Contacts of the helix formed by residues 11 - 23 (chain N) in PDB entry 4E45
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 ARG 11 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M TYR* 5.7 3.0 - - - -
26M THR* 5.4 3.7 + - - +
9N GLY 3.5 5.5 + - - +
10N PHE* 1.3 72.8 - - - +
12N LYS* 1.3 62.4 + - - +
13N GLU* 3.0 21.7 + - - +
14N LEU* 3.0 26.6 + - + +
15N VAL* 3.0 12.1 + - - +
676O LYS* 4.2 20.9 - - - +
677O ASP* 2.8 32.2 + - - +
678O TRP 4.7 2.4 + - - -
679O PHE 3.2 14.3 + - - -
680O LEU* 4.4 5.1 - - - +
684O GLU* 3.0 40.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N PHE 3.4 3.2 + - - -
11N ARG* 1.3 72.9 - - - +
13N GLU* 1.3 86.7 + - + +
15N VAL 3.8 0.2 - - - -
16N SER* 2.9 28.9 + - - -
32N GLY 6.1 0.2 - - - +
35N LEU* 3.5 27.1 - - + +
36N GLN* 5.8 10.5 - - + -
39N VAL* 3.5 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N ARG* 3.0 23.3 - - - +
12N LYS* 1.3 111.4 + - + +
14N LEU* 1.3 64.0 + - - +
16N SER* 3.7 7.1 + - - -
17N ARG* 3.4 20.8 + - - +
676O LYS 3.5 32.0 + - - +
678O TRP* 3.7 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M LEU* 3.6 34.3 - - + +
22M ALA* 3.8 38.1 - - + +
23M VAL* 4.2 6.3 - - + +
26M THR* 4.5 3.8 - - - +
10N PHE* 4.2 22.7 - - + -
11N ARG* 3.0 16.8 + - + +
13N GLU* 1.3 76.7 - - - +
15N VAL* 1.3 60.7 + - - +
17N ARG* 3.0 5.5 + - - +
18N LEU* 2.8 37.2 + - + +
678O TRP* 3.6 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M CYS* 5.4 1.6 - - - -
10N PHE* 3.5 34.1 - - + -
11N ARG 3.0 8.8 + - - +
12N LYS 3.5 2.2 + - - +
14N LEU* 1.3 74.4 - - - +
16N SER* 1.3 62.0 + - - +
18N LEU* 3.2 8.8 + - + +
19N LEU* 3.0 31.8 + - + +
35N LEU* 3.9 13.9 - - + -
38N MET* 4.0 23.6 - - + -
39N VAL* 3.8 19.5 - - + +
42N LEU* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 16 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N LYS 2.9 19.0 + - - -
13N GLU* 3.7 9.0 - - - -
14N LEU 3.1 0.2 - - - -
15N VAL* 1.3 76.7 - - - +
17N ARG* 1.3 64.1 + - - +
19N LEU* 3.4 3.6 + - - +
20N HIS* 3.0 43.6 + - - -
30N VAL* 5.8 3.3 - - - +
35N LEU* 3.7 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M TYR* 3.0 48.6 + - - +
19M LEU* 4.1 10.9 - - + +
13N GLU 3.4 8.8 + - - +
14N LEU* 3.0 8.7 + - - +
16N SER* 1.3 79.1 - - - +
18N LEU* 1.3 57.5 + - - +
20N HIS* 3.3 7.3 + - + +
21N LEU* 2.9 30.8 + - - +
678O TRP* 3.3 47.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M LEU* 4.2 19.1 - - + -
23M VAL* 3.8 26.2 - - + -
55M PHE* 3.5 34.5 - - + -
58M CYS* 3.8 26.7 - - + -
10N PHE* 5.1 1.3 - - + -
14N LEU* 2.8 31.3 + - + +
15N VAL* 3.2 13.9 + - + +
17N ARG* 1.3 76.6 - - - +
19N LEU* 1.3 62.5 + - - +
21N LEU* 3.4 6.9 + - + +
22N HIS* 3.1 27.0 - - + +
42N LEU* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M CYS* 3.9 17.9 - - - -
62M ALA* 3.6 33.1 - - + +
65M LEU* 4.3 13.5 - - + -
15N VAL* 3.0 33.5 + - + +
16N SER* 3.8 4.0 - - - +
18N LEU* 1.3 75.2 - - - +
20N HIS* 1.3 63.2 + - - +
22N HIS 3.0 12.5 + - - -
23N PHE* 3.3 32.2 + - + -
30N VAL* 4.2 20.6 - - + -
35N LEU* 4.2 12.3 - - + -
38N MET* 4.3 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 20 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N SER* 3.0 40.1 + - - +
17N ARG* 3.9 7.4 - - + +
19N LEU* 1.3 76.4 - - + +
21N LEU* 1.3 64.0 + - - +
22N HIS 3.1 0.9 + - - -
23N PHE* 3.5 34.7 + + - +
26N ASP 5.8 0.9 - - - -
28N THR 3.4 25.5 + - - -
29N LYS* 4.5 8.7 - - + +
30N VAL* 4.8 8.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M TYR* 4.5 22.0 - - + -
16M GLN* 4.1 24.2 - - + +
19M LEU* 3.9 20.4 - - + -
55M PHE* 3.9 17.9 - - + -
17N ARG 2.9 17.4 + - - +
18N LEU* 3.6 8.1 - - - +
19N LEU 3.1 0.4 - - - -
20N HIS* 1.3 79.0 - - - +
22N HIS* 1.3 82.9 + - + +
23N PHE 4.0 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 22 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M GLN* 5.3 2.7 - - - -
55M PHE* 4.4 20.9 + + - -
58M CYS* 4.2 5.5 - - + +
59M GLU* 3.5 57.2 + - + +
62M ALA* 3.8 12.1 - - + -
63M LYS* 3.7 29.0 + - + +
18N LEU* 3.1 26.2 + - - +
19N LEU 3.0 6.9 + - - +
21N LEU* 1.3 102.6 + - + +
23N PHE* 1.3 67.5 + - - +
24N LYS* 3.5 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M ALA* 3.5 33.0 - - + -
65M LEU* 5.1 0.4 - - + -
66M GLU* 3.4 20.0 - - + +
77M ILE* 3.6 27.1 - - + -
19N LEU* 3.3 21.0 + - + -
20N HIS* 3.5 50.2 + + - +
21N LEU 4.6 2.1 - - - +
22N HIS* 1.3 79.2 - - - +
24N LYS* 1.3 61.4 + - - +
25N ASP 4.0 9.9 - - - +
28N THR* 3.7 19.5 - - + -
30N VAL* 3.6 21.5 - - + -
----------------------------------------------------------
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