Contacts of the helix formed by residues 36 - 54 (chain C) in PDB entry 1P4A
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 ALA 36 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C SER* 4.8 0.2 - - - -
35C SER* 1.3 76.7 - - - +
37C LYS* 1.3 65.2 + - - +
38C SER* 4.2 15.3 - - - +
39C SER* 3.2 20.5 + - - +
40C ILE* 3.3 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.8 36.1 - - + +
27C THR* 4.2 23.8 - - + +
30C SER* 3.9 20.3 + - - +
35C SER 3.7 1.2 + - - -
36C ALA* 1.3 72.0 - - - +
38C SER* 1.3 64.7 + - - +
40C ILE* 3.0 12.2 + - - +
41C SER* 2.9 24.5 + - - -
64C GLY 5.8 3.8 - - - +
65C ALA 5.6 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ALA* 4.2 10.7 - - - +
37C LYS* 1.3 78.7 - - - +
39C SER* 1.3 60.6 + - - +
41C SER* 3.4 10.3 + - - -
42C GLU* 3.1 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 3.8 1.8 + - - +
8C ARG* 3.9 15.7 + - - -
35C SER* 4.6 6.3 - - - -
36C ALA* 3.2 24.0 + - - +
37C LYS 3.1 0.6 - - - -
38C SER* 1.3 78.8 + - - +
40C ILE* 1.3 63.9 + - - +
42C GLU* 3.3 13.8 + - - +
43C ASP* 3.1 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG* 4.3 8.5 - - - +
12C LEU* 4.5 7.6 - - + -
26C LEU* 4.7 7.4 - - + +
29C PHE* 3.7 30.7 - - + +
30C SER* 4.2 10.5 - - - +
33C TYR* 3.6 29.6 - - + -
35C SER* 4.2 15.5 - - - -
36C ALA 3.3 16.4 - - - +
37C LYS* 3.3 11.0 - - - +
39C SER* 1.3 76.9 - - - +
41C SER* 1.3 58.8 + - - +
43C ASP* 3.2 8.5 + - - +
44C LEU* 2.9 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.5 21.7 - - - +
37C LYS 2.9 14.3 + - - -
38C SER* 3.4 14.5 - - - -
39C SER 3.3 0.2 - - - -
40C ILE* 1.3 78.0 - - - +
42C GLU* 1.3 57.1 + - - +
44C LEU* 3.4 12.9 + - - +
45C THR* 3.0 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 3.5 19.9 + - - +
38C SER* 3.1 18.2 + - - +
39C SER* 3.6 10.1 + - - +
40C ILE 3.2 0.4 - - - -
41C SER* 1.3 75.0 - - - +
43C ASP* 1.3 64.8 + - - +
45C THR* 3.3 10.5 - - - -
46C ILE* 3.3 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 2.3 45.7 + - - +
8C ARG* 2.6 38.0 + - - +
9C LEU* 3.9 15.8 - - + +
12C LEU* 3.6 19.3 - - + +
39C SER 3.1 11.0 + - - +
40C ILE* 3.3 12.4 - - - +
42C GLU* 1.3 76.2 - - - +
44C LEU* 1.3 62.2 + - - +
46C ILE* 3.0 16.0 + - - +
47C ILE* 3.1 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.9 20.6 - - + -
16C LEU* 3.9 27.6 - - + -
26C LEU* 3.9 27.8 - - + -
29C PHE* 5.2 0.7 - - + -
40C ILE* 2.9 27.3 + - + +
41C SER* 3.7 11.0 - - - +
42C GLU 3.3 0.2 - - - -
43C ASP* 1.3 76.2 - - - +
45C THR* 1.3 54.0 + - - +
47C ILE* 3.3 3.5 + - + -
48C LYS* 2.8 36.4 + - - +
59C LEU* 3.4 12.9 - - + +
61C THR* 4.9 11.4 - - + -
69C VAL* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C SER 3.0 14.7 + - - -
42C GLU* 3.3 14.7 - - - +
44C LEU* 1.3 77.1 - - - +
46C ILE* 1.3 62.8 + - + +
48C LYS* 3.6 8.6 + - + +
49C GLN* 3.0 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 4.0 27.8 - - - +
9C LEU* 4.4 11.4 - - + -
42C GLU* 3.3 16.4 + - + +
43C ASP* 3.0 9.2 + - - +
45C THR* 1.3 79.6 - - + +
47C ILE* 1.3 62.0 + - - +
49C GLN* 3.3 10.7 + - - +
50C THR* 3.0 35.1 + - - +
4D ARG* 4.4 20.2 - - - +
6D SER* 3.8 39.5 - - - +
7D GLY* 4.4 1.3 - - - +
10D VAL* 4.6 2.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
9C LEU* 4.1 9.2 - - + +
12C LEU* 3.7 35.2 - - + -
13C THR* 3.7 14.4 - - - +
16C LEU* 4.1 11.9 - - + -
43C ASP 3.1 15.7 + - - +
44C LEU* 3.7 6.7 - - + +
46C ILE* 1.3 71.8 - - - +
48C LYS* 1.3 57.2 + - - +
50C THR* 3.3 0.5 + - - -
51C PHE* 2.7 73.2 + - + +
59C LEU* 3.9 11.0 - - + -
10D VAL* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU 2.8 22.1 + - - +
45C THR* 3.6 9.2 - - + +
47C ILE* 1.3 72.2 - - - +
49C GLN* 1.3 59.1 + - + +
51C PHE* 3.6 4.5 - - - +
52C GLU* 2.9 62.8 + - - +
58C THR* 3.8 2.6 + - - -
59C LEU* 2.7 50.3 + - + +
60C LEU* 4.9 6.1 - - - +
61C THR* 5.6 6.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C THR* 3.0 36.3 + - + +
46C ILE* 3.3 9.1 + - - +
48C LYS* 1.3 79.4 - - + +
50C THR* 1.3 58.6 + - - +
52C GLU* 3.4 7.9 + - - +
53C GLN* 3.0 30.0 + - - +
4D ARG* 4.2 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.0 19.7 + - - +
47C ILE 3.8 2.9 - - - -
49C GLN* 1.3 73.3 - - - +
51C PHE* 1.3 62.1 + - + +
53C GLN* 3.2 8.0 + - - +
54C GLN* 2.8 49.7 + - + +
56C ILE* 5.3 0.7 - - + -
3D PHE* 4.8 4.3 - - + -
7D GLY* 3.3 44.0 - - - +
10D VAL* 4.0 18.7 - - + +
11D ASP* 4.1 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C THR* 4.1 17.3 - - + -
16C LEU* 4.8 4.3 - - + -
17C LEU* 3.8 22.7 - - + -
47C ILE* 2.7 39.6 + - + +
48C LYS* 3.6 4.7 - - - +
50C THR* 1.3 72.2 - - - +
52C GLU* 1.3 61.5 + - - +
55C GLY 3.1 2.1 + - - -
56C ILE* 2.7 56.4 + - + -
57C GLY 3.2 16.5 + - - +
58C THR* 4.8 0.9 - - - +
59C LEU* 3.9 15.5 - - + -
71C TYR* 3.7 40.4 - + - -
10D VAL* 3.7 24.0 - - + -
14D ASN* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LYS* 2.9 46.2 + - - +
49C GLN* 3.9 6.5 - - - +
51C PHE* 1.3 75.0 - - - +
53C GLN* 1.3 63.6 + - - +
55C GLY* 3.2 10.2 + - - -
57C GLY 3.5 15.3 - - - +
58C THR* 2.4 27.2 + - - +
76C LYS* 3.3 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLN 3.0 19.5 + - - +
50C THR* 3.8 7.0 - - - +
52C GLU* 1.3 76.5 - - - +
54C GLN* 1.3 79.5 + - - +
55C GLY 3.2 0.4 - - - -
76C LYS* 3.0 18.9 + - - +
2D LYS* 4.4 14.4 + - - +
3D PHE* 3.5 29.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C THR* 2.8 29.9 + - + +
53C GLN* 1.3 105.8 + - - +
55C GLY* 1.3 63.3 + - - +
56C ILE* 3.4 15.9 + - + +
76C LYS* 4.6 0.9 - - - -
79C GLU* 5.3 1.6 - - - +
3D PHE* 3.4 21.9 - - + -
11D ASP* 2.9 31.3 - - - +
32D ARG* 3.5 16.4 + - - +
----------------------------------------------------------
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