Contacts of the helix formed by residues 13 - 37 (chain M) in PDB entry 2GTL
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 LEU 13 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M PHE 4.8 1.6 - - - +
11M GLN 3.0 0.4 - - - -
12M TYR* 1.3 94.7 - - + +
14M VAL* 1.3 64.3 + - + +
16M ASN* 3.3 24.9 - - - +
17M GLN* 3.6 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M PHE 4.2 13.5 - - - +
11M GLN* 3.0 12.9 + - + +
13M LEU* 1.3 79.9 - - + +
15M LYS* 1.3 64.2 + - - +
16M ASN 2.8 6.7 + - - -
17M GLN* 2.9 16.6 + - + +
18M ASN* 3.1 32.8 + - - +
14N LEU* 5.3 16.2 - - + -
13O ILE* 4.2 24.2 - - + +
14O ILE* 5.9 1.3 - - + -
17O LEU* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M GLN* 2.7 30.3 + - + +
12M TYR* 5.2 3.1 - - - +
14M VAL* 1.3 73.4 - - - +
16M ASN* 1.3 58.0 + - - +
18M ASN* 4.4 6.2 + - - +
19M LEU* 3.8 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 16 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M TYR 3.2 25.3 + - - -
13M LEU* 3.3 15.5 + - - +
14M VAL 2.9 1.0 - - - -
15M LYS* 1.3 78.8 - - + +
17M GLN* 1.3 74.7 + - - +
18M ASN 3.2 1.6 - - - -
19M LEU* 2.7 29.5 + - + +
20M HIS* 2.7 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M LEU 3.6 16.3 + - - +
14M VAL* 2.9 11.3 + - + +
16M ASN* 1.3 85.9 + - - +
18M ASN* 1.3 67.5 + - - +
19M LEU 3.0 0.9 + - - -
20M HIS* 3.0 18.3 + - + +
21M ILE* 3.1 14.7 + - + +
14N LEU* 4.0 29.9 + - - +
17N ASN* 3.9 20.9 + - - +
18N ALA* 4.6 10.4 - - - +
21N ILE* 4.1 20.2 - - + -
17O LEU* 4.1 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 18 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M VAL* 3.1 22.4 + - - +
15M LYS* 4.5 6.2 - - - +
17M GLN* 1.3 78.6 - - - +
19M LEU* 1.3 59.1 + - + +
21M ILE* 3.6 7.1 - - - +
22M ASP* 2.8 24.4 + - - +
16O LYS* 5.6 1.4 - - - +
17O LEU* 3.1 37.0 + - - +
20O ARG* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LYS 3.8 14.6 - - - +
16M ASN* 2.7 22.6 + - + +
18M ASN* 1.3 79.8 - - + +
20M HIS* 1.3 57.9 + - - +
21M ILE 2.9 1.3 - - - -
22M ASP* 3.1 12.5 + - + +
23M TYR* 2.7 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 20 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M ASN* 2.7 14.8 + - - +
17M GLN* 3.0 13.7 + - + +
19M LEU* 1.3 71.5 - - - +
21M ILE* 1.3 58.9 + - + +
23M TYR* 3.0 23.5 - + - +
24M LEU* 2.8 46.2 - - + +
21N ILE* 4.1 24.5 - - + +
22N ILE* 5.7 4.3 - - + -
25N ASP* 3.7 23.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M GLN* 3.1 15.2 + - + +
18M ASN* 3.6 11.0 - - - +
19M LEU 2.9 0.8 - - - -
20M HIS* 1.3 76.0 - - - +
22M ASP* 1.3 56.6 + - - +
23M TYR 2.7 14.8 + - - -
24M LEU* 2.9 20.2 + - + +
25M ALA* 3.0 13.5 + - + +
21N ILE* 3.9 23.3 - - + -
17O LEU 4.7 6.1 - - - +
20O ARG* 3.4 37.7 - - + +
21O THR* 3.3 41.5 - - + +
24O ILE* 4.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M ASN 2.8 18.1 + - - +
19M LEU* 3.1 18.6 + - + +
21M ILE* 1.3 72.9 - - - +
23M TYR* 1.3 62.5 - - - +
25M ALA* 3.7 8.6 - - - +
26M LYS* 3.6 14.9 + - - +
20O ARG* 3.2 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M LEU* 2.7 14.3 + - + +
20M HIS* 3.0 26.0 - + - +
21M ILE 2.7 0.8 + - - -
22M ASP* 1.3 73.2 - - - +
24M LEU* 1.3 72.8 + - + +
25M ALA 3.0 1.1 - - - -
26M LYS* 2.6 31.9 + - + +
27M LYS* 3.1 29.6 + - + +
25N ASP* 5.3 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M HIS* 2.8 44.9 - - + +
21M ILE* 2.9 11.9 + - + +
23M TYR* 1.3 86.5 - - + +
25M ALA* 1.3 64.4 + - - +
26M LYS 3.1 0.2 + - - -
27M LYS* 3.1 8.5 + - - +
28M LEU* 2.9 26.0 + - - +
21N ILE* 4.2 17.9 - - + +
24N LEU* 4.0 42.0 - - + +
25N ASP* 4.8 10.3 - - - +
28N ILE* 5.1 11.0 - - + +
24O ILE* 3.4 17.9 - - + -
28O ILE* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ILE* 3.0 12.6 + - + +
22M ASP* 3.7 14.8 - - - +
23M TYR 2.9 0.2 + - - -
24M LEU* 1.3 76.1 - - - +
26M LYS* 1.3 57.2 + - - +
28M LEU* 3.6 9.0 - - - +
29M HIS* 3.0 27.9 + - - +
20O ARG* 5.6 1.8 - - - +
24O ILE* 3.7 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M ASP 3.6 7.6 + - - +
23M TYR* 2.6 19.8 + - + +
25M ALA* 1.3 70.4 - - - +
27M LYS* 1.3 56.8 + - - +
28M LEU 2.9 4.9 - - - -
29M HIS* 3.7 5.9 - - - +
30M ASP* 2.8 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M TYR* 3.1 33.7 + - + +
24M LEU* 3.8 9.9 - - + +
26M LYS* 1.3 75.4 - - - +
28M LEU* 1.3 56.7 + - - +
30M ASP* 4.1 6.5 - - - +
31M ILE* 3.1 28.2 + - - +
28N ILE* 5.1 13.0 - - + -
32N ARG* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M LEU 2.9 16.7 + - - +
25M ALA* 3.6 7.2 - - - +
26M LYS 2.9 0.6 - - - -
27M LYS* 1.3 77.2 - - - +
29M HIS* 1.3 61.5 + - + +
30M ASP 3.1 1.3 - - - -
31M ILE* 2.7 14.6 + - + +
32M GLU* 2.7 50.5 + - + +
28N ILE* 4.1 12.1 - - + -
31N LEU* 6.1 0.9 - - + -
24O ILE* 4.6 8.1 - - + -
27O SER* 3.9 29.6 - - - +
28O ILE* 3.6 33.4 - - + +
31O VAL* 5.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 29 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M ALA 3.0 18.1 + - - +
26M LYS* 3.7 7.0 - - - +
28M LEU* 1.3 77.7 - - + +
30M ASP* 1.3 58.2 + - - +
31M ILE 2.8 5.2 - - - -
32M GLU* 3.8 17.4 + - + +
33M GLU* 2.9 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M LYS 2.8 17.3 + - - +
27M LYS* 4.2 7.2 - - - +
29M HIS* 1.3 76.7 - - - +
31M ILE* 1.3 59.4 + - - +
33M GLU* 4.2 7.9 - - - +
34M GLU* 3.7 20.4 + - - +
32N ARG* 5.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M LYS 3.1 22.9 - - - +
28M LEU* 2.7 15.7 + - + +
30M ASP* 1.3 80.7 - - + +
32M GLU* 1.3 65.9 + - - +
33M GLU 2.8 4.0 + - - -
34M GLU* 2.9 4.0 + - - +
35M TYR* 2.8 22.5 + - + +
28N ILE* 4.4 13.5 - - + +
31N LEU* 4.2 28.0 - - + -
32N ARG* 3.9 42.4 - - + +
35N LEU* 3.7 22.6 - - + +
31O VAL* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M LEU* 2.7 31.6 + - + +
29M HIS* 4.1 19.9 + - + +
31M ILE* 1.3 76.0 - - - +
33M GLU* 1.3 54.1 + - - +
35M TYR* 3.2 21.4 - - + +
36M ASN* 2.8 35.4 + - - +
30O HIS* 5.0 9.4 + - - -
31O VAL* 4.7 20.8 - - + +
34O LEU* 6.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M HIS* 2.9 42.6 + - + +
30M ASP* 4.2 6.7 - - - +
31M ILE 2.8 1.0 - - - -
32M GLU* 1.3 74.6 - - - +
34M GLU* 1.3 57.3 + - - +
35M TYR 2.8 9.9 + - - -
36M ASN* 3.1 25.7 + - - +
37M LYS* 3.4 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M ASP 3.7 13.7 + - - +
31M ILE 2.9 7.6 + - - +
33M GLU* 1.3 77.8 - - - +
35M TYR* 1.3 60.4 + - - +
37M LYS* 4.0 18.1 + - + +
38M LEU* 4.5 6.1 - - - +
32N ARG* 3.0 33.8 + - - -
35N LEU* 4.3 15.6 - - + +
36N ASP* 5.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M ILE* 2.8 12.6 + - + +
32M GLU* 3.2 20.9 - - + +
33M GLU 2.8 1.8 + - - -
34M GLU* 1.3 77.0 - - - +
36M ASN* 1.3 74.5 + - - +
37M LYS 3.0 1.3 - - - -
38M LEU* 2.8 38.4 + - + +
41M ASP* 5.5 1.7 + - - -
35N LEU* 4.2 22.2 - - + -
38N ALA* 6.4 0.9 - - + -
31O VAL* 5.8 2.9 - - + -
34O LEU* 3.9 41.5 + - + +
35O LEU* 4.3 20.9 - - + -
38O ARG* 4.5 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M GLU* 2.8 31.7 + - - +
33M GLU* 3.1 18.0 + - - +
35M TYR* 1.3 85.8 - - - +
37M LYS* 1.3 55.1 + - - +
38M LEU 2.8 20.2 + - - +
40M HIS* 4.8 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M GLU 3.4 11.1 + - - +
34M GLU* 4.1 12.7 - - + +
35M TYR 2.9 1.8 + - - -
36M ASN* 1.3 75.2 - - - +
38M LEU* 1.3 59.2 + - - +
----------------------------------------------------------
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