Contacts of the helix formed by residues 40 - 51 (chain N) 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 CYS 40 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N CYS* 3.0 9.6 - - - +
27N CYS* 2.0 44.9 - - - -
29N ARG* 3.5 28.0 - - + -
32N SER 4.5 2.0 - - - +
33N VAL* 4.0 14.6 - - + +
39N LEU* 1.4 72.1 - - - +
41N ARG* 1.3 53.8 + - - +
42N ILE* 4.2 7.4 - - - -
43N CYS* 2.1 64.6 - - - +
44N LEU* 2.6 14.2 + - - -
307N ZN 2.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973A G 2.7 26.9 + - - -
974A A 2.7 33.0 + - - -
49J VAL* 3.4 40.5 - - + +
50J ILE* 3.7 31.8 - - + +
52J GLY 3.2 14.9 + - - -
53J PRO* 3.4 9.1 - - - +
54J PHE 3.4 26.5 - - - +
29N ARG* 4.3 4.7 - - - +
32N SER* 3.2 36.1 + - - +
34N TYR* 5.4 1.8 - - + -
40N CYS* 1.3 71.4 - - - +
42N ILE* 1.3 86.2 + - + +
44N LEU* 3.2 9.3 + - - +
45N ARG* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202A G 3.2 74.7 - - + +
49J VAL* 5.7 0.2 - - - -
51J ARG 6.1 0.9 - - - +
52J GLY 5.4 3.1 - - - +
53J PRO* 4.3 24.7 - - + -
29N ARG* 3.8 18.2 - - - +
40N CYS* 4.2 6.1 - - - -
41N ARG* 1.3 88.4 - - + +
43N CYS* 1.3 70.6 + - - +
45N ARG* 3.8 2.1 - - - +
46N GLU* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 43 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202A G 4.1 3.8 - - - +
24N CYS* 3.4 6.1 - - - -
26N ARG* 3.7 16.4 - - - +
27N CYS* 3.3 2.7 - - - -
39N LEU* 3.8 10.1 - - + -
40N CYS* 2.1 60.6 - - - +
42N ILE* 1.3 75.0 - - - +
44N LEU* 1.3 66.5 + - - +
46N GLU* 3.2 3.6 + - - +
47N LEU* 3.1 20.8 + - - +
307N ZN 1.2 47.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J PHE* 4.1 15.7 - - + -
49J VAL* 5.0 7.4 - - + -
63J PHE* 4.2 20.9 - - + -
34N TYR* 4.0 35.2 - - + -
37N PHE* 4.4 20.6 - - + -
39N LEU* 3.9 15.6 - - + +
40N CYS 2.6 14.7 + - - +
41N ARG* 3.2 14.0 + - - +
43N CYS* 1.3 76.3 - - - +
45N ARG* 1.3 72.8 + - + +
47N LEU* 3.0 11.6 + - - +
48N ALA* 3.3 8.5 + - + -
53N LEU* 4.3 20.8 - - + +
56N VAL* 5.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A C 3.1 17.8 + - - -
1060A C 3.0 27.1 + - - -
5C ILE* 5.5 1.2 - - - +
49J VAL* 4.2 26.9 - - + -
51J ARG* 3.1 51.7 + - - +
61J GLU* 2.7 41.3 + - - +
63J PHE* 3.1 32.5 - - + -
41N ARG 3.0 13.3 + - - +
42N ILE* 4.0 2.0 - - - +
44N LEU* 1.3 78.4 - - - +
46N GLU* 1.3 65.4 + - - +
47N LEU 3.0 1.6 + - - -
48N ALA* 3.3 3.3 + - - +
49N HIS* 3.1 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058A G 4.3 13.7 + - - -
1059A C 5.4 7.5 - - - +
1202A G 3.5 37.2 + - - +
26N ARG* 4.2 18.8 + - - +
42N ILE* 2.8 24.8 + - - +
43N CYS 3.4 4.7 - - - +
45N ARG* 1.3 73.1 - - - +
47N LEU* 1.3 63.2 + - + +
49N HIS* 3.1 24.5 - - + +
50N LYS* 3.4 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 5.1 0.9 - - + -
37C GLN* 4.4 17.3 - - - +
26N ARG* 2.8 45.5 - - + +
39N LEU* 3.4 33.0 - - + -
43N CYS 3.5 4.3 - - - +
44N LEU 3.0 7.4 + - - +
46N GLU* 1.3 74.3 - - + +
48N ALA* 1.3 55.1 + - - +
49N HIS 2.6 4.4 + - - -
50N LYS* 2.5 33.8 + - + +
51N GLY 2.8 10.0 + - - -
52N GLN* 3.6 28.0 + - + +
53N LEU* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLY* 4.4 0.5 - - - +
12C LEU* 2.8 29.3 - - - +
63J PHE* 4.4 14.8 - - + -
44N LEU* 3.3 8.7 + - + +
45N ARG 3.3 7.7 + - - +
47N LEU* 1.3 76.0 - - - +
49N HIS* 1.3 58.0 + - - +
51N GLY* 3.6 4.6 + - - +
52N GLN 4.6 1.8 - - - +
53N LEU* 3.9 18.6 - - + +
56N VAL* 3.4 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 49 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A C 6.6 0.4 - - - -
5C ILE* 4.8 11.2 - - + -
6C HIS* 4.1 24.3 + - + +
8C ILE* 3.0 22.8 - - - +
9C GLY* 3.0 23.3 + - - -
12C LEU* 3.4 1.0 - - - +
61J GLU* 3.4 29.5 + - - -
63J PHE* 4.0 9.9 - + - -
45N ARG* 3.1 54.7 + - + +
46N GLU* 3.1 15.9 - - + +
47N LEU 2.6 4.6 + - - -
48N ALA* 1.3 75.9 - - - +
50N LYS* 1.3 63.1 + - + +
58N LYS* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C HIS* 4.1 18.8 - - + +
8C ILE* 3.8 17.8 - - - +
12C LEU* 4.9 0.3 - - - +
19C GLU* 4.0 19.4 + - - +
44C GLU* 5.7 4.6 + - - -
184C TYR* 6.2 3.8 - - - -
186C PHE* 5.4 15.5 + - - +
46N GLU 3.4 7.9 + - - +
47N LEU* 2.5 17.2 + - + +
49N HIS* 1.3 75.6 - - - +
51N GLY* 1.3 56.9 + - - +
52N GLN* 3.7 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.8 19.1 - - - -
18C TRP* 3.1 24.7 - - - -
19C GLU* 3.9 15.8 + - - -
20C SER 4.4 2.1 + - - -
47N LEU 2.8 8.1 + - - -
48N ALA* 3.8 11.7 - - - -
49N HIS 3.2 0.8 - - - -
50N LYS* 1.3 75.5 - - - +
52N GLN* 1.3 57.7 + - - +
53N LEU 3.1 10.1 + - - -
54N PRO 4.4 0.2 - - - -
----------------------------------------------------------
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