Contacts of the helix formed by residues 44 - 63 (chain V) in PDB entry 3CME
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 GLY 44 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910 G 3.5 6.6 + - - -
920 G 3.7 37.7 - - - -
42V ASN 2.5 12.3 + - - -
43V PRO* 1.3 70.6 - - - +
45V ARG* 1.3 58.6 + - - -
47V LYS* 2.8 12.7 + - - +
48V GLU* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1V THR* 6.1 3.1 - - + -
2V VAL* 5.6 11.4 - - + +
26V GLU* 2.8 41.7 + - - +
42V ASN* 3.4 8.1 + - + +
44V GLY* 1.3 68.2 - - - +
46V ILE* 1.3 54.6 + - - +
47V LYS 2.6 11.6 + - - -
48V GLU* 3.8 13.7 - - + -
49V LEU* 2.4 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570 C 3.6 29.9 + - - +
27V LEU* 4.1 15.0 - - + +
30V ALA* 4.5 20.4 - - + +
31V ARG* 5.2 4.3 - - + +
34V GLN* 3.6 40.2 - - + +
41V GLU* 5.6 1.8 - - - +
42V ASN 4.3 2.3 + - - +
43V PRO* 3.0 38.1 - - + +
45V ARG* 1.3 77.4 - - - +
47V LYS* 1.3 56.3 + - + +
49V LEU* 4.4 10.1 - - - +
50V ARG* 3.6 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570 C 3.7 25.8 - - - +
830 C 3.6 35.0 + - - -
910 G 5.3 6.7 - - - +
920 G 5.7 4.5 + - - +
43V PRO 3.8 7.2 - - - +
44V GLY* 2.8 9.3 + - - +
45V ARG 2.6 1.6 + - - -
46V ILE* 1.3 79.7 - - - +
48V GLU* 1.3 73.6 + - - +
49V LEU 3.2 0.9 - - - -
50V ARG* 3.3 16.2 + - - +
51V LYS* 3.4 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920 G 4.1 8.1 + - - +
930 C 4.0 27.0 + - - +
1V THR* 3.3 41.1 + - + +
44V GLY 2.8 21.2 + - - +
45V ARG* 3.8 11.2 - - + +
47V LYS* 1.3 85.1 - - - +
49V LEU* 1.3 56.0 + - - +
51V LYS* 3.0 21.7 + - - +
52V ALA* 2.6 37.6 + - - +
55V ARG* 4.7 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V LEU* 3.4 44.6 - - + +
26V GLU* 3.5 33.0 - - + +
27V LEU* 3.4 46.9 - - + +
30V ALA* 4.6 5.6 - - + -
45V ARG* 2.4 43.5 + - + +
46V ILE* 4.5 2.5 - - - -
48V GLU* 1.3 68.8 - - - +
50V ARG* 1.3 55.7 + - - +
52V ALA* 3.3 4.8 - - - +
53V ILE* 3.0 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550 U 3.3 11.6 + - - -
560 G 2.8 42.7 + - - -
570 C 4.3 8.0 + - - -
680 U 4.4 1.6 - - - +
690 A 3.1 74.4 + - - +
700 A 3.4 13.1 + - - -
27V LEU* 4.5 16.4 - - + -
31V ARG* 5.1 9.4 - - - +
46V ILE 3.6 20.4 - - - +
47V LYS* 3.3 8.9 + - - +
48V GLU 3.1 0.4 - - - -
49V LEU* 1.3 78.0 - - - +
51V LYS* 1.3 63.2 + - + +
53V ILE* 3.3 10.9 + - - +
54V ALA* 3.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690 A 4.7 1.6 - - - +
710 G 3.4 27.6 + - - +
720 C 3.1 35.7 + - - +
47V LYS* 3.4 31.5 + - - +
48V GLU* 3.0 24.3 + - - +
50V ARG* 1.3 76.0 - - + +
52V ALA* 1.3 66.7 + - - +
54V ALA* 3.2 8.0 + - - +
55V ARG* 3.0 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1V THR 6.4 0.2 - - - +
3V LEU* 4.5 15.2 - - + +
8V ILE* 4.8 0.5 - - - +
23V LEU* 3.7 27.4 - - + -
48V GLU 2.6 21.2 + - - +
49V LEU* 3.3 11.2 - - - +
51V LYS* 1.3 75.4 - - - +
53V ILE* 1.3 62.7 + - - +
55V ARG* 3.2 19.9 + - - +
56V ILE* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 U 4.5 11.0 - - - -
20V LEU* 4.2 19.7 - - + -
23V LEU* 4.1 19.5 - - + -
24V LYS* 4.0 33.4 - - + +
27V LEU* 3.6 29.2 - - + -
49V LEU* 3.0 19.0 + - + +
50V ARG* 3.3 6.5 + - - +
52V ALA* 1.3 77.5 - - - +
54V ALA* 1.3 59.6 + - - +
56V ILE* 4.2 2.0 - - - +
57V LYS* 3.4 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 U 3.2 41.8 + - - +
690 A 4.4 1.6 - - - +
710 G 5.4 2.0 - - - +
720 C 3.6 16.8 - - - +
50V ARG 3.0 13.4 + - - +
51V LYS* 3.6 10.3 - - - +
52V ALA 3.2 0.2 - - - -
53V ILE* 1.3 75.6 - - - +
55V ARG* 1.3 52.8 + - - +
57V LYS* 3.2 3.1 + - - +
58V THR* 2.5 39.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720 C 3.2 43.2 + - - +
730 U 3.6 17.5 + - - +
1V THR* 3.8 15.4 - - - +
3V LEU* 3.5 23.5 + - - -
4V HIS* 5.2 1.2 - - - +
5V VAL* 4.6 9.6 - - + +
8V ILE* 3.5 23.1 - - + -
48V GLU* 4.7 5.3 + - - -
51V LYS* 3.0 46.1 + - - +
52V ALA* 3.5 9.9 - - - +
54V ALA* 1.3 72.0 - - - +
56V ILE* 1.3 69.5 + - - +
58V THR* 2.8 14.3 + - - -
59V ILE* 2.8 18.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3V LEU* 4.5 2.5 - - + -
8V ILE* 3.9 27.1 - - + +
11V MET* 5.5 0.4 - - - -
16V ARG* 3.8 22.0 - - + +
19V GLU* 3.5 39.0 - - + +
20V LEU* 3.9 13.7 - - + +
23V LEU* 3.6 21.1 - - + -
52V ALA 3.2 10.6 + - - +
53V ILE 4.2 0.7 - - - +
55V ARG* 1.3 77.1 - - - +
57V LYS* 1.3 53.1 + - - +
59V ILE* 3.0 4.2 + - - +
60V GLN* 2.8 65.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 U 3.1 87.5 + - + +
1S SER* 5.8 4.6 - - - -
20V LEU* 4.7 9.4 - - + +
24V LYS* 4.7 15.2 - - - +
53V ILE* 3.4 20.3 + - - +
54V ALA 3.2 8.0 + - - +
55V ARG 3.2 0.8 - - - -
56V ILE* 1.3 78.4 - - - +
58V THR* 1.3 61.9 + - - +
60V GLN* 3.9 19.3 - - - +
61V GLY* 3.3 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 U 3.1 20.1 + - - +
720 C 2.6 29.3 + - - +
730 U 3.1 31.0 - - - +
1050 G 4.2 4.7 - - - +
1060 A 4.8 10.7 + - - +
54V ALA 2.5 21.8 + - - -
55V ARG 2.8 10.4 + - - -
57V LYS* 1.3 78.5 - - - +
59V ILE* 1.3 56.8 + - - +
61V GLY* 3.7 1.0 + - - -
62V GLU* 3.2 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730 U 4.6 5.8 - - - -
5V VAL* 3.8 13.2 - - + -
8V ILE* 3.5 26.5 - - + -
9V ARG* 3.3 46.9 - - + +
16V ARG* 3.9 13.5 - - - +
55V ARG* 2.8 17.5 + - + +
56V ILE 3.5 5.4 - - - +
58V THR* 1.3 74.9 - - - +
60V GLN* 1.3 54.5 + - - +
61V GLY 3.0 2.5 - - - -
62V GLU* 2.6 14.2 + - - +
63V GLU* 2.6 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16V ARG* 4.2 14.8 + - + +
17V GLU* 3.4 27.7 + - - +
20V LEU* 3.3 24.5 - - - +
56V ILE* 2.8 53.7 + - + +
57V LYS* 3.9 16.2 - - - +
58V THR 3.5 0.2 - - - -
59V ILE* 1.3 71.1 - - - +
61V GLY* 1.3 56.7 + - - +
64V GLY 3.4 0.2 + - - -
65V ASP* 2.6 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680 U 5.9 0.9 - - - -
1060 A 5.8 3.1 - - - -
57V LYS 3.3 12.0 + - - -
58V THR 4.1 1.1 - - - -
59V ILE 3.0 0.4 - - - -
60V GLN* 1.3 79.4 - - - +
62V GLU* 1.3 64.1 + - - +
64V GLY* 3.2 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730 U 2.6 39.4 + - - +
740 G 5.3 0.5 - - - +
1050 G 5.1 0.7 + - - -
1060 A 6.1 3.6 - - - +
9V ARG* 3.1 26.3 + - - -
58V THR* 3.2 23.3 + - + +
59V ILE* 2.6 20.2 + - - +
61V GLY* 1.3 73.3 - - - +
63V GLU* 1.3 68.8 + - - +
64V GLY 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V ARG* 4.2 24.6 + - - +
13V PRO* 5.6 1.7 - - + +
16V ARG* 3.2 32.5 + - - +
59V ILE* 2.6 37.4 + - + +
62V GLU* 1.3 89.1 - - - +
64V GLY* 1.3 59.2 - - - +
65V ASP* 3.1 7.9 - - - +
----------------------------------------------------------
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