Contacts of the helix formed by residues 70 - 91 (chain q) in PDB entry 3J9X
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 GLY 70 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2678 A 3.4 26.3 + - - +
2688 T 4.1 1.8 + - - -
69q THR* 1.3 75.9 - - - +
71q PRO* 1.3 69.4 - - - +
73q ARG* 2.9 32.1 + - - +
90s ILE* 5.5 0.8 - - - +
99s MET* 5.3 0.4 - - - +
111t PHE* 3.6 18.3 - - - -
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Residues in contact with PRO 71 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2678 A 3.7 30.7 - - + +
2688 T 3.6 26.9 - - - +
70q GLY* 1.3 83.5 - - - +
72q ASN* 1.3 63.7 + - - +
73q ARG 3.1 0.2 - - - -
74q ALA* 3.0 6.0 + - + +
75q ILE* 3.0 24.6 + - - +
71t PRO* 3.6 19.0 - - + +
74t ALA* 4.8 0.9 - - + -
75t ILE* 3.6 38.6 - - + +
107t TYR* 6.5 0.7 - - + -
111t PHE* 4.6 6.3 - - + -
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Residues in contact with ASN 72 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68q ILE* 3.5 16.4 - - + -
69q THR 3.3 14.1 + - - +
70q GLY 3.0 1.0 - - - -
71q PRO* 1.3 75.4 - - - +
73q ARG* 1.3 65.7 + - - +
75q ILE* 3.3 18.8 + - + +
76q TYR* 3.1 26.1 - - + -
72t ASN* 3.1 24.4 - - - +
75t ILE* 3.5 11.6 - - - +
111t PHE 3.2 26.1 + - - -
112t ASN* 4.6 10.7 + - - +
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Residues in contact with ARG 73 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2678 A 2.9 38.6 + - - +
60q SER* 2.7 45.9 + - - +
63q LEU* 3.5 18.1 - - + +
64q THR* 3.0 31.5 + - - +
68q ILE* 2.8 56.9 + - + +
69q THR* 3.8 8.1 - - - +
70q GLY 2.9 13.9 + - - +
72q ASN* 1.3 76.2 - - - +
74q ALA* 1.3 58.3 + - - +
76q TYR 3.1 3.3 + - - -
77q GLN* 2.8 32.2 + - - +
89s ARG 4.6 0.4 + - - -
90s ILE* 3.7 26.6 + - - +
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Residues in contact with ALA 74 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837 A 4.1 25.2 - - + +
2668 T 4.3 5.3 - - - +
2678 A 3.8 37.4 + - + +
70q GLY 3.7 0.6 + - - -
71q PRO* 3.0 11.7 + - + +
73q ARG* 1.3 80.7 - - - +
75q ILE* 1.3 62.0 + - - +
77q GLN* 3.6 8.9 - - - +
78q GLY* 2.9 21.1 + - - -
71t PRO* 4.8 3.6 - - + -
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Residues in contact with ILE 75 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837 A 5.9 0.2 - - - -
71q PRO 3.0 15.2 + - - +
72q ASN* 3.4 23.1 - - - +
73q ARG 3.2 0.4 - - - -
74q ALA* 1.3 76.9 - - - +
76q TYR* 1.3 71.8 + - + +
78q GLY* 3.3 1.0 + - - -
79q PHE* 3.2 16.8 + - - +
107q TYR* 3.5 31.5 - - + -
111q PHE* 4.8 11.0 - - + +
113q ALA* 4.2 19.3 - - + -
71t PRO* 3.5 27.6 - - + -
72t ASN* 3.5 35.4 - - - +
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Residues in contact with TYR 76 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59q VAL* 4.3 6.3 - - - +
63q LEU* 3.6 33.0 - - + -
68q ILE* 4.0 19.0 - - + +
72q ASN* 3.1 27.1 + - + -
73q ARG 3.1 3.7 + - - +
75q ILE* 1.3 80.2 - - + +
77q GLN* 1.3 60.6 + - - +
79q PHE* 3.2 7.3 + - - +
80q GLY* 2.9 25.1 + - - -
113q ALA* 4.0 8.0 - - + -
114q ASN* 2.9 38.9 + - - +
117q VAL* 3.7 27.1 - - + +
118q LEU* 3.6 30.7 - - + -
121q VAL* 4.4 8.7 - - + +
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Residues in contact with GLN 77 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2668 T 3.2 34.3 + - + +
2678 A 3.2 19.9 + - - +
55q VAL* 4.8 0.7 - - - +
56q ASN* 3.1 41.3 + - - +
59q VAL* 3.3 24.8 - - - +
60q SER* 3.4 11.7 - - - +
63q LEU* 4.0 3.9 - - + +
73q ARG 2.8 22.2 + - - +
74q ALA* 3.6 7.9 - - - +
75q ILE 3.3 0.2 - - - -
76q TYR* 1.3 77.8 - - - +
78q GLY* 1.3 55.5 + - - +
80q GLY* 3.2 1.6 + - - -
81q LEU* 2.9 36.6 + - + +
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Residues in contact with GLY 78 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837 A 5.6 1.1 - - - -
847 T 3.7 30.0 + - - +
2668 T 5.3 0.2 + - - -
74q ALA 2.9 14.5 + - - -
75q ILE 3.8 3.6 - - - -
77q GLN* 1.3 77.2 - - - +
79q PHE* 1.3 61.9 + - - +
81q LEU* 3.3 5.5 + - - +
82q LYS* 3.0 23.6 + - - +
107q TYR* 3.5 11.0 + - - -
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Residues in contact with PHE 79 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75q ILE 3.2 12.8 + - - +
76q TYR 3.4 8.3 - - - +
78q GLY* 1.3 76.3 - - - +
80q GLY* 1.3 64.8 + - - +
82q LYS* 3.2 6.0 + - - +
83q VAL* 3.1 30.1 + - + +
100q ILE* 5.0 0.9 - - + -
103q LEU* 3.6 32.1 - - + -
104q LYS* 3.8 28.3 - - + -
107q TYR* 3.5 26.9 + + + -
118q LEU* 3.3 50.5 - - + -
121q VAL* 3.8 15.7 - - + -
122q VAL* 3.6 24.0 - - + -
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Residues in contact with GLY 80 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55q VAL* 4.1 7.0 - - - -
59q VAL* 4.7 2.0 - - - -
76q TYR 2.9 12.6 + - - -
77q GLN 3.7 2.9 - - - -
79q PHE* 1.3 76.4 - - - +
81q LEU* 1.3 62.3 + - - +
83q VAL* 3.1 3.1 + - - -
84q ALA* 3.1 19.2 + - - +
121q VAL* 3.6 14.4 - - - -
125q ILE* 3.2 29.6 - - - +
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Residues in contact with LEU 81 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847 T 3.6 20.9 - - + +
857 A 3.4 33.6 - - + +
2658 A 4.9 7.0 - - + -
2668 T 5.2 2.7 - - - +
52q PHE* 3.7 37.2 - - + +
55q VAL* 4.3 6.5 - - + +
56q ASN* 3.3 30.5 - - - +
77q GLN* 2.9 25.8 + - + +
78q GLY* 3.6 4.3 - - - +
80q GLY* 1.3 76.0 - - - +
82q LYS* 1.3 56.9 + - - +
84q ALA* 3.3 6.7 + - - +
85q ARG* 2.9 28.4 + - - +
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Residues in contact with LYS 82 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847 T 4.0 13.8 + - - +
857 A 2.9 31.5 + - - +
2568 T 5.6 1.6 - - - -
2578 A 3.8 13.6 + - - -
78q GLY 3.0 13.6 + - - +
79q PHE* 3.4 9.9 - - - +
81q LEU* 1.3 75.5 - - - +
83q VAL* 1.3 64.5 + - - +
85q ARG* 3.2 11.6 + - - +
86q ALA* 3.1 23.6 + - - +
99q MET* 4.7 16.8 - - + -
103q LEU* 3.5 29.8 - - + +
106q TYR* 5.5 4.6 - - - -
107q TYR* 5.2 0.9 - - + -
106r TYR* 2.7 38.2 + - - -
111r PHE* 6.1 0.2 - - - -
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Residues in contact with VAL 83 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79q PHE* 3.1 35.0 + - + +
80q GLY* 3.1 8.5 + - - +
82q LYS* 1.3 77.5 - - - +
84q ALA* 1.3 62.7 + - - +
86q ALA* 3.4 5.5 + - - +
87q LEU* 3.0 21.3 + - + +
96q LEU* 4.3 4.4 - - + +
99q MET* 6.3 0.7 - - - -
100q ILE* 4.3 18.2 - - + -
103q LEU* 3.6 18.6 - - + -
122q VAL* 4.5 9.2 - - + -
125q ILE* 3.7 27.8 - - + -
126q THR* 4.3 15.3 - - + -
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Residues in contact with ALA 84 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51q LYS 5.5 0.9 - - - +
52q PHE* 3.6 20.2 - - + -
55q VAL* 4.0 21.1 - - + -
80q GLY 3.1 8.3 + - - +
81q LEU* 3.5 8.3 - - - +
83q VAL* 1.3 79.4 - - - +
85q ARG* 1.3 65.6 + - - +
87q LEU* 3.1 11.0 + - + +
88q ASN* 2.9 27.9 + - - +
125q ILE* 4.5 8.5 - - + +
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Residues in contact with ARG 85 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857 A 3.0 35.4 + - - +
867 T 3.1 33.5 + - - +
2568 T 3.8 34.2 + - - +
2578 A 3.9 20.9 + - - -
52q PHE* 3.6 10.3 - - - -
81q LEU 2.9 14.2 + - - +
82q LYS* 3.2 17.2 + - + +
84q ALA* 1.3 76.6 - - - +
86q ALA* 1.3 63.1 - - - +
88q ASN* 3.1 5.9 + - - +
89q ARG* 3.0 52.3 + - - +
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Residues in contact with ALA 86 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2568 T 5.4 3.4 - - - +
82q LYS* 3.1 11.6 + - - +
83q VAL* 3.7 9.4 - - - +
85q ARG* 1.3 77.8 - - - +
87q LEU* 1.3 57.4 + - - +
89q ARG* 4.5 3.4 - - - +
90q ILE* 2.7 51.2 + - + +
96q LEU* 3.9 9.4 - - + -
99q MET* 3.8 33.2 - - + -
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Residues in contact with LEU 87 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83q VAL* 3.0 15.2 + - + +
84q ALA* 3.1 12.8 + - + +
86q ALA* 1.3 76.1 - - - +
88q ASN* 1.3 65.2 + - - +
91q GLY* 2.7 31.8 + - - +
92q SER* 3.6 33.0 - - - +
96q LEU* 3.8 23.2 - - + +
125q ILE* 4.8 22.4 - - + +
126q THR* 6.1 2.7 - - + -
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Residues in contact with ASN 88 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867 T 5.9 0.9 - - - +
7p SER* 3.8 18.5 + - - +
48q ASN* 4.9 5.8 + - - -
51q LYS* 3.9 30.6 + - - +
52q PHE* 3.3 33.7 - - + -
84q ALA* 2.9 13.4 + - - +
85q ARG* 3.6 7.6 - - - +
87q LEU* 1.3 86.4 - - - +
89q ARG* 1.3 64.3 + - + +
90q ILE 5.0 0.2 - - - -
91q GLY 4.8 0.9 + - - -
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Residues in contact with ARG 89 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867 T 3.8 18.2 + - - -
877 A 4.3 14.1 + - - -
2548 T 4.7 4.0 + - - -
2558 A 3.6 26.6 + - - +
2568 T 3.5 37.1 + - - +
60o SER* 4.7 2.1 + - - -
73o ARG* 4.6 4.0 + - - -
7p SER* 3.6 36.9 - - - +
8p ARG* 5.5 3.6 - - - +
85q ARG* 3.0 52.6 + - - +
86q ALA* 4.2 2.5 - - - +
88q ASN* 1.3 80.2 - - + +
90q ILE* 1.3 61.9 + - + +
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Residues in contact with ILE 90 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2558 A 5.4 1.1 - - - +
2568 T 4.4 11.0 - - - +
60o SER* 4.7 2.6 + - - -
64o THR* 2.6 36.9 + - + +
69o THR* 4.4 17.9 - - + -
70o GLY 5.5 0.4 - - - +
73o ARG* 3.7 20.1 + - - +
86q ALA* 2.7 28.0 + - + +
88q ASN 5.0 0.4 - - - -
89q ARG* 1.3 79.9 - - + +
91q GLY* 1.3 68.2 + - - +
95q ALA* 3.5 26.2 - - + +
96q LEU* 4.2 4.3 - - - +
99q MET* 3.7 31.4 - - + -
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Residues in contact with GLY 91 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64o THR* 3.7 2.0 - - - +
86q ALA 3.6 0.6 + - - -
87q LEU* 2.7 30.6 + - - -
88q ASN 4.6 0.6 - - - -
90q ILE* 1.3 88.4 - - - +
92q SER* 1.3 68.8 + - - +
96q LEU* 3.6 10.2 - - - +
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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) + - + + + + + -
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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