Contacts of the helix formed by residues 57 - 76 (chain N) in PDB entry 5A0Q
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 TYR 57 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H MET* 1.9 52.5 - - + -
121H VAL* 5.1 5.8 - - + -
6N VAL* 2.9 15.0 + - + +
8N GLY 5.1 1.6 - - - +
39N ILE* 3.4 45.6 - - + +
40N SER 3.3 18.9 + - - -
41N ARG* 4.1 15.3 - - + -
53N ALA* 5.9 0.7 - - + -
55N GLY 3.2 6.4 + - - +
56N ASP* 1.3 71.3 - - - +
58N ALA* 1.3 57.9 + - - +
60N PHE* 3.1 36.5 + + + +
61N GLN* 3.0 50.4 + - + +
64N LYS* 5.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H TYR* 3.3 20.4 + - + -
91H ARG* 6.3 1.3 - - - -
117H GLY* 4.3 12.6 - - - +
118H GLY 3.3 29.6 - - - +
119H MET* 3.9 12.8 - - + -
5N MET* 5.7 4.3 - - + -
56N ASP* 3.3 4.6 - - + -
57N TYR* 1.3 77.0 - - - +
59N ASP* 1.3 59.8 + - - +
61N GLN* 3.2 5.1 + - - +
62N TYR 3.0 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H TYR* 3.7 15.4 + - - -
56N ASP* 3.3 17.5 + - - +
58N ALA* 1.3 77.3 - - - +
60N PHE* 1.4 55.8 + - - +
62N TYR* 3.4 2.3 + - - +
63N LEU* 2.9 30.0 + - - +
99N ARG* 4.0 11.1 + - - -
105N PRO 4.4 0.3 - - - +
106N LEU* 3.6 28.5 - - + +
107N TRP* 3.1 16.3 + - - +
108N ASN* 2.3 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N SER 3.9 8.7 - - - -
41N ARG* 3.1 32.5 - - - -
42N ILE 4.5 0.2 - - - -
43N MET* 3.6 44.2 - - + -
51N LEU 4.5 1.1 - - - -
52N GLY 4.7 0.4 - - - -
53N ALA* 3.2 30.3 - - + -
55N GLY 5.5 0.4 - - - +
57N TYR* 3.1 55.4 + + + +
59N ASP* 1.4 71.7 - - - +
61N GLN* 1.3 64.1 + - - +
63N LEU* 3.7 2.0 - - - +
64N LYS* 2.8 42.9 + - + +
108N ASN* 2.6 12.5 + - - +
110N MET* 4.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H LYS* 4.2 25.0 + - + +
88H TYR* 5.9 0.2 - - + -
118H GLY 5.4 0.2 - - - +
119H MET* 3.8 21.1 - - + -
120H MET* 3.2 26.1 + - - +
121H VAL* 5.4 0.2 - - - +
57N TYR* 3.0 39.8 + - + +
58N ALA* 3.2 8.0 + - - +
60N PHE* 1.3 84.6 - - - +
62N TYR* 1.3 66.1 + - - +
64N LYS* 3.8 10.7 - - - +
65N GLN* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H LYS* 5.5 0.7 - - - +
88H TYR* 1.9 57.4 - + + +
58N ALA 3.0 4.2 + - - -
59N ASP* 3.5 5.2 - - - +
61N GLN* 1.3 78.3 - - - +
63N LEU* 1.3 66.7 + - + +
65N GLN* 3.4 9.1 - - + +
66N VAL* 3.0 52.8 + - + +
95N ALA* 6.0 1.4 - - - +
99N ARG* 3.8 40.7 + - - +
106N LEU* 3.4 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N MET* 4.0 4.4 - - + +
59N ASP 2.9 11.0 + - - +
60N PHE 3.7 1.6 - - - +
62N TYR* 1.3 101.6 - - + +
64N LYS* 1.3 60.8 + - - +
66N VAL* 3.8 14.8 - - + +
67N LEU* 3.0 30.2 + - - +
92N LEU* 4.0 13.9 - - + -
95N ALA* 4.4 16.4 - - + -
96N MET* 3.5 25.8 - - - -
106N LEU* 3.4 28.7 - - + -
110N MET* 3.6 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N SER* 5.0 5.5 + - - -
42N ILE 5.2 1.4 + - - -
43N MET* 3.8 45.3 - - + +
44N ARG 5.5 0.7 - - - +
57N TYR* 5.8 0.6 + - - -
60N PHE* 2.8 43.3 + - + +
61N GLN* 3.8 12.1 - - - +
62N TYR 3.3 0.2 - - - -
63N LEU* 1.3 75.8 - - - +
65N GLN* 1.4 58.1 + - - +
67N LEU* 4.2 0.9 - - - +
68N GLY* 3.1 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G ARG 4.9 0.9 - - - +
100G SER* 3.5 34.4 - - - +
84H LYS* 3.5 29.9 + - - +
85H GLU* 3.9 15.2 + - - -
88H TYR* 5.3 4.9 - - - -
61N GLN 3.1 14.8 + - - +
62N TYR* 3.4 17.4 - - - +
64N LYS* 1.4 77.9 - - - +
66N VAL* 1.4 63.0 + - + +
68N GLY* 3.8 2.3 + - - -
69N GLN* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N TYR* 3.0 39.7 + - + +
63N LEU* 4.3 16.6 - - + -
64N LYS 3.3 0.2 - - - -
65N GLN* 1.4 81.5 - - + +
67N LEU* 1.3 65.3 + - - +
68N GLY 3.2 1.3 - - - -
69N GLN* 3.0 16.2 + - + +
70N MET* 3.0 28.8 + - + +
91N TRP* 5.6 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N MET* 4.1 8.7 - - + -
45N VAL* 3.4 40.6 - - + -
51N LEU* 3.5 38.4 - - + -
63N LEU* 3.0 18.4 + - + +
64N LYS 4.2 1.6 - - - +
66N VAL* 1.3 75.9 - - - +
68N GLY* 1.3 62.5 + - - +
70N MET* 3.3 9.0 + - + +
71N VAL* 3.1 33.5 + - + +
88N ILE* 3.7 22.0 - - + -
91N TRP* 6.3 0.2 - - - -
92N LEU* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64N LYS 3.1 18.1 + - - -
65N GLN* 3.9 2.7 - - - -
67N LEU* 1.3 76.3 - - - +
69N GLN* 1.3 56.6 + - - +
71N VAL* 4.6 4.7 - - - -
72N ILE* 2.9 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G SER* 3.3 41.0 + - - -
97G ASN* 5.3 1.8 + - - -
100G SER* 5.8 2.2 + - - -
65N GLN 3.2 14.5 + - - +
66N VAL* 3.0 14.5 + - + +
68N GLY* 1.3 76.4 - - - +
70N MET* 1.4 70.2 + - + +
72N ILE* 3.9 6.4 - - - +
73N ASP* 2.9 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F PHE* 5.1 14.6 - - + -
66N VAL* 3.0 24.6 + - + +
67N LEU* 3.3 12.3 + - + +
69N GLN* 1.4 94.8 - - + +
71N VAL* 1.3 65.4 + - + +
73N ASP* 3.6 8.6 + - - +
74N GLU* 3.1 25.6 + - - +
88N ILE* 5.5 6.3 - - + -
91N TRP* 3.2 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N VAL* 3.7 23.3 - - + +
46N ASN* 3.2 40.2 - - - +
67N LEU* 3.1 17.6 + - + +
68N GLY* 4.1 4.7 - - - +
70N MET* 1.3 74.1 - - - +
72N ILE* 1.3 69.7 + - + +
74N GLU* 3.4 7.5 + - - +
75N GLU* 3.0 31.3 + - + +
88N ILE* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ASP* 4.4 13.7 - - - +
71G ARG* 4.7 20.0 - - + +
96G SER* 6.4 1.1 - - - -
99G ARG* 4.1 32.1 - - - +
68N GLY* 2.9 29.9 + - - +
69N GLN* 4.0 8.1 - - - +
71N VAL* 1.3 80.3 - - + +
73N ASP* 1.4 59.8 + - - +
75N GLU* 3.7 8.9 + - - +
76N LEU* 3.1 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ARG* 5.1 7.4 - - - +
96G SER* 4.8 5.7 - - - -
69N GLN* 2.9 50.7 + - - +
70N MET* 3.8 11.2 - - - +
72N ILE* 1.4 77.3 - - - +
74N GLU* 1.3 65.0 + - - +
75N GLU 3.3 0.3 + - - -
76N LEU* 3.2 18.5 - - + +
77N LEU* 3.2 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F ARG* 4.8 11.0 - - - +
107F ARG* 3.0 34.6 + - - +
46N ASN* 5.6 1.0 + - - -
70N MET 3.1 17.1 + - - +
71N VAL* 4.0 7.8 - - - +
73N ASP* 1.3 80.3 - - + +
75N GLU* 1.3 76.7 + - - +
76N LEU 3.3 0.3 + - - -
77N LEU* 3.4 24.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G ARG* 5.4 10.1 - - - +
46N ASN* 3.8 22.4 + - - -
47N ASN* 5.0 8.0 + - - -
71N VAL* 3.0 22.1 + - + +
72N ILE* 3.9 9.0 - - - +
73N ASP 3.2 0.2 - - - -
74N GLU* 1.3 88.1 - - - +
76N LEU* 1.3 57.6 - - + +
77N LEU 5.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASN* 3.5 36.9 - - + +
69G VAL 4.4 0.9 - - - +
70G ASP* 3.9 25.6 - - - +
71G ARG* 4.2 2.9 - - + +
92G ARG* 3.3 53.0 + - + -
72N ILE* 3.1 32.5 - - + +
73N ASP* 3.2 22.0 - - + +
75N GLU* 1.3 76.2 - - + +
77N LEU* 1.4 66.7 + - + +
----------------------------------------------------------
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