Contacts of the helix formed by residues 39 - 56 (chain B) in PDB entry 1G2X
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 ASP 39 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 2.4 34.4 + - - -
37B PRO* 3.3 2.2 - - - +
38B VAL* 1.3 81.4 - - - +
40B LYS* 1.3 66.9 + - - +
41B LEU* 4.1 5.0 - - - +
42B ASP* 2.9 25.9 + - - +
43B ARG* 2.9 35.6 + - - +
105B PRO* 4.5 0.8 - - + +
107B ASN* 2.7 23.1 + - - +
110B ASN* 3.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASP* 1.3 74.3 - - - +
41B LEU* 1.3 64.7 + - - +
43B ARG* 2.9 43.5 + - + +
44B CYS* 3.0 15.7 + - - -
100B CYS* 4.8 4.7 - - - -
103B SER* 3.3 30.1 + - - -
104B ALA* 3.7 12.3 - - + +
105B PRO* 3.6 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 5.3 0.9 - - - +
22B TYR* 3.5 35.7 - - + -
25B TYR* 3.5 33.0 - - + -
29B CYS* 4.5 2.9 - - - -
39B ASP* 3.4 2.7 + - - +
40B LYS* 1.3 78.3 - - - +
42B ASP* 1.3 58.9 + - - +
44B CYS* 2.9 26.9 + - + +
45B CYS* 3.2 5.7 + - - -
101B PHE* 3.5 38.4 - - + +
104B ALA* 3.7 11.9 - - + +
105B PRO 3.8 18.1 + - - +
106B TYR* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.8 5.5 - - + +
26B GLY* 3.9 2.7 - - - -
27B CYS* 2.9 25.7 + - - +
28B TYR* 3.0 25.9 + - - +
29B CYS* 3.7 11.6 + - - -
37B PRO* 3.3 9.3 - - + +
38B VAL* 3.0 33.6 + - + +
39B ASP* 2.9 23.5 + - - +
41B LEU* 1.3 72.9 - - - +
43B ARG* 1.3 60.6 + - - +
45B CYS* 3.2 1.6 + - - +
46B TYR* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 5.3 11.9 - - - +
76A ASN* 2.8 36.8 - - - +
37B PRO* 3.7 12.1 + - + +
39B ASP* 2.9 16.6 + - - +
40B LYS* 3.1 46.8 - - - +
42B ASP* 1.3 75.9 - - - +
44B CYS* 1.3 62.4 + - - +
46B TYR* 3.0 6.6 + - + +
47B THR* 2.8 28.3 + - - +
100B CYS* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 3.0 18.4 + - - -
41B LEU* 2.9 20.5 + - - +
43B ARG* 1.3 77.7 - - - +
45B CYS* 1.3 55.6 + - - +
47B THR* 3.3 5.9 + - - -
48B HIS* 2.9 28.8 + - - +
97B ALA* 5.0 2.1 - - - +
100B CYS* 2.0 66.4 - - + -
101B PHE* 3.2 20.6 - - + -
104B ALA* 4.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 4.9 0.9 - - - -
28B TYR* 3.9 4.2 - - - +
29B CYS* 2.0 66.2 - - - +
41B LEU* 3.2 5.0 + - - -
42B ASP 3.2 4.5 + - - +
44B CYS* 1.3 76.3 - - - +
46B TYR* 1.3 57.0 + - - +
48B HIS* 3.7 5.1 + - - +
49B ASP* 2.7 37.7 + - - +
101B PHE* 3.3 31.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 4.2 8.0 - - - +
73A THR* 2.8 39.3 + - + -
76A ASN* 3.6 27.5 + - + +
77A ILE 5.2 0.7 - - - -
78A THR* 3.3 25.0 + - - -
28B TYR* 3.6 44.8 - + + +
37B PRO* 3.7 15.9 - - + -
42B ASP 2.9 14.5 + - - +
43B ARG* 3.1 10.1 - - + +
45B CYS* 1.3 77.8 - - - +
47B THR* 1.3 70.7 + - - +
49B ASP* 3.3 3.6 + - - +
50B HIS* 3.1 49.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 5.9 0.7 - - - -
95A ARG* 4.8 13.4 + - - +
43B ARG* 2.8 17.5 + - - +
44B CYS* 3.6 9.8 - - - -
46B TYR* 1.3 80.0 - - - +
48B HIS* 1.3 69.7 + - - +
50B HIS* 2.9 9.8 + - - +
51B CYS* 2.9 25.3 + - + +
96B THR* 4.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.8 21.2 - + - -
44B CYS 2.9 16.1 + - - +
45B CYS* 3.8 7.9 + - - +
47B THR* 1.3 78.8 - - - +
49B ASP* 1.3 65.6 + - - +
51B CYS* 3.1 17.2 + - - +
52B TYR* 3.0 49.8 + + - +
93B CYS* 3.6 15.9 - - + -
94B ASP* 2.7 26.7 + - - -
96B THR* 6.5 0.4 - - - -
97B ALA* 3.5 31.9 - - + -
101B PHE* 5.4 1.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 4.3 16.7 - - + +
30B GLY 5.8 1.3 - - - -
32B GLY* 3.8 23.4 - - - +
33B GLY* 5.0 0.2 - - - -
45B CYS 2.7 21.8 + - - +
46B TYR* 3.4 8.3 - - - +
47B THR 3.1 0.2 - - - -
48B HIS* 1.3 78.4 + - - +
50B HIS* 1.3 61.4 + - + +
52B TYR* 3.4 8.6 + - - +
53B ASN* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 4.5 9.4 - - + -
78A THR* 3.4 33.2 + - + +
28B TYR* 5.8 0.8 - - - -
46B TYR* 3.1 55.0 + + - -
47B THR* 2.9 9.9 + - - +
49B ASP* 1.3 78.3 - - + +
51B CYS* 1.3 55.8 + - - +
53B ASN* 3.4 15.7 + - - +
54B GLN* 2.7 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 2.9 17.0 + - + +
48B HIS* 3.1 14.6 + - - +
50B HIS* 1.3 76.0 - - - +
52B TYR* 1.3 58.9 + - - +
54B GLN* 3.4 8.3 + - - +
55B ALA* 3.0 22.5 + - - +
89B PHE* 3.2 23.2 - - - -
92B ASP* 6.1 0.4 - - - -
93B CYS* 2.0 53.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ASN 4.6 1.9 + - - -
2B LEU* 4.2 11.8 - - + +
5B PHE* 3.9 9.7 - - - +
48B HIS* 3.0 44.6 + + - +
49B ASP* 3.7 11.7 - - - +
51B CYS* 1.3 74.7 - - - +
53B ASN* 1.3 58.6 + - - +
55B ALA* 3.2 15.7 + - - +
56B ASP* 2.7 24.1 - - - +
63B PRO* 3.4 40.0 + - + +
64B ASN* 4.0 18.8 - - - -
90B LEU* 4.1 17.0 - - + -
93B CYS* 4.2 5.6 - - + -
94B ASP* 2.7 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A THR* 5.5 7.3 - - - +
49B ASP* 3.2 11.2 + - - +
50B HIS* 3.5 21.4 + - - +
52B TYR* 1.3 81.0 - - - +
54B GLN* 1.3 64.4 + - - +
56B ASP* 3.0 25.3 + - - +
57B SER* 4.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 3.8 7.9 - - - +
79A CYS 3.2 25.6 + - - +
80A THR* 4.0 22.4 - - + +
81A ARG 5.0 2.4 - - - +
82A THR* 3.8 14.1 + - - +
50B HIS* 2.7 44.6 + - - +
51B CYS* 3.7 8.9 - - - +
52B TYR 3.3 0.2 - - - -
53B ASN* 1.3 79.8 - - - +
55B ALA* 1.3 65.7 + - - +
57B SER* 3.0 24.3 + - - -
58B ILE* 4.2 4.2 + - - +
89B PHE* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B CYS 3.0 12.3 + - - +
52B TYR 3.3 12.1 - - - +
53B ASN 3.2 0.4 - - - -
54B GLN* 1.3 76.7 - - - +
56B ASP* 1.3 61.4 + - - +
57B SER 3.1 0.2 - - - -
58B ILE* 3.1 8.6 + - - +
61B CYS* 3.1 32.1 - - - +
63B PRO* 4.5 4.9 - - + -
89B PHE* 3.6 16.1 - - + -
90B LEU* 3.3 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR 2.7 25.9 - - - +
53B ASN* 3.0 17.1 - - - +
54B GLN 3.1 0.6 - - - -
55B ALA* 1.3 72.2 - - - +
57B SER* 1.3 57.5 + - - +
58B ILE 3.0 15.2 + - - +
61B CYS 3.6 12.2 - - - +
62B ASN* 4.8 3.3 + - - -
63B PRO* 3.6 20.5 - - - +
----------------------------------------------------------
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