Contacts of the helix formed by residues 40 - 49 (chain N) in PDB entry 2I2X
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 ILE 40 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N PRO* 4.4 22.2 - - + -
37N ASP* 3.3 34.4 + - + +
39N LEU* 1.3 78.9 - - + +
41N TYR* 1.3 53.3 + - - +
43N ILE* 2.7 34.9 + - + +
44N ALA* 3.1 8.2 + - + -
72N LEU* 5.1 5.6 - - + -
75N ASP* 3.1 36.3 - - + +
76N ALA* 3.7 36.6 - - + +
79N VAL* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 41 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N GLU* 3.2 33.9 + - - -
34N TYR* 3.6 30.7 - + + -
35N PRO 3.9 18.6 + - - +
36N LYS* 5.3 2.0 - - - -
38N GLU* 4.0 19.1 - - - +
40N ILE* 1.3 76.3 - - - +
42N PRO* 1.4 79.4 - - + +
43N ILE 3.2 0.2 + - - -
44N ALA* 3.3 5.9 + - - +
45N LYS* 3.0 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 42 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N GLU 3.5 17.5 - - - +
39N LEU 3.5 11.0 - - - +
41N TYR* 1.4 105.8 - - + +
43N ILE* 1.3 59.3 + - + +
45N LYS* 4.1 5.1 - - + +
46N ALA* 3.2 24.4 + - - +
54N ASP 4.9 1.4 - - - +
58N GLY* 5.4 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 43 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N LEU 3.9 7.2 - - - +
40N ILE* 2.7 30.5 + - - +
42N PRO* 1.3 71.8 - - + +
44N ALA* 1.3 59.5 + - - +
46N ALA* 3.2 6.7 + - - +
47N ILE* 3.2 28.7 + - + +
54N ASP 5.4 1.1 - - - -
55N VAL* 5.0 4.5 - - + +
58N GLY* 3.4 35.2 - - - +
59N LEU* 4.4 7.4 - - + +
62N ALA* 4.2 15.5 - - + -
72N LEU* 4.5 4.3 - - + -
76N ALA* 3.6 40.6 - - + +
77N LEU* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N TYR* 4.1 15.6 - - + -
35N PRO* 4.3 22.0 - - + -
40N ILE* 3.1 13.7 + - + +
41N TYR* 3.8 7.6 - - - +
43N ILE* 1.3 76.5 - - - +
45N LYS* 1.3 61.0 + - - +
47N ILE* 3.3 7.4 + - - +
48N PHE* 3.2 21.1 + - - +
76N ALA 4.3 1.7 + - - -
80N GLY* 3.8 30.3 - - - +
83N VAL* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N GLU* 5.0 5.4 - - - -
34N TYR* 3.3 37.3 - - + +
41N TYR* 3.0 45.5 + - + +
42N PRO* 4.2 5.4 - - + +
44N ALA* 1.3 75.8 - - - +
46N ALA* 1.3 57.6 + - - +
48N PHE* 3.7 1.4 + - - +
49N GLU* 3.2 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42N PRO 3.2 19.7 + - - +
43N ILE 3.5 5.4 - - - +
44N ALA 3.2 0.4 - - - -
45N LYS* 1.3 75.2 - - - +
47N ILE* 1.3 65.1 + - - +
49N GLU* 3.2 6.3 + - - +
50N GLY 3.1 16.5 + - - -
51N GLU* 3.2 14.7 + - - +
54N ASP* 3.8 27.1 - - + +
55N VAL* 3.6 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N ILE* 3.2 31.9 + - + +
44N ALA* 3.3 6.9 + - - +
46N ALA* 1.3 75.7 - - - +
48N PHE* 1.3 56.3 + - - +
50N GLY* 3.1 8.1 + - - -
55N VAL* 3.8 17.0 - - + -
76N ALA 4.4 1.8 - - - +
77N LEU* 3.7 39.0 - - + +
80N GLY* 3.8 26.0 - - - +
81N MET* 3.8 22.4 - - - -
84N VAL* 4.1 4.9 - - + -
101N SER* 2.6 32.9 + - - +
104N ALA* 4.6 3.6 - - - +
105N MET* 4.3 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 48 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N PRO* 3.6 31.2 - - + -
27N GLU* 4.0 22.0 - - + -
30N ALA* 3.8 18.8 - - + -
34N TYR* 3.5 29.6 - - + +
44N ALA 3.2 11.1 + - - +
45N LYS 3.8 2.7 - - - +
46N ALA 3.3 0.2 - - - -
47N ILE* 1.3 76.1 - - - +
49N GLU* 1.3 73.8 + - + +
50N GLY 3.0 5.9 + - - -
80N GLY 5.8 0.7 - - - +
83N VAL* 5.0 3.4 - - + -
84N VAL* 3.8 20.0 - - + -
87N LEU* 3.9 17.0 - - + -
93N ILE* 4.2 17.3 - - + -
97N ASN* 4.7 4.5 - - - +
100N MET* 5.7 1.6 - - - +
101N SER* 3.2 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N LYS* 3.2 47.0 + - + +
46N ALA* 3.2 7.3 + - - +
48N PHE* 1.3 91.8 - - + +
50N GLY* 1.3 61.0 + - - +
51N GLU* 3.2 20.8 + - + +
100N MET* 4.1 15.1 - - - +
----------------------------------------------------------
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