Contacts of the helix formed by residues 69 - 83 (chain C) in PDB entry 3P9K
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 GLU 69 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASN* 3.1 16.4 + - - +
68C PRO* 1.3 83.3 - - + +
70C ALA* 1.3 65.8 + - - +
71C PRO* 3.3 2.5 - - - -
72C ASP* 3.2 14.9 + - + +
73C MET* 3.0 41.9 + - + +
147D GLY* 5.3 0.2 - - - -
148D GLY 4.8 6.8 + - - -
271D GLN* 5.8 0.2 - - - +
323D GLY* 5.9 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ALA* 4.2 5.6 - - + -
64C SER* 3.4 26.0 - - - +
67C ASN* 2.9 28.3 + - - +
69C GLU* 1.3 77.7 - - - +
71C PRO* 1.4 61.4 - - + +
73C MET* 3.2 6.0 + - - +
74C VAL* 2.8 34.5 + - - +
144D VAL* 3.7 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO* 3.3 17.8 - - + +
56C THR* 4.0 32.8 - - + +
59C ALA* 3.8 20.2 - - + -
67C ASN 4.1 1.3 - - - +
68C PRO* 3.4 18.6 - - + +
69C GLU 3.4 0.7 - - - -
70C ALA* 1.4 95.9 - - + +
72C ASP* 1.3 54.7 + - - +
74C VAL* 3.3 1.3 + - + +
75C ASP* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLU* 3.2 17.2 + - + +
71C PRO* 1.3 79.5 - - - +
73C MET* 1.3 66.5 + - - +
75C ASP* 3.1 11.0 + - - +
76C ARG* 3.0 40.6 + - - +
325D ARG* 2.7 46.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASN* 3.6 13.7 - - - +
69C GLU* 3.0 36.7 + - + +
70C ALA 3.6 6.1 - - - +
72C ASP* 1.3 79.7 - - - +
74C VAL* 1.3 63.0 - - - +
76C ARG* 3.2 8.9 + - - +
77C ILE* 3.1 29.4 + - - +
140D LEU* 5.9 0.9 - - - -
143D ALA* 3.6 28.3 - - + +
144D VAL* 3.7 22.7 - - + -
148D GLY 3.7 25.1 - - - +
150D PRO* 5.9 0.7 - - + -
318D LEU* 4.1 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 4.3 11.4 - - + -
55C PRO* 4.3 7.2 - - + +
58C VAL* 3.7 23.3 - - + -
59C ALA* 4.3 7.2 - - + -
62C LEU* 4.1 26.5 - - + -
70C ALA 2.8 23.2 + - - +
71C PRO* 3.6 7.0 - - + +
73C MET* 1.3 75.5 - - - +
75C ASP* 1.3 61.5 + - - +
77C ILE* 3.5 9.0 + - + +
78C LEU* 3.1 46.2 + - + +
144D VAL* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO* 3.5 23.2 - - + +
71C PRO 2.9 14.6 + - - +
72C ASP* 3.3 15.7 - - - +
73C MET 3.1 0.2 - - - -
74C VAL* 1.3 78.7 - - - +
76C ARG* 1.3 60.8 + - + +
78C LEU 3.5 0.2 + - - -
79C ARG* 2.9 26.8 + - - +
101C ARG* 2.8 36.6 + - - +
103C TYR* 2.5 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASP* 3.0 35.7 + - - +
73C MET* 3.2 8.9 + - - +
75C ASP* 1.3 78.1 - - + +
77C ILE* 1.3 62.0 + - - +
79C ARG* 3.9 18.4 + - - +
80C LEU* 3.2 22.3 + - - +
314D ASP* 2.8 59.8 + - - +
315D MET* 3.6 12.7 - - - +
318D LEU* 3.4 32.7 - - + +
323D GLY* 5.0 2.0 + - - -
324D GLY 2.9 28.6 + - - -
325D ARG* 3.5 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C THR* 3.6 18.4 - - + +
35C ASN* 5.7 0.9 - - + -
36C ALA* 4.2 14.6 - - + -
39C LEU* 4.4 11.7 - - + -
41C LEU* 4.0 18.4 - - + -
73C MET 3.1 19.6 + - - +
74C VAL* 3.8 7.9 - - - +
76C ARG* 1.3 76.7 - - - +
78C LEU* 1.3 58.3 + - - +
80C LEU* 3.4 4.2 + - - +
81C LEU* 3.0 29.7 + - + +
140D LEU* 4.3 14.8 - - + -
144D VAL* 4.0 26.2 - - + -
315D MET* 3.9 26.0 - - + -
318D LEU* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 4.2 22.0 - - + -
42C LEU* 5.2 0.9 - - + -
45C LEU* 4.1 22.2 - - + -
58C VAL* 4.4 15.7 - - + -
74C VAL* 3.1 35.6 + - + +
77C ILE* 1.3 73.9 - - - +
79C ARG* 1.3 59.8 + - - +
81C LEU* 4.3 11.7 - - + -
82C ALA* 2.8 31.9 + - - +
87C VAL* 3.7 15.9 - - + +
103C TYR* 3.6 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ASP* 2.9 18.9 + - - +
76C ARG* 3.9 19.8 + - - +
78C LEU* 1.3 76.2 - - - +
80C LEU* 1.3 62.8 + - - +
82C ALA* 3.4 4.4 + - - +
83C SER* 3.2 21.3 + - - -
89C CYS* 5.5 1.8 - - - -
101C ARG* 3.6 32.4 - - - +
103C TYR* 3.5 15.8 + - - +
297D LEU* 3.6 24.0 - - - +
311D PHE* 3.6 38.7 - - + +
314D ASP* 3.0 36.2 + - - +
325D ARG* 5.7 3.2 - - - +
326D GLU 5.2 0.8 + - - -
328D TYR* 3.1 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 3.9 11.7 - - + -
29C LEU* 4.5 6.7 - - - -
32C THR* 4.0 14.1 - - + -
76C ARG 3.2 12.3 + - - +
77C ILE 3.5 7.9 - - - +
78C LEU 3.2 0.4 - - - -
79C ARG* 1.3 80.2 - - - +
81C LEU* 1.3 82.4 + - + +
83C SER* 2.6 29.4 + - - +
84C TYR* 3.6 15.9 - - + -
311D PHE* 3.7 27.8 - - + +
312D HIS* 4.0 23.8 - - + -
315D MET* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 4.2 14.8 - - + -
32C THR* 4.2 5.4 - - + -
33C LEU* 4.1 32.1 - - + +
36C ALA* 3.6 30.1 - - + -
42C LEU* 4.6 9.6 - - + -
77C ILE* 3.0 26.3 + - + +
78C LEU* 3.4 15.9 + - + +
80C LEU* 1.3 89.5 - - + +
82C ALA* 1.3 60.4 + - - +
84C TYR* 3.2 7.8 + - - +
86C VAL* 2.9 40.2 + - + +
87C VAL* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU 2.8 22.6 + - - +
79C ARG* 3.6 8.1 - - - +
80C LEU 3.2 0.2 - - - -
81C LEU* 1.3 69.6 - - - +
83C SER* 1.3 58.3 + - - +
84C TYR 3.0 5.4 - - - -
85C ASN* 2.8 25.1 + - - +
87C VAL* 3.5 23.2 - - + +
89C CYS* 3.6 31.2 - - + +
103C TYR* 4.3 0.2 - - + -
303D ALA* 5.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ARG 3.2 2.4 + - - -
80C LEU* 2.6 23.2 + - - +
82C ALA* 1.3 77.6 - - - +
84C TYR* 1.3 65.9 + - - +
85C ASN* 3.3 1.8 + - - -
303D ALA* 2.9 30.0 - - - +
308D GLN* 2.9 33.0 + - - +
311D PHE* 3.6 34.0 - - - -
----------------------------------------------------------
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