Contacts of the helix formed by residues 22 - 41 (chain F) 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 SER 22 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TYR 3.7 1.2 + - - -
21F GLY* 1.3 76.1 - - - -
23F GLY* 1.3 68.3 + - - +
24F HIS 3.3 2.9 + - - -
25F ASP* 3.4 20.1 + - - +
26F ARG* 3.9 19.7 - - - +
20G ASP* 3.7 25.9 + - - -
83G ASN* 4.0 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F SER* 1.3 75.6 - - - +
24F HIS* 1.3 63.2 + - - -
26F ARG* 3.5 5.7 - - - +
27F GLU* 3.3 18.8 + - - +
66F ASP* 5.2 0.7 - - - +
16G GLN* 5.2 12.6 - - - -
83G ASN* 3.4 30.6 + - - +
84G LEU* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F SER 3.3 1.2 + - - -
23F GLY* 1.3 69.0 - - - -
25F ASP* 1.3 73.1 + - - +
26F ARG 2.9 3.1 + - - -
27F GLU* 2.9 32.5 + - - +
28F ALA* 2.9 15.1 + - - +
86G ASP* 3.5 41.7 + - + +
63N GLU* 5.2 10.8 - - - +
78N SER* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TYR 4.6 4.0 - - - +
21F GLY* 5.1 2.7 - - - -
22F SER 3.4 18.3 + - - +
24F HIS* 1.3 77.5 + - - +
26F ARG* 1.3 52.3 + - - +
28F ALA* 3.4 4.9 + - - +
29F PHE* 2.7 37.2 + - - +
120F GLN* 4.7 20.1 + - - +
63N GLU* 4.2 14.6 - - - +
64N LYS 5.5 1.0 - - - +
65N ARG* 5.2 9.5 - - - +
78N SER* 5.3 7.4 + - - -
80N LEU* 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TYR* 3.2 61.6 + - + +
21F GLY 3.1 21.0 + - - -
22F SER* 3.6 17.7 + - - +
23F GLY 3.5 10.1 - - - +
24F HIS 2.9 0.2 - - - -
25F ASP* 1.3 75.4 - - - +
27F GLU* 1.3 55.4 + - - +
28F ALA 2.7 15.8 + - - -
29F PHE* 2.9 12.2 + - + -
30F SER* 3.0 17.4 + - - +
66F ASP* 3.2 28.4 + - - +
69F LEU* 5.8 0.4 - - + -
23G TRP* 5.7 5.1 - - - -
79G ASP* 3.4 19.0 + - - +
80G LEU* 5.1 3.6 - - - +
83G ASN* 3.0 37.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLY 3.3 10.1 + - - +
24F HIS* 2.9 30.0 + - - +
26F ARG* 1.3 75.2 - - - +
28F ALA* 1.3 55.1 + - - +
30F SER* 3.2 9.0 + - - -
31F GLN* 3.0 24.2 - - + +
62F ILE* 4.0 31.4 - - + +
66F ASP* 3.7 15.2 + - - +
83G ASN 5.3 1.7 - - - +
84G LEU* 4.5 10.0 - - + +
86G ASP 4.4 2.4 - - - +
87G ASP* 3.2 35.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS 2.9 12.7 + - - +
25F ASP 3.6 3.6 - - - +
26F ARG 2.7 4.2 + - - -
27F GLU* 1.3 73.9 - - - +
29F PHE* 1.3 59.4 + - - +
30F SER 3.0 1.6 - - - -
31F GLN* 2.6 29.0 + - + +
32F ALA* 2.6 16.8 + - - +
78N SER* 3.7 31.4 - - - +
80N LEU* 5.4 1.6 - - + -
81N LEU* 4.9 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TRP* 3.8 28.7 - + - -
19F ALA* 3.5 27.4 - - + +
20F TYR* 4.2 18.8 - + - +
25F ASP 2.7 23.4 + - - +
26F ARG* 3.4 8.3 - - + +
28F ALA* 1.3 72.8 - - - +
30F SER* 1.3 62.4 + - - +
32F ALA* 3.5 6.2 + - - +
33F ILE* 3.1 45.7 + - + +
69F LEU* 3.9 9.2 - - + -
116F VAL* 3.7 26.7 - - + -
117F VAL* 3.8 28.9 - - + -
120F GLN* 4.0 15.7 - - + +
80N LEU* 5.2 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F ARG* 3.0 17.3 + - - -
27F GLU* 3.2 11.6 + - - -
29F PHE* 1.3 74.2 - - - +
31F GLN* 1.3 75.5 + - - +
33F ILE* 3.0 6.4 + - - +
34F TRP* 2.9 27.1 + - - -
62F ILE* 5.1 1.7 + - - +
65F ALA* 3.9 20.6 - - - +
66F ASP* 4.3 7.7 + - - -
69F LEU* 3.6 36.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F GLU* 3.0 19.7 - - + +
28F ALA* 2.6 17.5 + - - +
30F SER* 1.3 79.7 + - - +
32F ALA* 1.3 63.6 + - - +
34F TRP* 3.2 5.1 + - - +
35F ARG* 3.0 47.4 + - - +
56F THR* 2.5 29.1 + - - +
57F SER* 3.5 23.2 + - - +
61F PHE* 5.2 1.8 - - - -
62F ILE* 3.6 28.4 - - + +
65F ALA* 5.6 2.5 - - + -
81N LEU* 5.0 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ALA 2.6 12.8 + - - +
29F PHE 3.6 8.5 - - - +
31F GLN* 1.3 72.6 - - - +
33F ILE* 1.3 65.1 + - - +
35F ARG* 3.2 6.6 + - - +
36F ALA* 3.0 22.9 + - - +
116F VAL* 3.9 16.8 - - + +
80N LEU* 3.7 35.4 - - + +
81N LEU* 4.3 8.2 - - + +
141N PHE* 5.0 5.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TRP* 5.6 0.2 - - + -
29F PHE* 3.1 45.3 + - + +
30F SER* 3.0 9.7 + - - +
32F ALA* 1.3 79.6 - - - +
34F TRP* 1.3 60.6 + - + +
36F ALA* 3.1 5.9 + - - +
37F THR* 2.9 24.9 + - - -
69F LEU* 4.0 16.6 - - + -
109F PHE* 4.1 20.2 - - + -
112F ALA* 3.4 9.8 - - + +
113F ILE* 4.0 36.1 - - + -
116F VAL* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F SER 2.9 19.0 + - - +
31F GLN* 3.8 6.3 - - - +
33F ILE* 1.3 78.9 - - + +
35F ARG* 1.3 59.1 + - + +
37F THR* 2.9 21.8 + - + -
38F PHE* 2.8 71.4 + + + +
48F PHE* 3.5 21.5 - + - -
56F THR* 5.7 0.7 - - - +
61F PHE* 3.7 26.2 - + + -
64F HIS* 4.1 6.7 - - - -
65F ALA* 3.5 37.4 - - + +
68F VAL* 4.2 4.7 - - + +
69F LEU* 4.4 10.2 - - + +
109F PHE* 3.4 29.8 - + - -
160F HEM 4.9 4.7 - + + -
161F CMO 3.2 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F GLN* 3.0 52.8 + - - +
32F ALA* 3.5 7.6 - - - +
34F TRP* 1.3 74.6 - - - +
36F ALA* 1.3 56.9 + - - +
38F PHE* 4.1 4.6 - - - +
39F ALA* 3.0 31.4 + - - +
45F ARG* 6.0 1.3 - - - +
56F THR* 3.7 18.7 + - + +
57F SER* 3.7 11.7 + - - -
81N LEU* 4.0 12.4 - - - +
84N ASP* 2.7 36.2 + - - -
86N HIS* 3.5 45.4 + - + +
88N ASP* 2.8 32.7 + - - -
140N PHE 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F ALA 3.0 13.6 + - - +
33F ILE* 3.3 10.1 - - - +
35F ARG* 1.3 74.3 - - - +
37F THR* 1.3 66.4 + - - +
39F ALA* 3.6 2.1 + - - +
40F GLN* 3.3 24.4 + - - +
112F ALA* 3.8 19.7 - - + -
115F HIS* 5.9 0.7 - - + -
116F VAL* 4.7 6.7 - - + -
140N PHE* 3.6 28.4 - - + +
141N PHE* 4.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F ILE 2.9 10.2 + - - -
34F TRP* 2.9 31.4 + - + -
36F ALA* 1.3 76.9 - - - +
38F PHE* 1.3 65.6 + - + +
40F GLN* 2.9 24.9 + - - +
41F VAL* 3.1 22.8 + - + +
44F SER* 4.6 1.6 - - - +
105F TYR 5.4 1.1 - - - +
108F ALA* 4.8 0.9 - - + -
109F PHE* 3.4 33.1 - - + +
112F ALA* 3.2 21.1 - - - +
160F HEM 5.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F TRP* 2.8 43.2 + + - +
35F ARG* 4.2 3.6 - - - +
37F THR* 1.3 78.2 - - + +
39F ALA* 1.3 62.2 + - - +
41F VAL 4.3 3.1 - - - -
42F PRO* 3.0 28.4 - - - +
44F SER* 3.4 22.2 - - - -
45F ARG* 3.7 54.1 + - + +
48F PHE* 3.6 31.9 - + + -
53F GLY 4.0 15.7 - - - -
56F THR* 5.3 4.5 - - + -
61F PHE* 3.6 28.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ARG 3.0 20.4 + - - +
36F ALA 3.7 5.8 - - - +
37F THR 3.1 0.2 - - - -
38F PHE* 1.3 78.9 - - - +
40F GLN* 1.3 61.6 + - - +
42F PRO* 4.1 5.9 - - - +
45F ARG* 5.8 0.7 - - - +
139N LYS 5.3 0.7 - - - +
140N PHE* 4.0 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F ALA 3.3 15.6 + - - +
37F THR* 2.9 8.4 + - - +
39F ALA* 1.3 80.9 - - - +
41F VAL* 1.3 65.1 + - + +
42F PRO* 3.5 7.6 - - - +
108F ALA* 2.9 41.3 - - + +
111F THR* 3.6 30.7 + - - +
112F ALA* 3.8 4.9 + - - +
140N PHE* 3.9 27.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F THR* 3.1 16.5 + - + +
38F PHE* 3.3 3.3 - - - +
40F GLN* 1.3 84.1 - - + +
42F PRO* 1.3 61.2 - - - +
43F GLU* 2.8 10.8 + - + +
44F SER* 2.7 46.3 + - - +
104F ASN* 4.2 24.9 - - - +
105F TYR* 3.9 19.7 - - + -
108F ALA* 4.1 22.4 - - + -
----------------------------------------------------------
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