Contacts of the helix formed by residues 28 - 44 (chain C) in PDB entry 2F4V
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 GLN 28 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLY* 2.7 17.8 + - - +
26C LYS 3.4 0.4 + - - -
27C LYS* 1.3 104.0 - - + +
29C TYR* 1.3 55.3 + - - +
30C ARG 3.0 2.2 - - - -
31C HIS* 2.6 37.0 + - + +
32C LEU* 2.9 28.9 + - + +
62C ASP* 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C TRP* 4.4 12.6 - + - -
24C ALA 4.7 8.7 - - - -
25C GLY* 2.7 21.8 + - - +
26C LYS 5.0 2.7 - - - +
28C GLN* 1.3 70.7 - - - +
30C ARG* 1.3 56.9 + - - +
32C LEU* 3.0 10.2 + - - +
33C LEU* 2.9 56.3 + - + +
11J PHE* 4.0 26.5 - + - -
65J LEU* 3.7 10.3 - - + +
36N PHE* 3.3 44.6 - + + +
37N PHE* 4.6 5.6 - + - -
53N LEU* 3.7 5.9 - - + +
54N PRO* 2.6 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LYS 3.3 24.7 + - - -
27C LYS* 3.8 27.1 + - - +
28C GLN 2.8 3.6 + - - +
29C TYR* 1.3 76.2 - - - +
31C HIS* 1.3 79.1 + - + +
33C LEU* 4.3 3.9 - - - +
34C LEU* 4.4 16.1 + - - +
25N VAL* 5.0 5.2 - - - +
35N ARG* 3.2 31.5 + - - +
36N PHE* 3.6 24.8 - - - +
37N PHE* 4.0 16.1 - - - +
38N GLY* 5.0 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LYS 3.1 27.1 + - - -
28C GLN* 2.6 18.2 + - + +
30C ARG* 1.3 97.0 + - + +
32C LEU* 1.3 58.5 - - + +
33C LEU 3.2 5.4 + - - -
34C LEU* 3.5 21.8 + - - +
35C GLU* 3.6 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C TRP* 2.7 54.0 - - + -
23C TYR 6.0 0.9 - - - +
25C GLY* 6.4 1.1 - - - -
28C GLN* 2.9 32.4 + - + +
29C TYR* 3.6 3.1 - - - +
31C HIS* 1.3 76.6 - - + +
33C LEU* 1.3 55.3 + - - +
35C GLU* 2.8 29.6 - - - +
36C ASP* 2.9 0.9 - - - +
59C ARG* 3.2 46.7 - - + +
97C LYS* 4.1 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C TRP* 4.3 10.3 - - + -
29C TYR* 2.9 43.0 + - + +
30C ARG* 4.9 5.2 - - - -
31C HIS 3.2 0.6 - - - -
32C LEU* 1.3 77.5 - - - +
34C LEU* 1.3 58.4 + - - +
35C GLU* 2.8 5.4 + - - -
36C ASP* 4.1 6.5 - - - +
37C GLN* 3.4 36.2 + - + +
25N VAL* 5.6 2.8 - - - +
37N PHE* 4.5 18.2 - - + +
39N LEU* 5.3 7.2 - - + -
47N LEU* 5.1 2.9 - - + -
52N GLN 3.7 18.6 - - - +
53N LEU* 3.6 31.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
30C ARG 4.4 11.3 + - - +
31C HIS* 3.5 16.4 + - - +
33C LEU* 1.3 74.8 - - - +
35C GLU* 1.3 65.7 + - - +
37C GLN* 4.4 5.6 - - + -
38C ARG* 2.9 65.2 + - + +
25N VAL* 3.8 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C HIS 3.6 4.1 + - - +
32C LEU* 2.8 30.8 - - - +
33C LEU 2.8 0.6 - - - -
34C LEU* 1.3 74.6 - - - +
36C ASP* 1.3 61.5 + - - +
37C GLN 2.5 15.8 + - - -
38C ARG* 2.6 18.0 + - - +
39C ILE* 3.1 24.5 + - + +
59C ARG* 2.7 36.6 + - - +
64C VAL* 5.2 2.0 - - - +
94C LEU* 5.8 0.3 - - - +
95C THR* 2.9 37.4 + - - +
97C LYS* 3.5 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C SER* 2.8 34.8 + - - -
22C TRP* 3.0 15.9 - - - -
32C LEU 2.9 20.8 - - - +
33C LEU* 3.9 7.2 + - + +
35C GLU* 1.3 69.5 - - - +
37C GLN* 1.3 58.8 + - - +
39C ILE* 3.1 13.4 + - - +
40C ARG* 2.8 58.5 + - - +
57C ILE* 3.5 12.8 - - + +
59C ARG* 3.7 0.7 + - - -
52N GLN 4.4 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.4 35.1 + - + +
34C LEU* 4.1 7.4 - - + +
35C GLU 2.5 6.9 + - - -
36C ASP* 1.3 78.2 + - - +
38C ARG* 1.3 58.2 + - + +
40C ARG* 3.5 7.8 - - - +
41C GLY* 2.8 26.9 + - - -
25N VAL* 5.4 8.3 - - + -
26N ARG* 4.7 28.9 - - + +
39N LEU* 6.1 1.8 - - + -
47N LEU* 4.4 13.7 - - + +
52N GLN* 3.4 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 2.9 47.5 - - + +
35C GLU* 2.6 9.4 + - - +
37C GLN* 1.3 74.5 - - + +
39C ILE* 1.3 54.6 + - + +
41C GLY* 2.7 26.2 + - - -
42C LEU* 3.3 5.7 + - - +
94C LEU* 5.1 34.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
35C GLU* 3.1 31.3 + - + +
36C ASP* 3.2 12.1 - - - +
38C ARG* 1.3 73.3 - - + +
40C ARG* 1.3 56.0 + - - +
41C GLY 2.7 13.3 + - - -
42C LEU* 3.3 1.4 + - - +
43C LEU* 2.9 42.1 + - + +
57C ILE* 3.6 31.2 - - + -
59C ARG* 5.1 0.9 - - - +
64C VAL* 5.2 5.4 - - + -
66C VAL* 4.4 24.7 - - + -
91C LEU* 6.5 0.9 - - + -
94C LEU* 5.4 12.3 - - + +
95C THR* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU* 3.2 32.6 + - - +
20C SER* 2.8 28.9 + - - -
36C ASP* 2.8 39.6 + - - +
37C GLN* 3.5 8.3 - - - +
39C ILE* 1.3 73.2 - - + +
41C GLY* 1.3 56.8 + - - +
43C LEU* 3.4 13.0 - - + -
44C GLU* 3.1 45.9 - - - +
55C VAL* 2.8 51.7 + - + +
56C ASP 4.3 2.4 + - - -
57C ILE* 4.4 4.3 - - + -
52N GLN* 3.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLN 2.8 13.2 + - - -
38C ARG* 2.7 13.7 + - - -
39C ILE 2.7 6.5 - - - -
40C ARG* 1.3 79.4 - - - +
42C LEU* 1.3 60.0 + - - +
44C GLU* 4.3 2.9 + - - +
45C LYS* 4.9 6.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
38C ARG 3.3 7.9 + - - +
39C ILE 4.5 1.3 - - - +
41C GLY* 1.3 72.1 - - - +
43C LEU* 1.3 70.4 + - - +
44C GLU 2.5 4.9 + - - -
45C LYS* 2.8 42.2 + - - +
46C GLU* 3.6 24.9 + - + +
87C LEU* 6.4 2.7 - - + -
90C GLU* 4.3 28.9 - - + +
94C LEU* 4.8 18.8 - - + -
----------------------------------------------------------
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 ILE* 2.9 33.9 + - + +
40C ARG* 3.4 15.7 - - - -
42C LEU* 1.3 76.5 - - - +
44C GLU* 1.3 57.3 + - - +
45C LYS 3.0 3.5 + - - -
46C GLU 3.4 5.1 - - - +
47C LEU* 3.0 50.7 - - + +
52C LEU* 4.6 1.7 - - + +
55C VAL* 3.7 37.2 - - + -
66C VAL* 4.8 2.9 - - + -
68C VAL* 3.7 27.6 - - + -
87C LEU* 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ARG* 3.1 35.4 + - - +
41C GLY 4.7 2.2 - - - +
42C LEU 2.5 7.5 + - - -
43C LEU* 1.3 72.5 - - + +
45C LYS* 1.3 57.7 + - - +
47C LEU 4.6 1.3 - - - -
48C TYR* 5.1 9.8 + - - -
52C LEU* 4.2 28.8 - - + +
55C VAL* 5.5 3.5 - - - +
50N LYS* 5.7 5.0 + - - -
52N GLN* 5.8 1.6 + - - -
----------------------------------------------------------
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