Contacts of the helix formed by residues 70 - 91 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2507 T 3.5 25.5 + - - +
2517 A 4.4 2.2 + - - -
111O PHE* 3.5 18.8 - - - -
90P ILE* 5.6 0.4 - - - +
99P MET* 5.3 0.4 - - - +
69R THR* 1.3 75.5 - - - +
71R PRO* 1.3 66.1 - - - +
73R ARG* 2.9 36.2 + - - +
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Residues in contact with PRO 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2507 T 3.6 24.0 - - + +
2517 A 3.9 32.5 - - - +
71O PRO* 3.6 19.1 - - + +
74O ALA* 4.8 2.5 - - + -
75O ILE* 3.5 37.7 - - + +
107O TYR* 6.5 0.9 - - + -
111O PHE* 4.6 7.2 - - + -
69R THR 4.4 0.2 - - - +
70R GLY* 1.3 83.0 - - - +
72R ASN* 1.3 65.0 + - - +
73R ARG 3.1 0.2 - - - -
74R ALA* 3.1 4.3 + - - +
75R ILE* 3.0 24.6 + - - +
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Residues in contact with ASN 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72O ASN* 3.1 24.6 - - - +
75O ILE* 3.5 11.6 - - - +
111O PHE* 3.3 25.1 + - - +
112O ASN* 4.8 8.7 + - - +
68R ILE* 3.5 15.3 - - + -
69R THR* 3.3 14.5 + - - +
70R GLY 3.0 1.0 - - - -
71R PRO* 1.3 75.6 - - - +
73R ARG* 1.3 65.4 + - - +
75R ILE* 3.3 18.8 + - + +
76R TYR* 3.0 26.0 - - + -
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Residues in contact with ARG 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2507 T 3.0 36.0 + - - +
89P ARG 4.6 0.8 + - - -
90P ILE* 3.7 27.3 + - - +
60R SER* 2.7 46.9 + - - -
63R LEU* 3.5 16.5 - - + +
64R THR* 2.9 32.3 + - - +
68R ILE* 2.7 55.8 + - + +
69R THR* 3.8 8.1 - - - +
70R GLY 2.9 15.6 + - - +
72R ASN* 1.3 76.4 - - - +
74R ALA* 1.3 52.9 + - - +
76R TYR* 3.0 5.0 + - - -
77R GLN* 2.8 35.8 + - - +
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Residues in contact with ALA 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2497 A 4.1 16.6 - - + +
2507 T 3.0 41.0 + - + +
998 A 4.7 4.9 - - + -
1008 T 4.4 6.5 - - - +
71O PRO* 4.8 4.0 - - + -
70R GLY 3.6 0.6 + - - -
71R PRO 3.1 9.9 + - - +
73R ARG* 1.3 76.3 - - - +
75R ILE* 1.3 65.2 + - - +
77R GLN* 3.6 10.7 - - - +
78R GLY* 2.9 21.7 + - - -
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Residues in contact with ILE 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008 T 5.8 0.2 - - - -
71O PRO* 3.6 26.5 - - + -
72O ASN* 3.5 36.1 - - - +
71R PRO 3.0 14.8 + - - +
72R ASN* 3.4 23.3 - - - +
74R ALA* 1.3 76.9 - - - +
76R TYR* 1.3 66.6 + - + +
78R GLY* 3.4 0.5 + - - -
79R PHE* 3.1 21.8 + - - +
107R TYR* 3.5 30.8 - - + -
111R PHE* 4.6 10.1 - - + +
112R ASN 5.9 0.4 - - - +
113R ALA* 4.1 20.2 - - + -
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Residues in contact with TYR 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59R VAL* 4.4 2.7 - - - +
63R LEU* 3.6 28.9 - - + -
68R ILE* 4.0 17.8 - - + +
72R ASN* 3.0 28.3 - - + -
73R ARG 3.0 6.0 + - - +
75R ILE* 1.3 80.8 - - + +
77R GLN* 1.3 60.2 + - - +
79R PHE* 3.3 6.0 + - - +
80R GLY* 2.8 26.7 + - - -
112R ASN 5.0 0.2 + - - -
113R ALA* 3.9 9.8 - - + -
114R ASN* 2.9 37.5 + - - +
117R VAL* 3.7 33.4 - - + +
118R LEU* 3.7 30.7 - - + -
121R VAL* 4.2 12.4 - - + +
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Residues in contact with GLN 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2497 A 3.4 34.1 + - + +
2507 T 3.1 21.7 + - - +
55R VAL* 5.4 0.7 - - - +
56R ASN* 3.4 23.7 + - - +
59R VAL* 3.3 20.9 - - - +
60R SER* 3.5 26.1 - - - +
63R LEU* 4.0 2.1 - - + +
73R ARG 2.8 21.9 + - - +
74R ALA* 3.2 9.8 + - - +
76R TYR* 1.3 77.4 - - - +
78R GLY* 1.3 57.1 + - - +
80R GLY* 3.3 0.7 + - - -
81R LEU* 2.9 42.4 + - + +
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Residues in contact with GLY 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2497 A 5.4 1.5 + - - -
1008 T 5.1 3.6 - - - -
1018 A 4.1 25.2 - - - +
74R ALA 2.9 15.0 + - - -
75R ILE 3.8 2.0 - - - -
77R GLN* 1.3 76.2 - - - +
79R PHE* 1.3 61.2 + - - +
81R LEU* 3.8 5.5 - - - +
82R LYS* 3.0 25.5 + - - +
107R TYR* 3.5 12.7 + - - -
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Residues in contact with PHE 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R ILE 3.1 13.4 + - - +
76R TYR 3.5 7.6 - - - +
78R GLY* 1.3 75.3 - - - +
80R GLY* 1.3 64.5 + - - +
82R LYS* 3.1 4.9 + - - +
83R VAL* 2.9 33.3 + - + +
100R ILE* 5.1 2.2 - - + -
103R LEU* 3.7 23.6 - - + -
104R LYS* 3.8 23.8 - - + -
107R TYR* 3.5 34.5 + + + -
118R LEU* 3.3 53.8 - - + -
121R VAL* 3.8 16.4 - - + -
122R VAL* 3.7 24.2 - - + -
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Residues in contact with GLY 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R VAL* 4.5 6.3 - - - -
59R VAL* 5.0 2.0 - - - -
76R TYR 2.8 16.7 + - - -
77R GLN 3.8 0.9 - - - -
79R PHE* 1.3 73.6 - - - +
81R LEU* 1.3 63.3 + - - +
83R VAL* 3.1 2.4 + - - -
84R ALA* 3.0 19.2 + - - +
121R VAL* 3.5 26.2 - - - -
125R ILE* 3.1 17.6 - - - +
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Residues in contact with LEU 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2487 T 5.5 1.3 - - - +
2497 A 5.6 3.4 - - - +
1018 A 4.1 19.7 - - + +
1028 T 3.4 36.1 - - - +
52R PHE* 3.5 43.3 - - + +
55R VAL* 4.5 7.1 - - + +
56R ASN* 3.4 30.7 - - - +
77R GLN* 2.9 29.1 + - + +
78R GLY* 3.8 4.9 - - - +
80R GLY* 1.3 74.6 - - - +
82R LYS* 1.3 57.3 + - - +
84R ALA* 3.2 4.2 + - - -
85R ARG 2.9 23.2 + - - -
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Residues in contact with LYS 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2397 A 4.9 0.2 + - - -
2407 T 3.2 14.6 + - - -
1018 A 3.7 26.7 + - - +
1028 T 3.3 28.8 + - - +
106Q TYR* 2.8 33.1 + - - -
78R GLY 3.0 17.1 + - - +
79R PHE* 3.1 5.4 + - - +
81R LEU* 1.3 73.7 - - - +
83R VAL* 1.3 65.4 + - - +
85R ARG* 3.3 11.0 + - - +
86R ALA* 3.1 22.6 + - + +
99R MET* 5.9 3.1 - - - -
103R LEU* 3.5 35.3 - - + +
106R TYR* 5.0 5.6 - - - -
107R TYR* 4.6 3.8 - - + -
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Residues in contact with VAL 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R PHE* 2.9 42.7 + - + +
80R GLY* 3.1 8.7 + - - +
82R LYS* 1.3 76.4 - - - +
84R ALA* 1.3 61.5 + - - +
86R ALA* 3.3 8.6 + - - +
87R LEU* 3.0 20.4 + - + +
96R LEU* 4.5 2.9 - - + +
100R ILE* 4.3 27.4 - - + -
103R LEU* 3.7 18.8 - - + -
122R VAL* 4.6 8.5 - - + -
125R ILE* 3.9 26.2 - - + -
126R THR* 4.5 6.3 - - + -
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Residues in contact with ALA 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R LYS 5.7 0.4 - - - +
52R PHE* 3.6 19.7 - - + -
55R VAL* 4.2 20.6 - - + -
80R GLY 3.0 11.4 + - - +
81R LEU* 3.5 8.3 - - - +
83R VAL* 1.3 73.4 - - - +
85R ARG* 1.3 66.9 + - - +
87R LEU* 3.1 12.1 + - + +
88R ASN* 3.0 25.4 + - - +
125R ILE* 4.4 9.9 - - + -
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Residues in contact with ARG 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2397 A 3.8 36.3 + - - -
2407 T 2.9 33.5 + - - +
1028 T 3.0 36.5 + - - +
1038 A 3.4 30.5 + - - +
52R PHE* 3.5 11.1 - - - -
81R LEU 2.9 13.7 + - - +
82R LYS* 3.3 20.2 - - - +
84R ALA* 1.3 75.9 - - - +
86R ALA* 1.3 64.1 + - - +
88R ASN* 3.0 6.7 + - - +
89R ARG* 3.0 44.9 + - - +
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Residues in contact with ALA 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2397 A 5.6 2.5 - - - -
82R LYS 3.1 8.7 + - - +
83R VAL* 3.3 9.4 + - - +
85R ARG* 1.3 79.0 - - - +
87R LEU* 1.3 58.3 + - - +
89R ARG* 4.5 2.7 - - - +
90R ILE* 2.7 47.6 + - + +
96R LEU* 3.8 17.3 - - + -
99R MET* 3.8 27.8 - - + -
100R ILE* 6.0 0.4 - - + -
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Residues in contact with LEU 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R VAL* 3.0 13.6 + - + +
84R ALA* 3.1 12.8 + - + +
86R ALA* 1.3 76.7 - - - +
88R ASN* 1.3 63.9 + - - +
91R GLY* 2.7 30.6 + - - +
92R SER* 3.6 30.3 - - - +
96R LEU* 3.6 23.3 - - + +
125R ILE* 4.5 25.6 - - + +
126R THR* 6.0 2.2 - - + -
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Residues in contact with ASN 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038 A 5.4 1.7 + - - +
48R ASN* 4.9 5.6 + - - +
51R LYS* 3.8 31.5 + - - +
52R PHE* 3.4 33.5 - - + -
84R ALA* 3.0 12.9 + - - +
85R ARG* 3.0 7.6 + - - +
87R LEU* 1.3 85.2 - - - +
89R ARG* 1.3 63.8 + - + +
90R ILE 4.8 0.2 - - - -
91R GLY* 4.5 1.6 + - - -
7S SER* 4.6 12.8 - - - +
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Residues in contact with ARG 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2377 A 4.6 10.1 + - - -
2387 T 3.6 28.9 + - - +
2397 A 3.3 32.9 + - - +
1038 A 4.1 17.5 + - - +
1048 T 4.3 15.6 + - - -
85R ARG* 3.0 45.8 + - + +
86R ALA* 4.3 2.9 - - - +
88R ASN* 1.3 80.0 - - + +
90R ILE* 1.3 62.2 + - - +
7S SER* 4.1 34.2 - - - +
60T SER* 4.5 5.5 + - - -
73T ARG* 4.6 1.9 + - - -
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Residues in contact with ILE 90 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2387 T 5.6 0.4 - - - +
2397 A 4.5 10.1 - - - +
86R ALA* 2.7 28.9 + - + +
88R ASN 4.8 0.9 - - - -
89R ARG* 1.3 79.9 - - + +
91R GLY* 1.3 67.0 + - - +
95R ALA* 3.6 26.5 - - + +
96R LEU* 4.0 5.8 - - + +
99R MET* 3.8 38.6 - - + -
60T SER* 4.9 1.9 + - - -
61T ALA* 5.8 0.7 - - - -
64T THR* 2.6 37.1 + - - +
69T THR* 4.4 9.9 - - + -
70T GLY 5.6 0.4 - - - +
73T ARG* 3.7 19.0 + - - +
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Residues in contact with GLY 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R ALA 3.6 0.4 + - - -
87R LEU* 2.7 31.0 + - - -
88R ASN 4.5 0.9 - - - -
90R ILE* 1.3 89.0 - - - +
92R SER* 1.3 69.2 + - - +
96R LEU* 3.4 9.0 - - - +
64T THR* 3.6 1.3 - - - +
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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