Contacts of the helix formed by residues 31 - 49 (chain C) in PDB entry 4JCQ
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 ASN 31 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLU* 3.3 36.4 + - - +
30C ILE* 1.3 74.6 - - - +
32C GLN* 1.3 58.5 + - - +
33C GLU* 3.3 20.8 + - - +
34C LEU* 2.9 34.9 + - - +
35C ALA 2.9 24.1 + - - -
63C HIS* 4.0 12.3 - - + +
66C ALA* 3.4 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASN* 1.3 76.5 - - - +
33C GLU* 1.3 65.3 + - - +
35C ALA* 3.4 7.4 + - - +
36C GLU* 2.9 30.4 + - - +
63C HIS* 5.5 1.0 - - - +
65C GLU* 4.4 15.6 - - + +
66C ALA* 3.8 7.4 - - + +
27D TYR* 3.8 9.5 - - + +
28D GLY* 3.4 25.1 - - - +
58D ASN* 3.2 39.6 + - - +
60D GLN* 3.2 30.4 + - - +
88D TRP* 3.5 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASN* 3.3 26.8 + - - +
32C GLN* 1.3 84.2 + - - +
34C LEU* 1.3 62.0 + - - +
36C GLU* 3.4 9.0 + - - +
37C ASP* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU 4.9 9.4 - - - +
26C ILE* 3.7 26.2 - - + -
27C TYR 5.0 10.3 - - - +
28C GLY 5.8 0.4 - - - +
29C GLU 4.0 13.9 - - - +
30C ILE* 4.1 10.8 - - + -
31C ASN* 2.9 20.4 + - - +
33C GLU* 1.3 73.4 - - - +
35C ALA* 1.3 59.5 + - - +
37C ASP* 3.2 13.2 + - + +
38C VAL* 2.8 48.0 + - + +
70C ILE* 3.7 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASN 2.9 15.9 + - - +
32C GLN* 3.6 11.0 - - - +
34C LEU* 1.3 77.1 - - - +
36C GLU* 1.3 53.6 + - - +
38C VAL* 4.0 0.9 - - - +
39C SER* 2.7 38.1 + - - -
66C ALA* 3.9 26.2 - - + +
69C THR* 4.5 4.5 - - + -
70C ILE* 3.8 16.1 - - + +
27D TYR* 3.7 14.1 - - + -
58D ASN* 5.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLN 2.9 16.5 + - - +
33C GLU* 3.7 8.6 - - - +
35C ALA* 1.3 74.7 - - - +
37C ASP* 1.3 60.6 + - - +
39C SER* 3.4 1.7 + - - -
40C LYS* 2.9 56.6 + - + +
25D LEU* 3.8 28.6 - - + +
27D TYR* 3.6 33.6 + - + +
37D ASP* 5.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU* 5.5 2.3 - - - +
33C GLU 3.1 13.9 + - - +
34C LEU* 3.2 19.4 + - + +
36C GLU* 1.3 77.5 - - - +
38C VAL* 1.3 56.7 + - - +
40C LYS* 3.5 9.7 + - - +
41C GLN* 3.1 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 4.4 13.0 - - + -
25C LEU 4.8 2.0 - - - +
26C ILE* 3.8 30.1 - - + -
34C LEU* 2.8 42.3 + - + +
35C ALA 4.0 2.5 - - - +
37C ASP* 1.3 69.2 - - - +
39C SER* 1.3 61.0 + - - +
41C GLN* 3.3 10.3 + - - +
42C LEU* 2.9 48.7 + - + +
55C ILE* 5.5 1.1 - - + -
70C ILE* 4.0 26.0 - - + -
73C MET* 6.3 0.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
35C ALA 2.7 24.6 + - - -
36C GLU 3.6 3.6 - - - -
38C VAL* 1.3 77.8 - - - +
40C LYS* 1.3 57.1 + - - +
42C LEU* 3.4 5.8 + - - +
43C LEU* 3.0 37.1 + - - +
69C THR* 4.0 2.9 - - - +
70C ILE* 5.5 1.4 - - - +
73C MET* 3.7 25.0 - - - +
25D LEU* 3.7 13.9 - - - -
27D TYR* 3.0 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU* 2.9 49.5 + - + +
37C ASP* 3.7 9.6 - - - +
39C SER* 1.3 75.7 - - - +
41C GLN* 1.3 58.9 + - + +
43C LEU* 4.0 4.7 - - + +
44C LEU* 3.0 31.1 + - - +
18D LEU* 3.9 32.0 - - + +
25D LEU* 3.7 17.5 - - + -
41D GLN* 6.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 6.0 1.7 - - - +
23C THR 4.3 4.0 - - - +
24C VAL* 3.6 39.9 - - + +
25C LEU 4.6 6.1 + - - +
37C ASP* 3.1 50.6 + - - +
38C VAL* 3.3 9.3 + - - +
40C LYS* 1.3 77.1 - - + +
42C LEU* 1.3 56.8 + - - +
44C LEU* 3.4 6.6 + - - +
45C LEU* 3.0 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 4.2 15.5 - - + -
38C VAL* 2.9 36.5 + - + +
39C SER* 3.9 3.6 - - - +
41C GLN* 1.3 75.2 - - - +
43C LEU* 1.3 57.6 + - - +
45C LEU* 3.5 3.8 + - - +
46C GLU* 3.0 29.1 + - - +
53C ILE* 4.3 11.4 - - + -
55C ILE* 4.2 20.0 - - + -
70C ILE 4.9 0.4 - - - +
73C MET* 4.2 25.6 - - + +
74C ILE* 4.1 24.9 - - + +
77C ILE* 3.9 32.2 - - + +
81C VAL* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C SER 3.0 22.7 + - - +
40C LYS* 4.0 6.1 - - - +
42C LEU* 1.3 75.1 - - - +
44C LEU* 1.3 64.6 + - - +
46C GLU* 3.5 11.5 + - - +
47C SER* 3.1 23.7 + - - -
73C MET* 3.9 26.5 - - + -
76C PHE* 5.1 0.7 - - + -
77C ILE* 4.6 2.2 - - + -
18D LEU* 5.2 5.6 - - + -
21D THR* 4.3 14.5 - - + +
23D THR* 3.8 30.3 - - + +
25D LEU* 4.2 16.2 - - + -
56D PHE* 4.5 9.2 - - + -
186D ARG* 3.6 27.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
19C ILE* 3.8 31.0 - - + -
40C LYS 3.0 19.3 + - - +
41C GLN* 3.6 8.1 - - - +
43C LEU* 1.3 76.5 - - - +
45C LEU* 1.3 64.8 + - + +
47C SER* 2.7 26.5 + - - +
48C ILE* 3.3 29.3 + - + +
14D LEU* 3.5 35.0 - - + +
17D LYS* 4.4 8.3 - - + -
18D LEU* 4.2 23.3 - - + +
21D THR* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 3.5 42.0 - - + +
22C ARG* 2.8 53.0 + - - +
23C THR 4.6 2.2 - - - +
24C VAL* 3.8 26.9 - - + -
41C GLN* 3.0 22.8 + - + +
42C LEU* 3.9 0.9 - - - +
44C LEU* 1.3 75.1 - - + +
46C GLU* 1.3 64.7 + - - +
48C ILE* 3.4 4.2 + - + -
49C SER 3.2 8.0 + - - +
53C ILE* 3.8 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU 3.0 18.8 + - - +
43C LEU* 3.7 10.0 - - - +
44C LEU 3.3 0.2 - - - -
45C LEU* 1.3 77.2 - - - +
47C SER* 1.3 61.3 + - - +
49C SER* 3.2 20.3 + - - +
50C ASN* 4.8 4.4 + - - +
77C ILE* 3.4 20.0 - - + +
78C LYS* 3.0 29.4 + - + +
79C PRO* 3.7 23.7 - - + +
186D ARG* 3.1 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU 3.1 13.7 + - - -
44C LEU* 2.7 26.2 + - - +
46C GLU* 1.3 77.3 - - - +
48C ILE* 1.3 61.5 + - - +
17D LYS* 3.7 30.5 - - - +
20D ASP* 6.4 0.2 - - - -
21D THR* 3.6 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 3.7 30.5 - - + -
20C ASP* 6.2 0.2 - - - +
22C ARG* 4.1 9.0 - - - +
44C LEU* 3.3 32.5 + - + +
45C LEU* 3.7 11.9 - - + +
46C GLU 3.2 0.8 - - - -
47C SER* 1.3 81.9 - - - +
49C SER* 1.3 65.5 + - - +
14D LEU* 5.6 1.8 - - + -
17D LYS* 3.9 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ARG* 3.3 29.6 + - - -
45C LEU 3.2 10.0 + - - +
46C GLU 3.2 16.9 + - - +
48C ILE* 1.3 85.1 - - - +
50C ASN* 1.3 60.4 + - - +
51C ASP* 3.3 23.2 + - - +
79C PRO* 3.7 4.7 - - - +
----------------------------------------------------------
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