Contacts of the helix formed by residues 64 - 78 (chain C) in PDB entry 1SL0
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 TYR 64 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.3 19.5 - - + -
8C ALA* 2.9 32.8 + - + +
10C ALA 3.0 10.3 + - - -
11C LEU* 4.0 10.3 - - + -
12C LEU* 3.4 41.3 - - + -
15C VAL* 5.0 0.7 - - + -
60C ASN* 3.2 16.0 + - - +
61C GLY 3.2 2.2 + - - -
62C HIS 3.4 0.2 - - - -
63C LYS* 1.3 81.2 - - - +
65C ASP* 1.3 99.2 + - - +
66C VAL 2.7 3.6 + - - -
67C PRO* 2.8 5.8 - - - +
68C ALA* 2.6 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ASP* 3.9 4.0 - - - -
6C ILE* 3.2 33.9 + - + +
58C PHE* 4.0 21.8 - - + -
59C HIS 4.0 5.1 - - - +
60C ASN* 4.1 0.5 - - - +
61C GLY* 3.6 20.5 + - - -
64C TYR* 1.3 101.4 - - - +
66C VAL* 1.3 58.9 + - - +
68C ALA* 4.1 1.6 - - - +
69C LEU* 2.9 34.3 + - - +
4004C MG 2.9 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PHE* 3.4 26.7 - - + -
61C GLY 2.7 32.6 + - - +
62C HIS* 4.1 4.7 - - - +
64C TYR 2.7 4.0 + - - -
65C ASP* 1.3 71.4 - - - +
67C PRO* 1.3 67.0 - - + +
68C ALA 3.1 2.3 + - - -
69C LEU* 3.4 11.9 + - - +
70C THR* 3.3 15.8 + - - +
81C PHE* 5.0 1.4 - - + -
83C LEU* 4.1 28.3 - - + +
88C CYS* 4.9 6.1 - - + -
222C TRP* 4.0 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.9 9.0 - - + +
61C GLY 3.3 8.1 - - - +
62C HIS 3.6 8.5 - - - +
63C LYS 3.8 7.0 - - - +
64C TYR* 2.8 31.0 - - - +
66C VAL* 1.3 90.5 - - + +
68C ALA* 1.3 54.6 - - - +
69C LEU 3.2 0.4 - - - -
70C THR* 3.6 9.9 + - - +
71C LYS* 3.3 23.7 + - - +
229C ARG* 3.5 40.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.7 5.8 - - + -
12C LEU* 3.4 23.8 - - + -
15C VAL* 4.7 5.6 - - + -
64C TYR* 2.6 47.3 + - + +
65C ASP 4.1 2.9 - - - +
67C PRO* 1.3 71.6 - - - +
69C LEU* 1.3 60.5 + - - +
71C LYS* 3.7 2.2 - - - +
72C LEU* 2.8 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 3.7 30.5 - - + -
39C PHE* 3.9 26.2 - - + -
42C TYR* 3.9 18.8 - - + -
43C LEU* 4.0 7.4 - - + -
46C LEU* 4.3 8.3 - - + -
58C PHE* 4.3 11.9 - - + -
65C ASP 2.9 23.5 + - - +
66C VAL* 3.4 6.3 + - - +
67C PRO 3.2 0.4 - - - -
68C ALA* 1.3 76.6 - - - +
70C THR* 1.3 58.8 + - - +
71C LYS 3.1 1.1 - - - -
72C LEU* 4.3 2.5 - - + +
73C ALA* 2.6 38.6 + - - +
81C PHE* 4.0 30.3 - - + -
83C LEU* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL* 3.3 14.8 + - - +
67C PRO* 3.7 12.1 - - - +
68C ALA 3.4 0.2 - - - -
69C LEU* 1.3 79.6 - - - +
71C LYS* 1.3 63.1 + - - +
73C ALA* 3.5 3.5 - - - +
74C LYS* 3.4 17.7 + - - +
79C ARG 4.8 0.7 - - - +
81C PHE* 3.3 20.4 + - - +
82C HIS* 3.3 40.1 + - + +
83C LEU 5.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.9 21.4 + - + +
13C GLU* 5.3 4.5 - - - +
14C SER* 4.8 2.6 - - - +
15C VAL* 2.8 42.6 + - + +
16C THR* 4.1 5.1 - - - +
67C PRO 3.3 14.1 + - - +
68C ALA 3.7 5.8 - - - +
69C LEU 3.1 0.2 - - - -
70C THR* 1.3 82.8 - - - +
72C LEU* 1.3 64.1 + - - +
74C LYS* 3.3 3.2 + - - +
75C LEU* 3.1 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.5 16.2 - - + -
8C ALA* 4.7 0.7 - - + -
15C VAL* 3.7 36.3 - - + +
16C THR* 3.8 11.7 - - - +
17C LYS* 3.8 15.9 - - - +
18C PHE* 3.6 35.0 - - + +
39C PHE* 3.9 17.9 - - + -
68C ALA* 2.8 24.3 + - + +
69C LEU* 4.0 1.3 - - + +
71C LYS* 1.3 81.6 - - + +
73C ALA* 1.3 64.2 + - - +
75C LEU* 4.3 5.8 - - + -
76C GLN* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 4.2 11.2 - - - -
43C LEU* 3.7 11.4 - - + -
69C LEU 2.6 22.9 + - - +
70C THR 3.5 4.5 - - - +
72C LEU* 1.3 72.0 - - - +
74C LYS* 1.3 63.6 + - - +
77C LEU* 3.1 15.8 + - - -
79C ARG* 3.0 26.8 + - + +
81C PHE* 3.4 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C THR 3.4 7.4 + - - +
71C LYS* 3.3 6.9 + - - +
73C ALA* 1.3 78.6 - - - +
75C LEU* 1.3 64.7 + - + +
78C ASN* 2.6 30.7 + - - +
79C ARG 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL 4.5 1.3 - - - +
16C THR* 4.2 23.6 - - + +
71C LYS* 3.1 46.0 + - + +
72C LEU* 3.8 5.2 - - - +
74C LYS* 1.3 86.7 - - + +
76C GLN* 1.3 67.4 + - + +
77C LEU 3.4 0.2 + - - -
78C ASN* 3.9 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C THR 3.8 14.3 - - - +
17C LYS* 3.1 13.3 - - - +
18C PHE* 2.5 44.9 + - - +
36C PRO 5.6 3.6 + - - -
39C PHE* 4.9 6.3 - - + +
72C LEU* 2.8 23.3 + - + +
75C LEU* 1.3 76.4 - - + +
77C LEU* 1.3 78.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PHE* 3.4 40.4 - - + -
40C GLY* 3.7 22.4 - - - +
43C LEU* 4.6 7.9 - - + -
73C ALA 3.1 8.3 + - - +
76C GLN* 1.3 105.0 - - + +
78C ASN* 1.3 75.1 + - - +
79C ARG* 3.0 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LYS* 2.6 28.0 + - - +
75C LEU 3.9 1.9 + - - +
76C GLN 3.7 0.8 - - - -
77C LEU* 1.3 74.9 - - - +
79C ARG* 1.3 58.5 + - - +
80C GLU 4.4 0.2 + - - -
----------------------------------------------------------
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