Contacts of the helix formed by residues 37 - 56 (chain C) in PDB entry 1LE6
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 ASP 37 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 2.6 34.7 + - - -
35C PRO 3.4 1.0 - - - -
36C ARG* 1.3 79.5 - - - +
38C ALA* 1.3 65.8 + - - +
39C ILE* 3.3 5.4 + - - +
40C ASP* 2.9 23.4 + - - +
41C TRP* 2.9 31.1 + - - -
102C GLU 4.4 5.6 - - - +
104C ASN* 4.2 4.2 - - - +
107C TYR* 3.4 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASP* 1.3 74.4 - - + +
39C ILE* 1.3 63.8 + - - +
41C TRP* 3.0 13.9 + - - +
42C CYS* 3.0 26.5 + - - -
101C THR* 4.1 20.2 - - + -
102C GLU 5.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 4.2 0.9 - - - +
20C TYR* 3.8 14.8 - - + -
23C TYR* 3.5 33.7 - - + +
27C CYS* 3.8 11.7 - - - -
37C ASP* 3.2 8.3 + - - +
38C ALA* 1.3 77.7 - - - +
40C ASP* 1.3 64.7 + - - +
42C CYS* 2.9 15.6 + - - +
43C CYS* 3.1 11.4 + - - -
98C LEU* 3.9 19.1 - - + -
101C THR* 3.3 30.3 - - + +
102C GLU 3.7 20.9 - - - +
103C TYR* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 3.6 6.2 - - + +
24C GLY* 3.6 8.7 - - - -
25C CYS* 2.8 25.3 + - - +
26C PHE* 2.8 30.0 + - - +
27C CYS* 3.8 6.1 + - - -
35C PRO* 3.2 10.2 - - + +
36C ARG* 2.8 32.7 + - + +
37C ASP* 2.9 17.9 + - - +
39C ILE* 1.3 76.8 - - - +
41C TRP* 1.3 56.7 + - - +
43C CYS* 3.2 2.4 + - - +
44C HIS* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLN* 4.9 5.4 - - - -
35C PRO* 3.5 35.8 + - + +
37C ASP* 2.9 28.7 + - - -
38C ALA* 3.3 12.6 - - - +
40C ASP* 1.3 74.7 - - - +
42C CYS* 1.3 64.7 + - - +
44C HIS* 3.2 30.1 + + - +
45C GLY* 3.1 19.9 + - - -
97C CYS* 4.9 2.0 - - - -
120C PRO* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA* 3.0 19.6 + - - -
39C ILE* 2.9 9.6 + - - +
41C TRP* 1.3 77.6 - - - +
43C CYS* 1.3 56.5 + - - +
45C GLY* 3.4 2.1 + - - -
46C HIS* 2.9 27.5 + - - +
94C ILE* 3.8 8.6 - - + +
97C CYS* 2.0 69.5 - - + -
98C LEU* 3.6 21.8 - - + -
101C THR* 4.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 5.2 5.4 - - - -
26C PHE* 3.6 5.4 - - - +
27C CYS* 2.0 65.3 - - - +
39C ILE* 3.1 9.5 + - - -
40C ASP 3.2 4.2 + - - +
42C CYS* 1.3 75.7 - - - +
44C HIS* 1.3 60.6 + - - +
46C HIS* 3.6 7.7 - - - +
47C ASP* 2.8 36.6 + - - +
94C ILE* 4.1 15.3 - - - -
98C LEU* 5.2 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.4 37.6 - + + +
35C PRO* 4.2 9.4 - - + -
40C ASP 3.0 13.6 + - - +
41C TRP* 3.2 32.3 + + - +
43C CYS* 1.3 73.8 - - - +
45C GLY* 1.3 69.4 + - - +
47C ASP* 3.2 4.3 + - - +
48C CYS* 3.0 44.4 + - - -
119C SER* 4.7 2.0 - - - -
120C PRO* 2.9 42.5 + - + +
121C LYS 3.7 12.9 + - - -
122C CYS* 4.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TRP 3.1 10.6 + - - -
42C CYS 3.8 3.1 - - - -
44C HIS* 1.3 84.5 - - - +
46C HIS* 1.3 56.8 + - - +
48C CYS* 3.3 10.6 + - - +
49C CYS* 3.0 26.5 + - - +
52C ARG* 5.0 1.2 + - - -
93C GLU* 4.4 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 3.8 19.3 - - + -
42C CYS 2.9 17.6 + - - +
43C CYS* 3.6 4.7 - - - +
44C HIS 3.2 0.2 - - - -
45C GLY* 1.3 75.0 - - - +
47C ASP* 1.3 69.9 + - - +
49C CYS* 3.2 4.8 + - - +
50C TYR* 2.9 59.1 + + - +
90C CYS* 3.3 29.8 + - + -
91C ASP* 2.9 22.3 + - - -
93C GLU* 5.2 2.5 - - - -
94C ILE* 3.6 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.5 17.5 - - + +
30C GLY 3.0 14.0 - - - +
31C GLY* 4.2 1.0 - - - +
43C CYS* 2.8 27.2 + - - +
44C HIS* 3.5 7.6 - - - +
46C HIS* 1.3 81.5 + - - +
48C CYS* 1.3 63.1 + - - +
50C TYR* 3.4 7.5 + - - +
51C THR* 3.0 28.9 + - - +
463C CA 2.5 30.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C HIS* 3.0 38.6 + - - -
45C GLY* 3.3 11.2 - - - +
47C ASP* 1.3 78.9 - - - +
49C CYS* 1.3 62.7 + - - +
51C THR* 3.3 7.1 + - - -
52C ARG* 3.1 35.6 + - - +
122C CYS* 2.0 60.2 - - + -
123C ASP 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLY 3.0 13.0 + - - +
46C HIS* 3.2 8.7 + - - +
48C CYS* 1.3 77.0 - - - +
50C TYR* 1.3 61.4 + - - +
52C ARG* 3.3 30.6 + - - +
53C ALA* 3.1 17.7 + - - +
86C LEU 4.6 0.7 - - - -
89C LYS* 4.8 2.5 - - - -
90C CYS* 2.0 61.6 - - + -
93C GLU* 4.2 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C GLY 4.7 0.9 + - - -
5C LEU* 3.5 17.8 - - + +
46C HIS* 2.9 40.3 + + - +
47C ASP* 3.8 7.2 - - - +
49C CYS* 1.3 73.4 - - - +
51C THR* 1.3 60.6 + - - +
53C ALA* 3.3 6.0 + - - +
54C GLU* 2.9 37.6 + - + +
60C PRO* 3.3 44.9 + - + +
61C LYS* 5.7 0.4 - - - -
87C LEU* 4.1 10.0 - - + +
90C CYS* 3.8 19.7 - - + -
91C ASP* 2.7 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASP* 3.0 19.4 + - - +
48C CYS* 3.6 8.0 - - - -
49C CYS 3.2 0.2 - - - -
50C TYR* 1.3 74.5 - - - +
52C ARG* 1.3 66.7 + - + +
54C GLU* 3.2 16.6 + - + +
55C GLU* 2.9 40.9 + - + +
122C CYS* 6.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C GLY 5.0 1.2 + - - -
48C CYS* 3.1 30.7 + - - +
49C CYS* 3.3 40.2 + - - +
51C THR* 1.3 76.7 - - + +
53C ALA* 1.3 63.5 + - - +
55C GLU* 3.1 29.4 + - - +
56C ALA* 3.2 12.0 + - - +
86C LEU* 5.3 2.5 - - + -
93C GLU* 4.9 4.2 + - - -
122C CYS* 4.9 3.3 - - + +
123C ASP* 4.5 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C CYS 3.1 13.0 + - - +
50C TYR 3.5 8.7 - - - +
52C ARG* 1.3 76.9 - - - +
54C GLU* 1.3 56.9 + - - +
56C ALA* 2.9 19.1 + - - +
58C CYS* 3.0 25.6 + - + +
60C PRO* 4.5 1.3 - - + -
86C LEU* 4.0 25.3 - - + +
87C LEU* 3.9 28.5 - - + -
90C CYS* 5.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 2.9 23.3 + - - +
51C THR* 3.5 17.6 + - + +
53C ALA* 1.3 70.9 - - - +
55C GLU* 1.3 55.3 + - + +
56C ALA 2.9 4.5 - - - -
57C GLY* 2.7 23.7 + - - -
58C CYS 3.5 11.2 - - - +
60C PRO* 3.6 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C THR* 2.9 34.8 + - + +
52C ARG* 3.1 24.0 + - - +
54C GLU* 1.3 75.6 - - - +
56C ALA* 1.3 56.7 + - - +
57C GLY 3.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ARG 3.2 9.1 + - - +
53C ALA 2.9 12.6 + - - +
55C GLU* 1.3 77.4 - - - +
57C GLY* 1.3 59.7 + - - +
58C CYS* 3.5 8.0 + - - -
82C LYS* 5.9 3.1 - - + -
83C CYS* 4.5 2.8 - - - -
86C LEU* 4.0 20.4 - - + -
----------------------------------------------------------
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