Contacts of the helix formed by residues 31 - 42 (chain F) in PDB entry 6R90
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 THR 31 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F GLN 3.7 12.1 - - - +
29F GLY* 3.0 18.0 + - - +
30F ILE* 1.3 77.5 - - - +
32F LYS* 1.3 65.2 + - - +
33F PRO* 3.6 11.2 - - - +
34F ALA* 3.5 19.1 + - - +
35F ILE* 3.1 22.4 + - - +
56F ARG* 3.5 6.3 - - - +
60J C 3.1 41.6 + - - +
61J A 4.6 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F THR* 1.3 74.1 - - - +
33F PRO* 1.3 66.3 - - + +
35F ILE* 3.2 4.3 + - - +
36F ARG* 2.9 51.2 + - - +
49F GLY* 5.3 5.3 - - - -
52F TYR* 3.4 46.2 - - + -
56F ARG* 3.2 15.0 - - - +
80I G 5.6 7.7 - - - +
81I A 5.6 2.2 - - - -
61J A 5.6 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F THR* 3.6 8.3 - - - +
32F LYS* 1.3 98.4 - - + +
34F ALA* 1.3 57.3 + - - +
36F ARG* 3.2 29.6 + - - +
37F ARG* 2.9 39.6 + - - +
60J C 3.8 31.4 - - + +
61J A 5.0 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E LEU* 4.1 9.9 - - - +
63E ILE* 4.7 14.6 - - + -
30F ILE* 5.2 1.8 - - + -
31F THR* 3.5 24.3 + - - +
32F LYS 3.3 0.8 - - - -
33F PRO* 1.3 78.3 - - - +
35F ILE* 1.3 59.4 + - + +
37F ARG* 3.1 32.9 + - - +
38F LEU* 2.9 30.4 + - - +
60J C 4.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LEU* 5.7 1.1 - - + -
105E PHE* 3.8 26.0 - - + -
30F ILE* 3.4 36.1 - - + +
31F THR 3.1 21.1 + - - +
32F LYS 3.7 3.6 - - - +
34F ALA* 1.3 72.3 - - - +
36F ARG* 1.3 60.5 + - - +
38F LEU* 3.2 14.6 + - + +
39F ALA* 2.9 27.9 + - + +
47F ILE* 6.0 0.7 - - + -
51F ILE* 5.4 0.7 - - + -
52F TYR* 4.1 23.6 - - + +
55F THR* 4.1 22.7 - - + +
56F ARG* 4.3 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E GLU* 4.7 8.1 + - - +
32F LYS* 2.9 31.3 + - - +
33F PRO* 3.3 36.7 + - - +
35F ILE* 1.3 77.4 - - - +
37F ARG* 1.3 57.7 + - + +
39F ALA* 3.3 2.4 + - - +
40F ARG* 2.8 72.7 + - + +
47F ILE* 4.1 17.2 - - + +
52F TYR* 3.2 26.1 + - - +
81I A 4.4 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E GLU* 5.4 4.9 - - - +
55E TYR* 3.2 48.5 + - + +
62E LEU* 3.2 46.5 + - + +
64E ARG* 4.6 10.7 - - - +
33F PRO* 2.9 22.2 + - - +
34F ALA* 3.1 28.3 + - - +
36F ARG* 1.3 75.8 - - + +
38F LEU* 1.3 63.0 + - - +
40F ARG* 3.1 11.8 + - + +
41F ARG* 3.0 21.7 + - - +
59J G 4.6 9.5 + - - +
60J C 3.9 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E LEU* 4.4 15.5 - - + +
63E ILE* 4.0 19.7 - - + -
98E GLU* 3.5 41.3 - - + +
101E LEU* 3.9 26.2 - - + -
102E VAL* 4.2 19.8 - - + +
105E PHE* 4.3 11.6 - - + -
30F ILE* 5.4 0.2 - - + -
34F ALA 2.9 19.6 + - - +
35F ILE* 3.2 20.2 + - + +
37F ARG* 1.3 75.6 - - - +
39F ALA* 1.3 62.0 + - - +
41F ARG* 3.0 17.9 + - + +
42F GLY* 3.2 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E PHE* 3.5 37.8 - - + -
35F ILE 2.9 14.9 + - - +
36F ARG 3.8 3.8 - - - +
38F LEU* 1.3 76.0 - - - +
40F ARG* 1.3 56.5 + - - +
42F GLY* 2.9 15.6 + - - -
43F GLY 3.1 0.5 + - - -
44F VAL* 3.0 29.0 + - + +
47F ILE* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E ALA* 3.2 45.6 - - - +
51E GLU* 3.0 29.9 + - + +
52E ILE* 3.5 28.5 - - + +
55E TYR* 4.7 2.7 - - + -
36F ARG* 2.8 57.0 + - + +
37F ARG* 3.1 13.0 + - - +
39F ALA* 1.3 73.6 - - - +
41F ARG* 1.3 61.5 + - - +
43F GLY* 2.8 20.1 + - - -
44F VAL 3.1 26.4 + - - -
45F LYS 3.1 18.0 + - - -
47F ILE* 4.3 9.5 - - - +
81I A 3.9 13.1 + - - +
82I A 4.5 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLY* 4.5 11.8 - - - -
108C VAL* 3.7 34.0 - - + +
55E TYR* 2.5 29.0 + - + +
56E GLN* 2.6 38.3 + - + +
58E SER* 2.4 41.3 + - - -
59E THR* 3.5 13.7 + - - +
60E GLU* 4.0 7.9 + - - -
62E LEU* 3.6 27.9 - - + +
98E GLU* 5.3 0.4 + - - -
102E VAL* 4.4 20.8 - - + +
106E GLU* 4.5 1.6 - - - +
37F ARG 3.0 11.2 + - - +
38F LEU* 3.0 11.2 + - - +
40F ARG* 1.3 76.3 - - - +
42F GLY* 1.3 53.4 + - - +
43F GLY 3.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASN 5.4 0.4 - - - +
56E GLN* 4.2 1.1 - - - -
102E VAL* 4.5 17.2 - - - +
105E PHE* 4.8 2.0 - - - -
106E GLU* 3.0 40.1 - - - +
109E ASN* 4.3 6.6 + - - -
38F LEU 3.2 7.6 + - - -
39F ALA* 2.9 13.7 + - - -
41F ARG* 1.3 76.7 - - - +
43F GLY* 1.3 57.9 + - - +
44F VAL* 3.5 2.8 + - - +
----------------------------------------------------------
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