Contacts of the helix formed by residues 39 - 53 (chain S) in PDB entry 1KC8
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 THR 39 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S LYS* 1.3 73.6 - - - +
40S ALA* 1.3 66.3 + - - +
41S GLY* 3.0 11.2 - - - +
42S GLU* 2.6 47.7 + - + +
43S ALA* 2.7 10.4 + - - +
107S GLU 2.8 24.9 - - - +
108S ALA* 3.7 17.9 + - - -
109S MET 3.3 6.0 + - - -
110S THR* 4.5 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S LYS 3.7 1.8 + - - -
39S THR* 1.3 71.1 - - - +
41S GLY* 1.3 61.3 + - - +
43S ALA* 3.2 4.9 + - - +
44S VAL* 3.0 26.7 + - - +
92S LEU* 4.3 13.1 - - + +
96S VAL* 3.6 29.6 - - + -
106S GLY 3.7 8.7 - - - +
107S GLU* 3.6 9.4 - - - +
109S MET 2.8 13.7 + - - +
111S ILE* 4.3 3.9 - - - +
147S LEU* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 41 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S THR* 3.6 4.9 - - - -
40S ALA* 1.3 73.4 - - - +
42S GLU* 1.3 64.3 + - - +
44S VAL* 3.2 9.5 + - - +
45S ASP* 3.0 29.4 + - - +
107S GLU* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S GLY 4.8 0.5 - - - +
38S LYS* 3.4 20.2 - - + +
39S THR* 2.6 51.6 + - + +
41S GLY* 1.3 72.2 - - - +
43S ALA* 1.3 55.9 + - - +
45S ASP* 3.2 9.6 + - - +
46S TYR* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S ILE* 4.4 13.5 - - + -
38S LYS* 4.4 8.0 - - + +
39S THR 2.7 14.3 + - - +
40S ALA 3.3 9.4 - - - +
42S GLU* 1.3 73.1 - - - +
44S VAL* 1.3 62.4 + - - +
46S TYR* 3.1 7.8 + - - +
47S LEU* 2.9 28.5 + - - +
92S LEU* 3.8 15.5 - - + -
111S ILE* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S ALA* 3.0 18.0 + - + +
41S GLY* 3.2 8.9 + - - +
43S ALA* 1.3 76.3 - - - +
45S ASP* 1.3 65.8 + - - +
47S LEU* 3.3 1.2 + - - +
48S GLU* 2.9 45.5 + - - +
89S LEU* 3.8 22.2 - - + +
92S LEU* 4.3 22.2 - - + -
93S GLU* 6.5 0.2 - - - -
96S VAL* 5.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S GLY 3.0 16.9 + - - +
42S GLU* 3.7 8.8 - - - +
44S VAL* 1.3 78.0 - - - +
46S TYR* 1.3 65.3 + - - +
48S GLU* 3.3 17.5 + - - +
49S ALA* 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 46 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31S ILE* 5.7 1.1 - - + -
34S GLU* 3.2 35.6 + - + +
35S ILE* 3.9 10.8 - - + -
38S LYS* 3.3 26.9 - - - +
42S GLU 2.9 13.8 + - - +
43S ALA* 3.4 8.7 - - - +
44S VAL 3.1 0.2 - - - -
45S ASP* 1.3 75.2 - - - +
47S LEU* 1.3 74.7 + - + +
49S ALA* 2.7 25.8 + - - +
50S VAL* 2.9 28.5 + - + +
55S GLN* 3.2 35.2 - - + -
56S PRO 3.1 19.3 + - - -
57S VAL* 3.4 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31S ILE* 4.1 19.3 - - + -
35S ILE* 4.3 8.3 - - + -
43S ALA 2.9 18.5 + - - +
46S TYR* 1.3 95.1 - - + +
48S GLU* 1.3 56.9 + - - +
50S VAL* 3.2 6.4 + - + +
51S ILE* 2.9 34.6 + - - +
57S VAL* 5.6 0.2 - - + -
85S SER* 3.8 26.0 - - - +
88S PHE* 3.5 29.8 - - + -
89S LEU* 3.8 26.0 - - + -
92S LEU* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44S VAL* 2.9 37.0 + - + +
45S ASP* 3.7 20.9 - - - +
47S LEU* 1.3 77.2 - - - +
49S ALA* 1.3 57.0 + - - +
51S ILE* 3.4 10.6 + - - +
52S GLU* 2.9 28.4 + - - +
89S LEU* 4.1 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S ASP 3.1 11.8 + - - +
46S TYR* 2.7 11.6 + - - +
48S GLU* 1.3 74.0 - - - +
50S VAL* 1.3 57.0 + - - +
52S GLU* 3.2 7.1 + - - +
53S GLY 2.7 28.8 + - - -
54S ASP* 2.8 20.6 + - + +
55S GLN* 3.5 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S TYR* 2.9 49.4 + - + +
47S LEU* 3.3 12.6 - - + +
49S ALA* 1.3 77.3 - - - +
51S ILE* 1.3 58.6 - - - +
53S GLY* 2.9 20.1 + - - -
55S GLN* 3.2 18.8 - - + +
57S VAL* 3.8 19.1 - - + -
80S TYR* 3.6 31.8 - - - +
81S PRO* 3.9 2.9 - - + +
85S SER* 3.6 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S LEU 2.9 21.0 + - - +
48S GLU* 3.6 7.9 - - - +
50S VAL* 1.3 75.4 - - - +
52S GLU* 1.3 63.1 + - - +
53S GLY* 3.4 0.7 + - - -
80S TYR* 5.8 0.3 - - - +
82S GLU* 4.1 27.4 - - + +
85S SER* 3.7 19.7 - - - -
86S LYS* 3.7 36.1 - - + -
89S LEU* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48S GLU 2.9 18.5 + - - +
49S ALA* 3.4 4.5 - - - +
50S VAL 3.1 0.2 - - - -
51S ILE* 1.3 79.8 - - - +
53S GLY* 1.3 59.9 + - - +
54S ASP* 2.9 31.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 53 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S ALA 2.7 6.9 + - - -
50S VAL 2.9 13.0 + - - -
51S ILE 3.1 1.1 - - - -
52S GLU* 1.3 81.1 - - - +
54S ASP* 1.3 60.0 + - - +
55S GLN 3.4 2.2 - - - -
80S TYR* 3.5 30.3 + - - -
----------------------------------------------------------
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