Contacts of the helix formed by residues 69 - 87 (chain C) in PDB entry 2NRA
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 69 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A T 2.7 71.9 + - + +
18A A 4.5 13.2 + - - +
19A C 6.2 0.7 - - - -
68C ILE* 1.3 76.0 - - - +
70C PRO* 1.4 75.8 - - + +
71C SER* 4.4 7.6 + - - -
72C LEU 2.9 16.1 + - - -
73C ALA 3.3 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B A 5.8 1.3 - - - +
26B C 5.9 0.4 - - + +
59C ALA 6.0 0.4 - - - -
60C GLU* 5.9 6.1 - - + -
63C ALA* 4.0 19.5 - - + -
68C ILE 3.4 3.6 - - - +
69C THR* 1.4 81.5 - - + +
71C SER* 1.3 69.0 + - - +
73C ALA* 2.8 15.1 + - + +
74C TYR* 2.8 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A T 5.0 1.9 + - - -
18A A 3.5 12.5 + - - -
19A C 4.0 13.5 - - - -
26B C 4.1 9.8 - - - +
27B G 2.7 36.2 + - - +
28B T 4.0 2.6 + - - -
69C THR* 3.3 9.1 - - - -
70C PRO* 1.3 78.9 - - - +
72C LEU* 1.3 63.0 + - - +
74C TYR* 3.4 14.8 + - - +
75C ARG* 3.3 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A A 5.3 0.9 - - + -
16A G 3.8 37.2 - - + +
17A T 3.7 24.1 - - + +
68C ILE* 3.6 19.3 - - + -
69C THR* 2.9 12.9 + - - +
71C SER* 1.3 76.6 - - - +
73C ALA* 1.3 56.1 + - - +
75C ARG* 2.8 33.3 + - - +
76C GLN* 2.7 71.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ALA* 3.5 29.2 - - + +
62C LEU* 4.0 19.3 - - + +
63C ALA* 3.8 19.3 - - + +
68C ILE* 3.9 6.0 - - + +
69C THR 3.3 2.5 + - - +
70C PRO 2.8 14.2 + - - +
72C LEU* 1.3 74.8 - - - +
74C TYR* 1.3 55.7 - - - +
76C GLN* 3.9 2.6 - - - +
77C LEU* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B G 3.3 19.4 + - - -
25B A 2.7 59.7 + + + -
26B C 3.5 43.3 - + + -
59C ALA* 3.4 24.2 - - + +
60C GLU* 5.1 5.7 + - - +
70C PRO* 2.8 47.3 + - + +
71C SER* 3.5 10.5 - - - +
73C ALA* 1.3 77.3 - - - +
75C ARG* 1.3 63.6 + - - +
77C LEU* 3.7 1.9 - - - +
78C LYS* 3.0 23.9 + - - +
126C TYR* 3.6 12.7 + - - +
131C GLY* 4.0 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A A 5.8 0.6 + - - -
16A G 3.4 28.1 + - - -
17A T 3.4 24.7 + - - +
27B G 5.6 0.4 + - - -
28B T 4.0 25.4 + - - +
29B A 4.4 2.0 - - - +
71C SER* 3.3 13.5 + - - +
72C LEU* 2.8 29.2 + - + +
74C TYR* 1.3 77.7 - - - +
76C GLN* 1.3 66.9 + - + +
78C LYS* 3.1 4.4 + - - +
79C GLU* 2.9 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A A 3.9 8.7 + - - +
16A G 3.0 22.2 + - - -
30C LEU* 3.8 17.7 - - - +
31C PRO* 3.8 19.7 - - + +
34C ARG* 2.8 34.8 + - + +
62C LEU* 4.7 8.6 - - + +
68C ILE* 5.2 2.1 - - - +
72C LEU* 2.7 51.8 + - + +
73C ALA* 3.9 4.7 - - - +
75C ARG* 1.3 75.3 - - + +
77C LEU* 1.3 52.9 + - - +
79C GLU* 4.6 2.2 - - - -
80C GLY* 2.6 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL* 4.0 16.2 - - + -
38C MET* 6.1 0.2 - - + -
57C ILE* 3.5 42.0 - - + +
58C ARG 4.9 0.2 - - - -
59C ALA* 3.7 23.3 - - + +
62C LEU* 4.6 12.4 - - + +
73C ALA 2.8 21.0 + - - +
74C TYR* 3.7 4.9 - - - +
76C GLN* 1.3 72.9 - - - +
78C LYS* 1.3 65.4 + - - +
81C GLY* 2.8 22.3 + - - -
126C TYR* 3.9 13.7 - - + -
132C TYR* 4.1 1.1 - - - -
133C LEU* 3.7 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B C 5.4 4.9 + - - +
27B G 6.1 0.9 - - - +
74C TYR 3.0 14.7 + - - +
75C ARG* 3.7 4.5 - - - +
77C LEU* 1.3 80.5 - - - +
79C GLU* 1.3 64.1 + - - +
81C GLY* 3.1 8.0 + - - -
82C LYS* 3.2 34.1 + - - +
126C TYR* 3.8 43.5 - - + +
128C PRO* 3.8 31.7 - - - +
133C LEU* 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PRO* 4.7 7.9 - - + -
75C ARG* 2.9 24.6 + - + +
76C GLN* 3.9 4.7 - - - +
78C LYS* 1.3 75.3 - - - +
80C GLY* 1.3 65.5 - - - +
82C LYS* 3.2 26.9 + - - +
83C LEU* 3.0 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PRO* 3.7 4.7 - - - +
32C ALA* 3.7 27.4 - - - +
35C VAL* 3.7 12.8 - - - -
76C GLN 2.6 22.2 + - - -
79C GLU* 1.3 71.1 - - - +
81C GLY* 1.3 52.3 + - - +
83C LEU* 3.2 2.2 + - - -
84C LEU* 2.8 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL* 4.0 1.4 - - - +
77C LEU 2.8 13.7 + - - -
78C LYS 3.5 5.8 - - - -
80C GLY* 1.3 74.5 - - - +
82C LYS* 1.3 67.7 + - - +
84C LEU* 3.3 0.8 + - - -
85C GLY* 3.0 16.6 + - - -
124C ILE* 3.4 32.7 - - - +
133C LEU* 4.2 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LYS* 3.2 34.6 + - - +
79C GLU* 3.2 30.6 + - - +
81C GLY* 1.3 75.7 - - - +
83C LEU* 1.3 66.4 + - + +
85C GLY* 2.9 9.8 + - - -
86C ALA* 3.3 10.4 + - - +
124C ILE* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PRO* 3.5 37.0 - - + -
31C PRO* 4.6 15.5 - - + -
32C ALA* 4.0 9.6 - - + +
79C GLU* 3.0 31.9 + - - +
80C GLY 3.8 5.8 - - - +
82C LYS* 1.3 78.0 - - + +
84C LEU* 1.3 60.7 + - - +
86C ALA* 3.1 18.9 + - + +
87C SER* 2.8 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 4.0 8.1 - - + -
32C ALA* 4.0 15.5 - - + +
35C VAL* 3.7 26.2 - - + -
36C MET* 4.3 22.0 - - - +
80C GLY 2.8 20.1 + - - +
81C GLY 3.7 3.8 - - - +
83C LEU* 1.3 73.7 - - - +
85C GLY* 1.3 65.8 - - - +
87C SER* 2.8 21.3 + - - +
120C ILE* 3.9 22.7 - - + -
121C ILE* 3.5 35.5 - - + +
124C ILE* 4.4 5.2 - - + -
135C LEU* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLY 3.0 9.7 + - - -
82C LYS* 2.9 9.3 + - - -
84C LEU* 1.3 77.8 - - - +
86C ALA* 1.3 61.5 + - - +
87C SER 4.1 3.1 - - - +
88C LYS* 5.3 0.3 + - - -
119C ASN* 4.8 7.6 - - - +
121C ILE* 4.5 17.3 + - - +
124C ILE* 4.3 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LYS 3.3 7.4 + - - +
83C LEU* 3.1 14.4 + - + +
85C GLY* 1.3 77.5 - - - +
87C SER* 1.3 63.1 + - - +
88C LYS* 3.1 28.8 + - - +
119C ASN* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.4 22.2 - - - +
29C PRO* 5.4 4.2 - - - +
32C ALA* 4.9 0.5 - - - +
83C LEU* 2.8 19.7 + - - +
84C LEU* 2.8 17.5 + - - +
85C GLY 4.1 2.3 - - - +
86C ALA* 1.3 79.3 - - - +
88C LYS* 1.3 61.1 + - - +
119C ASN* 3.8 4.3 - - - +
120C ILE* 3.3 37.3 + - - -
121C ILE 4.7 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