* 3.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A G 5.1 8.4 + - - +
8A T 5.8 0.6 + - - +
8D ASN* 1.3 75.0 - - - +
10D PHE* 1.3 62.0 - - - +
12D VAL* 3.2 4.5 + - - +
13D TRP* 3.1 23.6 + - - +
41D TRP* 3.9 13.0 - - + -
52D PHE* 3.8 6.9 - - - +
53D ILE* 3.6 44.0 - - + +
56D ALA* 3.4 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A T 3.6 28.3 - + - -
6A T 3.4 40.2 - - - +
7A G 4.4 6.1 - - - -
8D ASN* 2.9 11.0 + - - +
9D ALA* 1.3 75.8 - - - +
11D MET* 1.3 60.4 + - - +
13D TRP* 3.7 14.4 - + - -
14D SER* 2.7 57.6 + - - -
18D ARG* 6.0 0.2 - - - -
34D SER* 5.7 0.2 - - - -
37D LEU* 3.9 9.0 - - + -
38D GLY* 4.0 20.4 - - - -
41D TRP* 3.4 57.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A T 5.1 1.6 - - - +
6A T 4.5 1.8 - - - +
44B A 3.5 43.7 - - + +
45B A 3.1 74.7 - - + +
7D MET* 4.0 17.3 - - + +
8D ASN* 2.7 33.6 + - - +
10D PHE* 1.3 86.2 - - - +
12D VAL* 1.3 60.8 + - - +
14D SER* 3.1 13.2 + - - +
15D ARG* 3.2 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D MET* 3.9 18.4 - - + +
8D ASN 3.1 14.6 + - - +
9D ALA* 3.2 8.7 + - - +
11D MET* 1.3 74.1 - - - +
13D TRP* 1.3 63.1 + - - +
15D ARG* 3.0 25.6 - - - +
16D GLY 3.8 1.7 + - - -
52D PHE* 4.1 17.2 - - + +
55D GLU* 3.8 27.6 - - + +
56D ALA* 4.6 4.0 - - - -
59D LEU* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ALA 3.1 5.1 + - - +
10D PHE* 3.7 9.0 - + - +
12D VAL* 1.3 76.2 - - - +
14D SER* 1.3 84.2 + - - +
15D ARG 3.0 1.8 - - - -
16D GLY* 2.8 23.6 + - - -
17D GLN* 3.5 36.0 + - + +
37D LEU* 3.7 41.5 - - + -
40D GLU* 3.6 29.6 - - + -
41D TRP* 3.5 36.8 - + + -
44D LEU* 3.8 22.7 - - + +
52D PHE* 3.5 47.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B A 5.2 3.0 + - - -
10D PHE* 2.7 45.2 + - - -
11D MET* 3.1 16.5 + - - +
13D TRP* 1.3 87.8 - - - +
15D ARG* 1.3 57.0 + - - +
16D GLY 2.9 0.3 + - - -
17D GLN 3.2 1.1 + - - +
18D ARG* 2.7 43.7 + - - +
37D LEU* 3.7 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B A 2.6 30.4 + - - -
46B A 2.4 34.8 + - - -
7D MET* 4.3 25.8 - - - +
11D MET 3.2 10.2 + - - +
12D VAL* 3.0 18.2 - - - +
14D SER* 1.3 82.1 + - - +
16D GLY* 1.3 61.4 + - - +
18D ARG* 3.6 13.3 - - - +
19D ARG* 4.1 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D VAL 3.8 1.8 + - - -
13D TRP 2.8 12.0 + - - -
15D ARG* 1.3 77.4 - - - +
17D GLN* 1.3 70.6 + - - -
18D ARG 3.1 2.2 + - - -
19D ARG* 3.1 15.4 + - - +
20D LYS* 3.4 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D TRP* 3.5 44.6 + - + +
14D SER 3.2 0.6 + - - +
16D GLY* 1.3 77.6 - - - +
18D ARG* 1.3 66.5 + - - +
20D LYS* 2.9 34.7 + - - +
21D MET* 3.2 7.0 + - + +
37D LEU* 3.2 25.8 - - + -
40D GLU* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A T 4.3 2.4 + - - -
45B A 3.8 19.3 + - - -
46B A 3.0 61.0 + - - +
10D PHE* 6.0 0.2 - - - -
14D SER* 2.7 27.1 + - - +
15D ARG* 3.6 11.7 - - - +
17D GLN* 1.3 71.1 - - - +
19D ARG* 1.3 59.3 + - - +
21D MET* 3.9 1.2 - - - +
22D ALA* 2.9 35.1 + - + +
30D ASN* 3.2 29.5 + - - +
33D ILE* 3.6 18.4 - - - +
34D SER* 3.2 28.5 + - - +
37D LEU* 3.8 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ARG 4.1 4.0 + - - +
16D GLY 3.1 9.4 + - - +
18D ARG* 1.3 75.5 - - + +
20D LYS* 1.3 54.0 - - - +
21D MET 2.6 18.5 + - - -
22D ALA* 4.2 4.9 - - - -
23D GLN* 3.0 31.3 + - + +
24D GLU 3.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLY 3.4 8.1 + - - +
17D GLN* 2.9 20.6 + - - +
19D ARG* 1.3 75.2 - - - +
21D MET* 1.3 61.8 + - - +
24D GLU* 4.2 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLN* 3.3 11.9 - - + +
18D ARG* 4.0 2.0 - - - +
19D ARG 2.6 3.0 + - - -
20D LYS* 1.3 77.2 - - - +
22D ALA* 1.3 64.9 + - - +
23D GLN 3.5 0.4 - - - -
24D GLU* 4.0 8.6 - - - +
25D ASN* 2.8 37.5 + - + +
28D MET* 3.9 26.7 - - + +
33D ILE* 4.0 29.6 - - + -
36D ARG* 3.6 33.0 - - + +
37D LEU* 4.1 15.5 - - + -
40D GLU* 4.9 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B G 6.4 1.6 - - - -
18D ARG* 2.9 27.4 + - + +
19D ARG* 3.9 4.7 - - - +
21D MET* 1.3 75.7 - - - +
23D GLN* 1.3 61.0 + - - +
25D ASN 4.5 1.8 - - - -
26D PRO* 2.9 33.8 - - - +
28D MET 6.0 0.7 - - - -
30D ASN* 5.4 2.0 - - - +
33D ILE* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ARG* 3.0 16.9 + - + +
22D ALA* 1.3 74.6 - - - +
24D GLU* 1.3 67.8 + - - +
26D PRO* 3.1 18.9 - - - +
----------------------------------------------------------
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