Contacts of the helix formed by residues 14 - 23 (chain N) in PDB entry 6CM9
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 PRO 14 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N VAL 3.5 13.0 - - - +
11N ILE* 4.2 8.3 - - - +
12N GLY 3.8 0.9 - - - -
13N TRP* 1.4 93.2 - - + +
15N ALA* 1.3 61.0 + - + +
16N VAL 3.6 0.2 - - - -
17N ARG* 3.5 24.5 + - - +
18N GLU* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N ILE 4.5 4.9 - - - +
12N GLY* 3.2 14.1 + - - +
14N PRO* 1.3 79.1 - - + +
16N VAL* 1.3 64.2 + - + +
18N GLU* 3.2 7.2 + - - +
19N ARG* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N GLY* 2.8 23.7 + - - +
15N ALA* 1.3 73.0 - - + +
17N ARG* 1.3 57.6 + - - +
19N ARG* 3.3 15.4 + - - +
20N MET* 2.8 42.0 + - - +
109N ILE* 4.5 16.2 - - + -
110N LEU* 4.7 7.2 - - + -
113N TRP* 3.5 57.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
13N TRP* 2.7 69.0 + - - +
14N PRO* 3.5 25.3 + - - +
15N ALA 3.2 0.6 - - - -
16N VAL* 1.3 78.2 - - - +
18N GLU* 1.3 56.1 + - - +
20N MET* 3.3 16.1 + - + +
21N ARG* 2.9 74.2 + - + +
95N GLY 4.5 3.2 + - - -
96N GLY* 3.5 19.1 - - - +
100N LEU* 5.0 2.7 - - + -
106N ARG* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N PRO 2.9 18.5 + - - +
15N ALA* 3.2 8.2 + - - +
17N ARG* 1.3 74.8 - - - +
19N ARG* 1.3 60.8 + - - +
21N ARG* 4.4 12.3 + - - +
22N ARG* 2.9 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N ALA 3.0 17.0 + - - +
16N VAL* 3.8 20.4 - - - +
18N GLU* 1.3 77.0 - - - +
20N MET* 1.3 61.8 + - - +
22N ARG* 4.1 5.1 - - - +
23N ALA* 3.2 22.5 + - - +
109N ILE* 3.4 43.0 + - + +
113N TRP* 4.9 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N VAL* 2.8 31.0 + - + +
17N ARG* 3.5 15.7 - - + +
18N GLU 3.2 0.2 - - - -
19N ARG* 1.3 77.6 - - - +
21N ARG* 1.3 56.9 + - - +
23N ALA* 3.1 29.2 + - - +
97N LEU* 5.0 14.1 - - + -
100N LEU* 5.2 4.0 - - + -
106N ARG* 3.2 66.5 + - + +
109N ILE* 4.9 9.9 - - + -
110N LEU* 3.7 30.7 - - + -
183N TRP* 5.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17N ARG* 2.9 53.8 + - + +
18N GLU* 4.1 13.2 + - - +
20N MET* 1.3 73.7 - - - +
22N ARG* 1.3 77.1 + - - +
23N ALA 3.6 5.5 - - - +
25N PRO* 5.5 1.2 - - - +
96N GLY* 3.6 11.3 + - - -
100N LEU* 3.4 31.6 - - + +
106N ARG* 3.5 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18N GLU* 2.9 44.2 + - + +
19N ARG* 4.2 5.4 - - - +
21N ARG* 1.3 85.1 + - - +
23N ALA* 1.3 63.1 + - - +
24N GLU* 3.6 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N ARG 3.2 16.7 + - - +
20N MET* 3.1 24.4 + - - +
21N ARG 3.6 5.2 - - - +
22N ARG* 1.3 77.8 - - - +
24N GLU* 1.3 64.8 - - - +
25N PRO* 3.4 9.9 - - - +
105N ARG* 3.8 37.7 - - + +
106N ARG* 4.7 4.5 + - + +
109N ILE* 4.8 6.3 - - + -
----------------------------------------------------------
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