Contacts of the helix formed by residues 27 - 47 (chain C) 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 GLU 27 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 3.4 29.6 - - - +
27A PHE* 4.2 21.1 - - + +
29A ASP* 4.3 12.2 - - + +
30A ARG* 3.6 26.4 + - + +
13B LYS* 3.2 27.5 + - - +
80B ASP* 4.8 4.5 - - - +
25C ASP* 3.0 11.4 + - - +
26C THR* 1.3 80.2 + - - +
28C SER* 1.3 62.2 + - - +
29C SER* 3.2 10.1 + - - -
30C LYS* 3.3 19.9 + - + +
31C ILE* 3.4 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 6.0 0.5 - - - -
73B ASP* 5.3 1.7 + - - -
77B SER* 4.7 9.9 - - - -
23C TRP* 4.6 18.2 - - - -
25C ASP 3.5 8.6 + - - -
26C THR 2.9 10.7 + - - -
27C GLU* 1.3 75.3 - - - +
29C SER* 1.3 58.2 + - - +
31C ILE* 3.0 9.4 + - - +
32C LYS* 2.7 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 3.5 20.3 + - - +
77B SER* 3.3 30.5 - - - -
78B THR* 4.7 5.6 - - - -
81B GLN* 3.7 15.1 + - - -
26C THR 4.8 0.2 + - - -
27C GLU* 3.7 6.8 + - - -
28C SER* 1.3 80.5 + - - +
30C LYS* 1.3 71.0 + - - +
32C LYS* 4.6 1.6 - - - -
33C ILE* 2.9 35.6 + - - +
72C LEU* 4.5 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.8 32.9 - - + -
29A ASP* 3.3 36.2 + - - +
80B ASP* 5.3 2.7 + - - -
81B GLN* 3.9 29.9 + - - +
27C GLU* 3.3 17.8 + - + +
29C SER* 1.3 83.2 + - - +
31C ILE* 1.3 58.3 + - - +
33C ILE* 4.0 6.8 - - + +
34C GLY* 3.1 23.9 + - - -
85D ASP* 4.9 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.0 20.0 - - + -
22C LEU* 3.9 19.1 - - + +
23C TRP* 3.4 24.2 - - + -
25C ASP* 3.6 27.8 - - - +
27C GLU 3.4 8.9 + - - +
28C SER* 3.0 8.1 + - - +
30C LYS* 1.3 73.3 - - - +
32C LYS* 1.3 69.9 + - - +
33C ILE 2.9 2.0 + - - -
34C GLY* 2.9 2.3 + - - -
35C PHE* 2.7 32.5 + - + +
15D LEU* 3.8 39.7 - - + -
19D LEU* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 5.9 0.2 - - - -
26B ARG* 6.1 0.4 - - - +
73B ASP* 3.1 18.2 + - - -
23C TRP* 3.8 34.0 - - + +
28C SER* 2.7 39.0 + - - +
29C SER* 5.2 0.4 - - - -
31C ILE* 1.3 74.3 - - - +
33C ILE* 1.3 53.4 + - - +
35C PHE* 4.6 1.8 - - - -
36C GLY* 2.7 34.7 + - - -
71C ALA 4.6 0.5 - - - +
72C LEU* 3.6 22.7 - - + -
75C LEU* 3.4 34.2 - - + +
76C ASN* 3.1 30.1 + - + +
79C ASP* 4.3 11.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 5.3 0.7 - - + -
81B GLN* 4.3 22.4 - - - +
84B THR* 5.1 3.4 - - + -
29C SER* 2.9 25.7 + - - +
30C LYS* 4.0 6.7 - - + +
32C LYS* 1.3 72.4 - - - +
34C GLY* 1.3 61.2 + - - +
37C ARG* 2.5 50.4 + - + +
68C SER* 3.9 39.5 - - - +
71C ALA* 4.0 9.7 - - + +
72C LEU* 3.3 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LYS 3.1 10.3 + - - -
31C ILE 2.9 7.5 + - - -
33C ILE* 1.3 77.9 - - - +
35C PHE* 1.3 56.7 + - - +
37C ARG* 3.4 14.2 - - - +
38C LEU* 2.9 30.3 + - - +
11D VAL* 4.6 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TRP* 4.7 8.7 - + - -
22C LEU* 5.3 7.9 - - + -
23C TRP* 5.8 0.7 - + - -
31C ILE* 2.7 29.5 + - + +
32C LYS* 3.9 3.6 - - - +
34C GLY* 1.3 68.7 - - - +
36C GLY* 1.3 59.7 + - - +
38C LEU* 3.2 9.8 + - + +
39C LEU* 2.8 65.0 + - + +
75C LEU* 3.9 16.2 - - + -
120C LEU* 4.4 1.3 - - + -
123C GLY* 4.3 9.0 - - - -
124C LEU* 3.8 41.1 - - + -
127C VAL* 3.9 31.2 - - + -
11D VAL* 5.0 3.7 - - - +
12D THR* 4.2 15.0 - - + -
15D LEU* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LYS 2.7 22.0 + - - -
33C ILE 3.6 0.2 - - - -
35C PHE* 1.3 74.1 - - - +
37C ARG* 1.3 61.0 + - - +
39C LEU* 3.3 6.4 + - - +
40C LEU* 3.0 30.9 + - - +
71C ALA* 4.3 10.3 - - - -
74C ILE* 5.4 3.8 - - - -
75C LEU* 4.2 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE* 2.5 38.6 + - + +
34C GLY* 3.4 11.0 - - - +
36C GLY* 1.3 72.4 - - - +
38C LEU* 1.3 68.6 + - - +
40C LEU* 3.2 1.9 + - - +
41C THR* 2.9 28.7 + - - +
62C ALA* 3.5 41.2 + - + +
63C GLU* 3.3 36.6 + - - +
67C PHE* 4.2 16.5 - - + -
68C SER* 4.9 0.8 + - - -
71C ALA* 4.0 5.6 - - + +
11D VAL* 6.1 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLY 2.9 18.0 + - - +
35C PHE* 3.5 8.3 - - + +
37C ARG* 1.3 81.1 - - - +
39C LEU* 1.3 74.2 + - + +
41C THR* 3.1 8.3 + - - -
42C LYS* 2.8 39.3 + - + +
119C ILE* 5.5 1.3 - - + -
123C GLY* 6.1 3.6 - - - -
126C GLN* 5.6 3.4 - - - +
10D LEU* 5.3 11.9 - - + -
11D VAL* 4.3 20.0 - - + -
12D THR* 4.1 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 2.8 51.9 + - + +
36C GLY* 3.6 6.1 - - - +
37C ARG 3.3 0.2 - - - -
38C LEU* 1.3 84.2 - - + +
40C LEU* 1.3 62.1 + - + +
42C LYS* 3.7 3.1 + - - +
43C LEU* 3.3 18.4 + - - +
74C ILE* 5.9 1.3 - - + -
75C LEU* 4.3 12.1 - - + -
78C LEU* 5.7 0.2 - - + -
116C PHE* 4.1 23.3 - - + -
119C ILE* 4.1 28.7 - - + +
120C LEU* 3.4 40.8 - - + -
123C GLY* 5.1 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLY 3.0 15.8 + - - +
37C ARG 3.8 2.5 - - - +
39C LEU* 1.3 73.1 - - - +
41C THR* 1.3 66.7 + - - +
43C LEU* 2.8 18.1 + - + +
44C ALA* 3.0 14.0 + - - +
54C PHE* 3.5 30.7 - - + -
59C ILE* 5.1 2.7 - - - +
67C PHE* 3.7 22.0 - - + -
70C HIS* 3.4 36.6 - - + +
71C ALA* 4.8 2.9 - - - -
74C ILE* 3.7 32.8 - - + -
116C PHE* 4.0 13.5 - - + -
160C HEM 5.8 1.1 - - + -
161C CMO 4.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ARG* 2.9 28.1 + - - +
38C LEU* 3.4 12.2 - - - -
40C LEU* 1.3 75.7 - - - +
42C LYS* 1.3 59.3 - - - +
43C LEU 2.8 6.2 + - - -
44C ALA* 2.8 19.7 + - + +
45C LYS* 2.9 15.9 + - + +
59C ILE* 5.4 5.5 - - - +
62C ALA* 4.8 8.0 - - - +
67C PHE* 4.9 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 2.8 28.5 + - + +
39C LEU 4.0 4.0 - - - +
41C THR* 1.3 73.3 - - + +
43C LEU* 1.3 61.1 + - - +
45C LYS* 3.8 18.4 - - + +
46C ASP* 3.6 39.7 + - - -
119C ILE* 3.6 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU 3.3 11.9 + - - +
40C LEU* 2.8 16.9 + - + +
42C LYS* 1.3 76.5 - - - +
44C ALA* 1.3 56.5 + - - +
45C LYS 3.0 4.6 + - - -
46C ASP* 3.1 3.5 + - - +
47C ILE* 2.9 31.6 + - + +
50C VAL* 4.2 23.1 - - + -
54C PHE* 4.7 5.8 - - + -
112C HIS* 4.1 19.1 - - + +
115C LYS* 4.1 10.3 - - + -
116C PHE* 4.1 22.7 - - + +
119C ILE* 3.6 19.3 - - + -
160C HEM 4.0 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU 3.0 8.4 + - - +
41C THR* 2.8 9.7 + - - +
43C LEU* 1.3 76.4 - - - +
45C LYS* 1.3 62.1 + - - +
47C ILE 3.5 11.2 - - - -
48C PRO* 3.4 22.7 - - - +
50C VAL* 4.2 9.8 - - + +
51C ASN* 3.5 31.1 + - - +
59C ILE* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 2.9 18.7 + - + +
42C LYS* 3.6 23.8 - - + +
44C ALA* 1.3 80.7 - - - +
46C ASP* 1.3 70.1 + - - +
48C PRO* 4.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LYS* 3.6 31.5 + - - +
43C LEU* 3.1 6.9 + - - +
45C LYS* 1.3 89.2 - - - +
47C ILE* 1.3 68.6 + - + +
48C PRO* 4.1 3.6 - - - +
115C LYS* 3.0 38.8 - - + +
119C ILE* 4.9 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 2.9 10.8 + - + +
44C ALA* 3.4 7.7 - - - +
45C LYS 3.4 0.2 - - - -
46C ASP* 1.3 89.5 - - + +
48C PRO* 1.3 63.2 - - + +
49C GLU* 3.5 32.8 - - + +
50C VAL* 3.0 29.6 - - + +
111C ALA* 4.5 11.0 - - + +
112C HIS* 3.7 24.9 - - + +
115C LYS* 4.1 27.4 - - + -
----------------------------------------------------------
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