Contacts of the helix formed by residues 1 - 19 (chain I) in PDB entry 1GQM
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 THR 1 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I LYS* 1.3 64.0 + - - +
3I LEU 3.3 6.1 + - - -
4I GLU* 2.7 37.1 + - - +
5I GLU* 2.9 39.2 + - - +
38J LYS 3.5 23.1 - - - +
39J GLU* 3.2 25.4 + - - +
41J ALA* 5.2 3.4 - - + +
42J ASN* 4.2 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 2 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I THR* 1.3 74.2 + - - +
3I LEU* 1.3 57.9 + - - +
4I GLU 3.0 1.8 - - - -
5I GLU* 2.5 51.5 + - - +
6I HIS* 2.9 51.1 + - - +
13J ILE* 4.0 14.1 - - + -
39J GLU* 3.9 7.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 3 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I THR* 3.3 2.2 + - - -
2I LYS* 1.3 78.2 - - - +
4I GLU* 1.3 62.9 + - - +
6I HIS* 3.1 4.8 + - - +
7I LEU* 2.9 57.4 + - + +
10J ILE* 4.4 21.5 - - + +
13J ILE* 3.1 45.1 - - + +
35J LEU* 5.4 1.3 - - + -
39J GLU* 3.5 32.3 + - + +
40J LEU* 4.7 12.3 - - + -
73J PHE* 5.2 9.0 - - + -
77J VAL* 5.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 4 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I THR* 2.7 35.8 + - - +
2I LYS 3.0 0.6 - - - -
3I LEU* 1.3 79.0 - - - +
5I GLU* 1.3 59.5 + - + +
7I LEU* 3.2 8.6 + - + +
8I GLU* 2.8 33.1 + - - +
39J GLU 3.5 14.1 - - - +
40J LEU* 3.4 8.1 - - + -
41J ALA 3.6 0.2 + - - -
42J ASN* 2.6 49.2 + - - +
43J THR* 2.9 23.7 + - + +
84J ALA* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 5 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I THR* 2.9 31.9 + - - +
2I LYS* 2.5 41.4 + - - +
4I GLU* 1.3 74.2 - - + +
6I HIS* 1.3 56.1 + - - +
8I GLU* 3.3 11.0 + - - +
9I GLY* 2.9 25.6 + - - -
6J HIS* 4.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 6 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I LYS* 2.9 53.8 + - + +
3I LEU* 3.7 6.3 - - - +
5I GLU* 1.3 77.0 - - - +
7I LEU* 1.3 65.0 + - - +
9I GLY* 3.1 1.6 + - - -
10I ILE* 2.9 28.5 + - - +
5J GLU* 4.4 3.4 - - + -
6J HIS* 2.6 57.4 + + + +
9J GLY* 3.6 31.0 - - - -
10J ILE* 4.1 10.8 - - + -
13J ILE* 4.1 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I LEU* 2.9 41.2 + - + +
4I GLU* 3.6 8.3 - - - +
6I HIS* 1.3 77.3 - - - +
8I GLU* 1.3 63.7 + - - +
10I ILE* 3.0 21.4 + - + +
11I VAL* 3.0 16.3 + - - +
10J ILE* 3.9 21.5 - - + -
40J LEU* 3.9 9.9 - - + -
43J THR* 4.9 3.1 - - + -
77J VAL* 4.4 14.1 - - + -
80J ALA* 3.2 43.5 - - + +
81J LEU* 4.2 9.6 - - + +
84J ALA* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I GLU 2.8 18.1 + - - +
5I GLU* 3.7 11.5 - - - +
7I LEU* 1.3 75.3 - - - +
9I GLY* 1.3 56.8 + - - +
11I VAL* 3.2 11.4 + - + +
12I ASN* 2.9 43.5 + - - +
84J ALA* 5.1 10.0 - - + +
87J HIS* 6.0 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 9 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I GLU 2.9 15.0 + - - -
6I HIS 3.5 4.3 - - - -
7I LEU 3.0 0.4 - - - -
8I GLU* 1.3 73.7 - - - +
10I ILE* 1.3 65.9 + - - +
12I ASN* 3.0 11.4 + - - +
13I ILE* 2.8 31.7 + - - +
6J HIS* 3.9 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I HIS 2.9 15.0 + - - +
7I LEU* 3.0 9.8 + - + +
9I GLY* 1.3 72.6 - - - +
11I VAL* 1.3 64.8 + - - +
13I ILE* 3.1 8.2 + - - +
14I PHE* 3.0 22.4 + - - +
70I PHE* 5.3 1.6 - - + -
73I PHE* 4.5 9.0 - - + -
77I VAL* 3.9 32.8 - - + -
3J LEU* 4.1 17.5 - - + -
6J HIS* 4.1 13.2 - - + -
7J LEU* 4.0 16.4 - - + -
10J ILE* 3.8 27.4 - - + -
81J LEU* 4.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I LEU 3.0 14.5 + - - +
8I GLU* 3.4 12.3 - - + +
10I ILE* 1.3 79.0 - - - +
12I ASN* 1.3 70.2 + - - +
14I PHE* 3.0 12.0 + - - +
15I HIS* 3.1 32.8 + - + +
70I PHE* 3.7 29.2 - - + -
81J LEU* 4.1 7.9 - - + -
84J ALA* 4.5 6.7 - - + +
85J HIS* 4.1 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 12 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I GLU* 2.9 32.2 + - - +
9I GLY* 3.0 11.0 + - - +
11I VAL* 1.3 80.8 - - - +
13I ILE* 1.3 66.5 + - + +
15I HIS* 3.0 8.5 + - - +
16I GLN* 2.9 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLY* 2.8 30.7 + - - +
10I ILE* 3.1 6.7 + - + +
12I ASN* 1.3 75.0 - - + +
14I PHE* 1.3 68.2 + - - +
16I GLN* 3.2 23.0 + - - +
17I TYR* 3.1 33.1 - - + -
35I LEU* 4.5 5.6 - - + -
39I GLU* 4.2 20.6 - - + +
73I PHE* 5.7 1.6 - - + -
2J LYS* 4.2 19.1 - - + -
3J LEU* 4.1 26.9 - - + +
6J HIS* 4.2 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 14 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ILE 3.0 11.9 + - - +
11I VAL 3.4 7.6 - - - +
13I ILE* 1.3 80.6 - - - +
15I HIS* 1.3 105.0 + + - +
17I TYR* 3.0 7.3 + - - +
18I SER* 3.0 23.9 + - - -
25I ASP 3.5 21.1 - - - -
27I LEU* 3.5 34.0 - - + +
35I LEU* 4.5 6.7 - - - -
68I VAL 4.1 9.0 - - - -
70I PHE* 3.7 33.2 - + + -
73I PHE* 3.5 45.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 15 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I VAL* 3.1 28.5 + - + +
12I ASN* 3.0 10.1 + - - +
14I PHE* 1.3 105.9 - + - +
16I GLN* 1.3 66.4 + - - +
17I TYR 2.8 3.6 + - - -
18I SER* 2.9 20.5 + - - +
19I VAL* 2.9 20.8 + - + +
24I PHE 4.4 5.8 - - - +
25I ASP* 4.6 9.7 + - - +
85J HIS* 4.2 21.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ASN* 2.9 11.5 + - - +
13I ILE* 3.2 33.1 + - - +
15I HIS* 1.3 75.6 - - - +
17I TYR* 1.3 72.1 + - + +
19I VAL* 3.2 16.9 - - - +
20I ARG* 3.5 23.7 + - - +
39I GLU* 5.1 5.2 + - - -
2J LYS* 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 17 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ILE* 3.1 25.8 - - + -
14I PHE 3.0 7.2 + - - +
15I HIS 2.8 0.8 + - - -
16I GLN* 1.3 92.1 + - + +
18I SER* 1.3 62.6 + - - +
19I VAL 3.2 3.3 + - - -
20I ARG* 3.6 42.4 + - - +
27I LEU* 3.8 15.3 - - + -
31I GLU* 3.1 24.5 - - - +
34I GLN* 3.8 10.8 - - + -
35I LEU* 3.6 38.1 - - + -
38I LYS* 3.8 21.8 + - + +
39I GLU* 2.6 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I PHE* 3.0 18.6 + - - -
15I HIS* 2.9 28.3 + - - -
17I TYR* 1.3 77.1 - - - +
19I VAL* 1.4 56.6 + - - +
23I HIS 2.9 11.4 - - - +
24I PHE 2.7 22.5 + - - -
26I THR 3.6 23.6 - - - -
27I LEU* 3.9 5.8 - - - +
31I GLU* 2.9 5.7 - - - +
1088I CA 2.2 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I HIS* 2.9 23.4 + - + +
16I GLN* 3.2 20.6 - - - +
18I SER* 1.4 79.4 + - - +
20I ARG* 1.3 69.5 + - + +
21I LYS* 3.3 3.0 + - - +
22I GLY 4.9 1.7 - - - +
24I PHE* 3.9 41.8 - - + +
----------------------------------------------------------
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