Contacts of the helix formed by residues 70 - 91 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2867 T 3.5 25.3 + - - +
2877 A 4.4 2.8 + - - -
111I PHE* 3.5 19.5 - - - -
90J ILE* 5.6 0.6 - - - +
99J MET* 5.3 0.2 - - - +
69L THR* 1.3 76.3 - - - +
71L PRO* 1.3 65.9 - - - +
73L ARG* 2.9 35.2 + - - +
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Residues in contact with PRO 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867 T 3.6 23.3 - - + +
2877 A 3.9 33.4 - - - +
71I PRO* 3.6 18.4 - - + +
74I ALA* 4.8 2.2 - - + -
75I ILE* 3.5 37.7 - - + +
107I TYR* 6.5 0.9 - - + -
111I PHE* 4.6 7.2 - - + -
69L THR 4.4 0.2 - - - +
70L GLY* 1.3 82.0 - - - +
72L ASN* 1.3 64.3 + - - +
73L ARG 3.1 0.2 - - - -
74L ALA* 3.1 4.5 + - - +
75L ILE* 3.0 24.8 + - - +
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Residues in contact with ASN 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ASN* 3.1 24.9 - - - +
75I ILE* 3.5 10.7 - - - +
111I PHE* 3.3 25.5 + - - +
112I ASN* 4.8 8.5 + - - +
68L ILE* 3.5 15.9 - - + -
69L THR* 3.3 13.9 + - - +
70L GLY 3.0 0.8 - - - -
71L PRO* 1.3 75.6 - - - +
73L ARG* 1.3 65.5 + - - +
75L ILE* 3.3 17.3 + - + +
76L TYR* 3.0 26.3 - - + -
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Residues in contact with ARG 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2867 T 3.0 36.1 + - - +
89J ARG 4.6 0.8 + - - -
90J ILE* 3.7 28.2 + - - +
95J ALA* 4.0 0.2 - - - +
60L SER* 2.7 46.3 + - - +
63L LEU* 3.5 15.8 - - + +
64L THR* 2.9 30.7 + - - +
68L ILE* 2.8 56.9 + - + +
69L THR* 3.8 8.5 - - - +
70L GLY 2.9 15.0 + - - +
72L ASN* 1.3 77.8 - - - +
74L ALA* 1.3 58.1 + - - +
76L TYR* 3.0 5.0 + - - -
77L GLN* 2.8 30.3 + - - +
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Residues in contact with ALA 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2857 A 4.1 16.8 - - + +
2867 T 3.0 41.2 + - + +
638 A 4.7 5.2 - - + -
648 T 4.4 6.5 - - - +
71I PRO* 4.8 3.4 - - + -
70L GLY 3.6 0.8 + - - -
71L PRO 3.1 8.6 + - - +
73L ARG* 1.3 77.4 - - - +
75L ILE* 1.3 64.1 + - - +
77L GLN* 3.6 10.5 - - - +
78L GLY* 2.9 21.1 + - - -
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Residues in contact with ILE 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I PRO* 3.6 26.4 - - + +
72I ASN* 3.5 36.8 - - - +
71L PRO 3.0 14.8 + - - +
72L ASN* 3.4 22.4 - - - +
74L ALA* 1.3 78.0 - - - +
76L TYR* 1.3 67.2 + - + +
78L GLY* 3.4 0.7 + - - -
79L PHE* 3.1 21.1 + - - +
107L TYR* 3.5 31.0 - - + -
111L PHE* 4.6 10.1 - - + +
112L ASN 5.9 0.9 - - - +
113L ALA* 4.1 19.1 - - + -
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Residues in contact with TYR 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L VAL* 4.4 2.7 - - - +
63L LEU* 3.6 28.9 - - + -
68L ILE* 4.0 18.0 - - + +
72L ASN* 3.0 28.3 - - + -
73L ARG 3.0 5.0 + - - +
75L ILE* 1.3 81.7 - - + +
77L GLN* 1.3 60.4 + - - +
79L PHE* 3.3 5.5 + - - +
80L GLY* 2.8 27.2 + - - -
112L ASN 5.0 0.2 + - - -
113L ALA* 3.9 8.8 - - + -
114L ASN* 2.9 38.5 + - - +
117L VAL* 3.7 31.1 - - + +
118L LEU* 3.7 31.0 - - + -
121L VAL* 4.2 11.3 - - + +
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Residues in contact with GLN 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2857 A 3.4 34.1 + - + +
2867 T 3.1 21.3 + - - +
55L VAL* 5.4 0.7 - - - +
56L ASN* 3.4 23.9 + - - +
59L VAL* 3.3 20.6 - - - +
60L SER* 3.5 26.3 - - - +
63L LEU* 4.0 2.1 - - + +
73L ARG 2.8 21.5 + - - +
74L ALA* 3.2 9.6 + - - +
76L TYR* 1.3 78.5 - - - +
78L GLY* 1.3 57.2 + - - +
80L GLY* 3.3 1.1 + - - +
81L LEU* 2.9 41.3 + - + +
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Residues in contact with GLY 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2857 A 5.4 0.8 + - - -
648 T 5.1 2.9 - - - -
658 A 4.1 24.6 - - - +
74L ALA 2.9 16.2 + - - -
75L ILE 3.8 1.8 - - - -
77L GLN* 1.3 77.9 - - - +
79L PHE* 1.3 61.6 + - - +
81L LEU* 3.4 5.3 + - - +
82L LYS* 3.0 25.1 + - - +
107L TYR* 3.5 14.7 + - - -
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Residues in contact with PHE 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ILE 3.1 13.4 + - - +
76L TYR* 3.5 7.9 - - - +
77L GLN 3.3 0.2 - - - -
78L GLY* 1.3 75.9 - - - +
80L GLY* 1.3 65.0 + - - +
82L LYS* 3.1 5.8 + - - +
83L VAL* 2.9 32.6 + - + +
100L ILE* 5.1 2.0 - - + -
103L LEU* 3.7 24.0 - - + -
104L LYS* 3.8 23.6 - - + -
107L TYR* 3.5 33.9 + + + -
118L LEU* 3.3 52.5 - - + -
121L VAL* 3.8 17.5 - - + -
122L VAL* 3.7 23.8 - - + -
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Residues in contact with GLY 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L VAL* 4.5 5.4 - - - -
59L VAL* 5.0 2.0 - - - -
76L TYR 2.8 16.6 + - - -
77L GLN* 3.8 0.9 - - - -
79L PHE* 1.3 75.3 - - - +
81L LEU* 1.3 64.5 + - - +
83L VAL* 3.1 2.5 + - - -
84L ALA* 3.0 19.4 + - - +
121L VAL* 3.5 26.5 - - - -
125L ILE* 3.1 17.7 - - - +
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Residues in contact with LEU 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2847 T 5.5 1.6 - - - +
2857 A 5.6 3.4 - - - +
658 A 4.1 19.1 - - + +
668 T 3.4 36.7 - - - +
52L PHE* 3.5 43.6 - - + +
55L VAL* 4.5 6.7 - - + +
56L ASN* 3.4 31.2 - - - +
77L GLN* 2.9 29.6 + - + +
78L GLY* 3.8 5.2 - - - +
80L GLY* 1.3 76.0 - - - +
82L LYS* 1.3 58.6 + - - +
84L ALA* 3.2 3.7 + - - -
85L ARG 2.9 22.9 + - - -
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Residues in contact with LYS 82 (chain L).
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 3.2 14.6 + - - -
658 A 3.7 26.2 + - - +
668 T 3.3 26.7 + - - +
106K TYR* 2.8 33.6 + - - -
78L GLY 3.0 17.9 + - - +
79L PHE* 3.5 5.2 - - - +
81L LEU* 1.3 75.0 - - - +
83L VAL* 1.3 63.7 + - - +
85L ARG* 3.3 10.6 + - - +
86L ALA* 3.1 22.2 + - - +
99L MET* 5.9 2.6 - - - -
103L LEU* 3.5 35.8 - - + +
106L TYR* 5.0 5.8 - - + -
107L TYR* 4.6 3.4 - - + -
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Residues in contact with VAL 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L PHE* 2.9 42.1 + - + +
80L GLY* 3.1 8.3 + - - +
82L LYS* 1.3 76.3 - - - +
84L ALA* 1.3 63.8 + - - +
86L ALA* 3.3 8.1 + - - +
87L LEU* 3.0 19.6 + - + +
96L LEU* 4.5 2.7 - - + +
100L ILE* 4.3 28.0 - - + -
103L LEU* 3.7 20.2 - - + +
122L VAL* 4.6 9.0 - - + -
125L ILE* 3.8 26.5 - - + -
126L THR* 4.5 6.1 - - + -
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Residues in contact with ALA 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L LYS 5.7 0.2 - - - +
52L PHE* 3.6 20.4 - - + -
55L VAL* 4.2 20.0 - - + -
80L GLY 3.0 12.0 + - - +
81L LEU* 3.5 8.7 - - - +
83L VAL* 1.3 73.7 - - - +
85L ARG* 1.3 66.9 + - - +
87L LEU* 3.1 11.9 + - + +
88L ASN* 3.0 25.3 + - - +
125L ILE* 4.4 10.8 - - + -
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Residues in contact with ARG 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2757 A 3.8 35.3 + - - -
2767 T 2.9 33.7 + - - +
668 T 3.0 37.0 + - - +
678 A 3.4 30.3 + - - +
52L PHE* 3.5 10.9 - - - -
81L LEU 2.9 14.2 + - - +
82L LYS* 3.3 19.5 - - - +
83L VAL 3.2 0.2 - - - -
84L ALA* 1.3 75.6 - - - +
86L ALA* 1.3 64.1 + - - +
88L ASN* 3.0 5.9 + - - +
89L ARG* 3.0 45.2 + - - +
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Residues in contact with ALA 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2757 A 5.6 2.0 - - - -
82L LYS 3.1 8.2 + - - +
83L VAL* 3.6 9.4 - - - +
85L ARG* 1.3 78.4 - - - +
87L LEU* 1.3 58.8 + - - +
89L ARG* 4.5 3.4 - - - +
90L ILE* 2.7 47.1 + - + +
96L LEU* 3.8 15.7 - - + -
99L MET* 3.8 28.5 - - + -
100L ILE* 6.0 0.2 - - + -
103L LEU* 6.2 0.4 - - + -
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Residues in contact with LEU 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L VAL* 3.0 12.7 + - + +
84L ALA* 3.2 12.3 - - + +
86L ALA* 1.3 76.7 - - - +
88L ASN* 1.3 64.2 + - - +
91L GLY* 2.7 30.9 + - - +
92L SER* 3.6 29.2 - - - +
96L LEU* 3.6 24.4 - - + +
125L ILE* 4.5 26.0 - - + +
126L THR* 6.0 2.2 - - + -
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Residues in contact with ASN 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678 A 5.4 1.3 + - - +
48L ASN* 4.9 5.6 + - - -
51L LYS* 3.8 30.6 + - - +
52L PHE* 3.4 34.1 - - - -
84L ALA* 3.0 12.7 + - - +
85L ARG* 3.0 8.0 + - - +
87L LEU* 1.3 85.8 - - - +
89L ARG* 1.3 64.6 + - + +
90L ILE 3.7 0.7 + - - -
91L GLY* 4.5 1.0 + - - -
7M SER* 4.6 13.3 - - - +
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Residues in contact with ARG 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2737 A 4.6 10.1 + - - -
2747 T 3.6 28.7 + - - +
2757 A 3.3 32.7 + - - +
678 A 4.1 17.5 + - - +
688 T 4.3 15.2 + - - -
85L ARG* 3.0 46.7 + - - +
86L ALA* 4.3 2.2 - - - +
88L ASN* 1.3 79.5 - - + +
90L ILE* 1.3 61.6 + - + +
7M SER* 4.1 33.8 - - - +
60N SER* 4.5 6.4 + - - -
73N ARG* 4.6 1.9 + - - -
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Residues in contact with ILE 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2747 T 5.6 0.2 - - - +
2757 A 4.5 11.0 - - - +
86L ALA* 2.7 29.5 + - + +
88L ASN 4.8 0.9 - - - -
89L ARG* 1.3 78.0 - - - +
91L GLY* 1.3 67.9 + - - +
95L ALA* 3.6 26.0 - - + +
96L LEU* 4.0 5.2 - - + +
99L MET* 3.8 38.1 - - + -
60N SER* 4.9 1.7 + - - -
61N ALA* 5.8 0.7 - - - -
64N THR* 2.6 36.6 + - + +
69N THR* 4.4 10.8 - - + -
73N ARG* 3.7 18.8 + - - +
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Residues in contact with GLY 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L ALA 3.6 0.6 + - - -
87L LEU* 2.7 30.6 + - - -
88L ASN 4.5 0.9 - - - -
90L ILE* 1.3 89.8 - - - +
92L SER* 1.3 68.1 + - - +
96L LEU* 3.4 9.2 - - - +
64N THR* 3.6 0.9 - - - +
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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) + - + + + + + -
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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