Contacts of the helix formed by residues 70 - 91 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758 A 3.4 26.7 + - - +
768 T 4.1 1.6 + - - -
69K THR* 1.3 75.7 - - - +
71K PRO* 1.3 69.5 - - - +
73K ARG* 2.9 31.8 + - - +
90M ILE* 5.5 0.8 - - - +
99M MET* 5.3 0.4 - - - +
111N PHE* 3.6 18.1 - - - -
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Residues in contact with PRO 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758 A 3.7 30.7 - - + +
768 T 3.6 26.7 - - - +
69K THR 4.4 0.4 - - - +
70K GLY* 1.3 83.6 - - - +
72K ASN* 1.3 64.0 + - - +
73K ARG 3.1 0.2 - - - -
74K ALA* 3.0 5.6 + - + +
75K ILE* 3.0 24.9 + - - +
71N PRO* 3.6 18.9 - - + +
74N ALA* 4.8 0.7 - - + -
75N ILE* 3.6 37.9 - - + +
107N TYR* 6.5 0.9 - - + -
111N PHE* 4.6 6.1 - - + -
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Residues in contact with ASN 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K ILE* 3.5 15.7 - - + -
69K THR 3.3 14.8 + - - +
70K GLY 3.0 1.0 - - - -
71K PRO* 1.3 74.7 - - - +
73K ARG* 1.3 65.8 + - - +
75K ILE* 3.3 19.7 + - + +
76K TYR* 3.1 26.5 - - + -
72N ASN* 3.1 23.9 - - - +
75N ILE* 3.5 11.6 - - - +
111N PHE* 3.2 26.1 + - - +
112N ASN* 4.6 10.7 + - - +
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Residues in contact with ARG 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758 A 2.9 38.1 + - - +
60K SER* 2.7 45.3 + - - +
63K LEU* 3.5 18.4 - - + +
64K THR* 3.0 31.3 + - - +
68K ILE* 2.8 56.9 + - + +
69K THR* 3.8 7.9 - - - +
70K GLY 2.9 14.1 + - - +
72K ASN* 1.3 76.4 - - - +
74K ALA* 1.3 58.4 + - - +
76K TYR 3.1 2.9 + - - -
77K GLN* 2.8 32.3 + - - +
89M ARG 4.6 0.4 + - - -
90M ILE* 3.7 27.5 + - - +
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Residues in contact with ALA 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757 A 4.1 25.8 - - + +
748 T 4.3 5.2 - - - +
758 A 3.8 37.6 + - + +
70K GLY 3.7 0.8 + - - -
71K PRO 3.0 12.1 + - - +
73K ARG* 1.3 80.3 - - - +
75K ILE* 1.3 62.4 + - - +
77K GLN* 3.6 9.1 - - - +
78K GLY* 2.9 21.1 + - - -
71N PRO* 4.8 3.8 - - + -
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Residues in contact with ILE 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757 A 5.9 0.2 - - - -
71K PRO 3.0 14.7 + - - +
72K ASN* 3.4 23.3 - - - +
73K ARG 3.2 0.2 - - - -
74K ALA* 1.3 78.1 - - - +
76K TYR* 1.3 71.4 + - + +
78K GLY* 3.3 0.7 + - - -
79K PHE* 3.2 17.5 + - - +
107K TYR* 3.5 31.4 - - + -
111K PHE* 4.8 10.5 - - + +
113K ALA* 4.2 19.3 - - + -
71N PRO* 3.5 26.9 - - + -
72N ASN* 3.5 35.4 - - - +
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Residues in contact with TYR 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K VAL* 4.3 6.1 - - - +
63K LEU* 3.6 33.4 - - + -
68K ILE* 4.0 19.4 - - + +
72K ASN* 3.1 27.1 + - + -
73K ARG 3.1 3.7 + - - +
75K ILE* 1.3 79.7 - - + +
77K GLN* 1.3 61.2 + - - +
79K PHE* 3.2 7.7 + - - +
80K GLY* 2.9 25.5 + - - -
113K ALA* 4.0 9.1 - - + -
114K ASN* 2.9 39.1 + - - +
117K VAL* 3.7 28.0 - - + +
118K LEU* 3.6 30.7 - - + -
121K VAL* 4.4 8.3 - - + +
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Residues in contact with GLN 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748 T 3.2 34.3 + - + +
758 A 3.2 19.8 + - - +
55K VAL* 4.8 0.7 - - - +
56K ASN* 3.1 41.4 + - - +
59K VAL* 3.3 23.9 - - - +
60K SER* 3.4 11.3 - - - +
63K LEU* 4.0 3.5 - - + +
73K ARG 2.8 22.4 + - - +
74K ALA* 3.6 7.6 - - - +
76K TYR* 1.3 77.7 - - - +
78K GLY* 1.3 56.1 + - - +
80K GLY* 3.2 1.6 + - - -
81K LEU* 2.9 37.2 + - + +
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Residues in contact with GLY 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757 A 5.6 1.3 - - - -
2767 T 3.7 30.8 + - - +
748 T 5.3 0.2 + - - -
74K ALA 2.9 14.7 + - - -
75K ILE 3.8 3.8 - - - -
77K GLN* 1.3 76.3 - - - +
79K PHE* 1.3 61.1 + - - +
81K LEU* 3.3 5.3 + - - +
82K LYS* 3.0 24.1 + - - +
107K TYR* 3.5 10.4 + - - -
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Residues in contact with PHE 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75K ILE 3.2 12.4 + - - +
76K TYR 3.4 7.9 - - - +
78K GLY* 1.3 75.4 - - - +
80K GLY* 1.3 64.5 + - - +
82K LYS* 3.2 5.7 + - - +
83K VAL* 3.1 30.4 + - + +
100K ILE* 5.0 0.7 - - + -
103K LEU* 3.6 31.2 - - + -
104K LYS* 3.8 28.7 - - + -
107K TYR* 3.5 26.5 + + + -
118K LEU* 3.3 50.9 - - + -
121K VAL* 3.8 15.5 - - + -
122K VAL* 3.6 24.7 - - + -
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Residues in contact with GLY 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K VAL* 4.1 6.7 - - - -
59K VAL* 4.7 2.0 - - - -
76K TYR 2.9 12.2 + - - -
77K GLN 3.7 3.1 - - - -
79K PHE* 1.3 76.2 - - - +
81K LEU* 1.3 63.3 + - - +
83K VAL* 3.1 3.3 + - - -
84K ALA* 3.1 18.9 + - - +
121K VAL* 3.6 13.9 - - - -
125K ILE* 3.2 29.9 - - - +
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Residues in contact with LEU 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2767 T 3.6 23.8 - - + +
2777 A 3.4 29.2 - - + +
738 A 4.9 6.5 - - + -
748 T 5.2 2.2 - - - +
52K PHE* 3.7 37.1 - - + +
55K VAL* 4.3 7.1 - - + +
56K ASN* 3.3 31.9 - - - +
77K GLN* 2.9 25.8 + - + +
78K GLY* 3.6 5.2 - - - +
80K GLY* 1.3 75.4 - - - +
82K LYS* 1.3 56.7 + - - +
84K ALA* 3.3 6.3 + - - +
85K ARG* 2.9 28.1 + - - +
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Residues in contact with LYS 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2767 T 4.0 14.4 + - - +
2777 A 2.9 31.5 + - - +
648 T 5.6 2.0 - - - -
658 A 3.8 13.6 + - - -
78K GLY 3.0 14.1 + - - +
79K PHE* 3.4 9.6 - - - +
81K LEU* 1.3 74.7 - - - +
83K VAL* 1.3 64.6 + - - +
85K ARG* 3.2 11.3 + - - +
86K ALA* 3.1 24.2 + - + +
99K MET* 4.7 16.4 - - + -
103K LEU* 3.5 29.3 - - + +
106K TYR* 5.5 4.0 - - - -
107K TYR* 5.2 0.9 - - + -
106L TYR* 2.7 38.7 + - - -
111L PHE* 6.1 0.2 - - - -
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Residues in contact with VAL 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K PHE* 3.1 33.9 + - + +
80K GLY* 3.1 8.7 + - - +
82K LYS* 1.3 76.9 - - - +
84K ALA* 1.3 62.4 + - - +
86K ALA* 3.4 5.8 + - - +
87K LEU* 3.0 21.2 + - + +
96K LEU* 4.3 4.8 - - + +
99K MET* 6.3 0.7 - - - -
100K ILE* 4.3 18.4 - - + -
103K LEU* 3.6 18.8 - - + -
122K VAL* 4.5 8.7 - - + -
125K ILE* 3.7 26.9 - - + -
126K THR* 4.3 15.5 - - + -
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Residues in contact with ALA 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K LYS 5.5 0.9 - - - +
52K PHE* 3.6 21.1 - - + -
55K VAL* 4.0 20.4 - - + -
80K GLY 3.1 8.8 + - - +
81K LEU* 3.5 8.1 - - - +
83K VAL* 1.3 78.6 - - - +
85K ARG* 1.3 65.2 + - - +
87K LEU* 3.1 10.9 + - + +
88K ASN* 2.9 27.7 + - - +
125K ILE* 4.5 9.6 - - + +
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Residues in contact with ARG 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2777 A 3.0 35.2 + - - +
2787 T 3.1 33.9 + - - +
648 T 3.8 35.0 + - - +
658 A 3.9 20.9 + - - -
52K PHE* 3.6 10.5 - - - -
81K LEU 2.9 14.0 + - - +
82K LYS* 3.2 16.2 + - + +
84K ALA* 1.3 76.3 - - - +
86K ALA* 1.3 62.5 - - - +
88K ASN* 3.1 5.8 + - - +
89K ARG* 3.0 52.5 + - - +
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Residues in contact with ALA 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648 T 5.4 3.4 - - - +
82K LYS* 3.1 11.8 + - - +
83K VAL* 3.7 8.5 - - - +
85K ARG* 1.3 77.8 - - - +
87K LEU* 1.3 57.8 + - - +
89K ARG* 4.5 2.9 - - - +
90K ILE* 2.7 50.6 + - + +
96K LEU* 3.9 10.3 - - + -
99K MET* 3.8 33.2 - - + -
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Residues in contact with LEU 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K VAL* 3.0 15.1 + - + +
84K ALA* 3.1 12.5 + - + +
86K ALA* 1.3 75.8 - - - +
88K ASN* 1.3 64.5 + - - +
91K GLY* 2.7 31.8 + - - +
92K SER* 3.6 32.5 - - - +
96K LEU* 3.8 23.3 - - + +
125K ILE* 4.8 22.0 - - + +
126K THR* 6.1 2.9 - - + -
57p GLU* 5.8 3.6 - - - +
58p ASN* 6.2 0.2 - - - +
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Residues in contact with ASN 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2787 T 5.9 0.9 - - - +
7J SER* 3.8 18.3 + - - +
48K ASN* 4.9 5.4 + - - -
51K LYS* 3.9 30.4 + - - +
52K PHE* 3.3 33.9 - - + -
84K ALA* 2.9 13.5 + - - +
85K ARG* 3.1 7.8 + - - +
87K LEU* 1.3 87.3 - - - +
89K ARG* 1.3 63.2 + - + +
90K ILE 5.0 0.2 - - - -
91K GLY 4.8 0.7 + - - -
57p GLU* 5.2 4.9 - - - +
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Residues in contact with ARG 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2787 T 3.8 18.8 + - - +
2797 A 4.3 14.1 + - - -
628 T 4.7 4.0 + - - -
638 A 3.6 26.7 + - - +
648 T 3.5 37.0 + - - +
60I SER* 4.7 2.1 + - - -
73I ARG* 4.6 3.8 + - - -
7J SER* 3.6 37.8 - - - +
8J ARG* 5.5 3.6 - - - +
85K ARG* 3.0 52.6 + - - +
86K ALA* 4.2 2.2 - - - +
88K ASN* 1.3 79.3 - - + +
90K ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638 A 5.4 1.1 - - - +
648 T 4.4 11.2 - - - +
60I SER* 4.7 2.6 + - - -
64I THR* 2.6 37.2 + - - +
69I THR* 4.4 17.9 - - + -
73I ARG* 3.7 19.8 + - - +
86K ALA* 2.7 28.0 + - + +
88K ASN 5.0 0.7 - - - -
89K ARG* 1.3 79.3 - - + +
91K GLY* 1.3 68.6 + - - +
95K ALA* 3.5 25.8 - - + +
96K LEU* 4.2 4.0 - - - +
99K MET* 3.7 31.2 - - + -
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Residues in contact with GLY 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I THR* 3.8 1.8 - - - +
86K ALA 3.6 0.4 + - - -
87K LEU* 2.7 30.8 + - - -
88K ASN 4.6 0.6 + - - -
90K ILE* 1.3 88.4 - - - +
92K SER* 1.3 68.9 + - - +
96K LEU* 3.6 9.9 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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