Contacts of the helix formed by residues 94 - 115 (chain B) in PDB entry 3JRV
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 ASP 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B TYR* 5.3 0.9 - - - -
92B VAL* 3.8 2.5 - - - +
93B HIS* 1.3 98.7 + - + +
95B GLN* 1.3 60.3 + - - +
96B GLU* 3.5 12.4 + - - +
97B SER* 2.8 42.2 + - - -
98B LEU* 2.9 30.5 + - - +
136B ASN* 5.3 1.2 + - - -
139B ILE* 4.5 11.7 - - - -
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ASP* 1.3 76.4 - - - +
96B GLU* 1.3 65.9 + - - +
98B LEU* 3.2 2.4 + - - +
99B PHE* 2.9 59.6 + - + -
139B ILE* 3.7 32.2 - - + +
143B PHE* 3.7 19.2 - - - +
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 3.8 15.5 - - + +
66B ARG* 5.1 6.1 + - - +
67B TYR* 3.6 36.7 + - + +
94B ASP* 3.4 12.5 + - - +
95B GLN* 1.3 81.5 - - - +
97B SER* 1.3 58.4 + - - +
99B PHE* 3.4 3.9 + - - -
100B ALA* 2.8 30.7 + - - +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 3.5 32.7 - - - -
91B LYS 5.4 0.2 - - - -
92B VAL* 4.2 7.4 - - - -
93B HIS* 3.1 34.1 + - - -
94B ASP* 2.8 27.6 + - - -
96B GLU* 1.3 74.4 - - - +
98B LEU* 1.3 62.8 + - - +
100B ALA* 3.8 1.9 - - - +
101B THR* 2.8 33.4 + - - -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 3.6 11.8 - - + +
94B ASP 2.9 18.3 + - - +
95B GLN 3.5 4.9 - - - +
96B GLU 3.2 0.2 - - - -
97B SER* 1.3 77.8 + - - +
99B PHE* 1.3 70.6 + - + +
101B THR* 3.2 3.5 + - - -
102B ILE* 3.0 37.1 + - + +
131B LEU* 3.8 25.4 - - + -
132B MSE 4.1 13.9 - - + -
136B ASN* 3.4 54.1 - - + +
139B ILE* 4.0 18.6 - - + -
140B LEU* 4.4 5.2 - - + +
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PHE* 3.4 43.9 - + + +
63B VAL* 3.8 22.2 - - + -
95B GLN* 2.9 44.3 + - + +
96B GLU* 5.3 1.1 - - - -
98B LEU* 1.3 95.4 - - + +
100B ALA* 1.3 66.8 + - - +
102B ILE* 3.3 2.6 + - + +
103B GLY 2.9 18.2 + - - -
139B ILE* 4.2 7.9 - - + -
140B LEU* 3.6 19.1 - - + -
143B PHE* 3.5 52.7 - + + -
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL* 3.6 4.4 - - + +
64B ALA* 3.5 17.9 - - - +
67B TYR* 3.7 39.7 - - + -
68B TYR* 3.8 8.1 - - + -
96B GLU 2.8 18.5 + - - +
97B SER 3.8 3.8 - - - +
98B LEU 3.2 0.2 - - - -
99B PHE* 1.3 77.0 - - - +
101B THR* 1.3 58.0 + - - +
103B GLY 3.2 1.0 + - - -
104B ILE* 2.8 30.8 + - - +
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B TYR* 3.7 15.5 + - - +
87B ILE* 4.8 7.4 - - + -
89B PHE* 3.7 35.9 - - + -
92B VAL* 3.5 17.5 - - + +
97B SER* 2.8 22.5 + - - -
98B LEU 3.6 4.0 - - - -
100B ALA* 1.3 74.6 - - - +
102B ILE* 1.3 64.9 + - - +
104B ILE* 3.3 10.2 + - + +
105B CYS* 3.0 23.7 + - - -
131B LEU* 3.8 11.2 - - + -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 4.2 32.3 - - + -
33B TYR* 4.5 10.1 - - + -
34B ILE* 3.8 12.7 - - + +
57B LEU* 5.2 0.4 - - + +
60B PHE* 3.9 32.5 - - + -
98B LEU* 3.0 37.2 + - + +
99B PHE* 3.7 6.1 - - + +
101B THR* 1.3 74.4 - - - +
103B GLY* 1.3 63.2 + - - +
105B CYS* 3.1 10.0 + - - +
106B ALA* 3.0 20.6 + - - +
131B LEU* 4.3 18.8 - - + -
132B MSE 4.4 4.7 - - - -
140B LEU* 4.3 10.3 - - + -
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PHE* 3.6 31.4 - - - +
61B ASP* 4.1 10.6 - - - +
64B ALA* 4.2 6.5 - - - +
99B PHE 2.9 11.3 + - - -
100B ALA 3.2 2.9 + - - -
102B ILE* 1.3 77.8 - - - +
104B ILE* 1.3 56.2 + - - +
106B ALA* 3.3 5.1 + - - +
107B LYS* 2.9 27.5 + - - +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ALA* 4.1 5.1 - - + +
68B TYR* 2.7 55.6 - - + +
73B ILE* 5.2 7.4 - - + -
76B ILE* 3.8 27.6 - - + -
77B VAL* 6.2 0.7 - - + -
87B ILE* 4.0 17.0 - - + -
100B ALA 2.8 11.6 + - - +
101B THR* 3.5 11.7 - - + +
102B ILE 3.2 0.2 - - - -
103B GLY* 1.3 71.7 - - - +
105B CYS* 1.3 68.2 + - - +
107B LYS* 3.2 7.5 + - - +
108B ILE* 2.9 43.4 + - + +
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Residues in contact with CYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 3.7 16.2 - - + -
87B ILE* 4.3 7.4 - - - -
89B PHE* 3.8 33.7 - - - -
101B THR 3.0 19.5 + - - -
102B ILE* 3.1 9.1 + - - +
104B ILE* 1.3 79.1 - - - +
106B ALA* 1.3 61.9 + - - +
108B ILE* 3.2 7.9 + - - +
109B THR* 3.0 29.1 + - - +
125B LEU* 4.0 19.3 - - + -
131B LEU* 4.7 4.7 - - - -
85D PHE* 4.2 8.7 - - + -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TYR* 4.0 7.4 - - + +
34B ILE* 3.5 15.9 - - + +
37B ARG* 3.7 36.2 - - + +
61B ASP* 3.9 4.7 - - - +
102B ILE 3.0 12.3 + - - +
103B GLY* 3.6 9.2 - - - +
104B ILE 3.2 0.2 - - - -
105B CYS* 1.3 75.1 - - - +
107B LYS* 1.3 59.8 + - - +
109B THR* 3.4 5.8 + - - -
110B GLU* 2.9 32.2 + - - +
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASP* 4.8 5.5 + - - -
65A ILE* 6.1 0.8 - - - +
37B ARG* 5.6 0.4 - - - +
61B ASP* 5.0 7.5 + - + +
64B ALA* 6.4 0.4 - - + -
65B ILE* 5.1 6.9 - - + +
70B ILE* 4.1 19.2 - - - +
73B ILE* 3.8 22.7 - - + -
74B ASN* 4.5 9.3 + - - -
77B VAL* 3.6 21.1 - - + -
103B GLY 2.9 14.2 + - - +
104B ILE* 3.2 11.9 + - - +
106B ALA* 1.3 75.5 - - - +
108B ILE* 1.3 58.8 + - - +
110B GLU* 3.5 21.5 + - - +
111B HIS* 2.8 31.0 + - + +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ILE* 4.4 3.4 - - + -
77B VAL* 4.1 22.2 - - + +
80B MSE 3.8 36.1 - - + -
87B ILE* 3.8 13.7 - - + -
104B ILE* 2.9 40.0 + - + +
105B CYS 3.7 4.0 - - - +
106B ALA 3.2 0.2 - - - -
107B LYS* 1.3 76.8 - - - +
109B THR* 1.3 58.6 + - - +
111B HIS* 3.2 9.5 + - + +
112B TRP* 3.0 62.9 + - + -
125B LEU* 3.9 9.2 - - + -
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Residues in contact with THR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 2.8 42.5 + - + +
37B ARG* 3.8 6.2 - - - +
38B ASN* 3.1 24.7 + - - +
105B CYS 3.0 16.5 + - - +
106B ALA* 3.5 6.6 + - - -
108B ILE* 1.3 73.3 - - - +
110B GLU* 1.3 61.7 + - - +
112B TRP* 3.4 12.6 + - + -
113B GLY 2.9 22.7 + - - -
125B LEU* 4.0 6.5 - - + -
84D PHE* 3.6 28.0 - - + -
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ARG* 2.9 50.5 + - + +
41B ILE* 4.6 5.7 - - + +
47B ILE* 5.3 3.5 - - - +
61B ASP* 5.2 0.3 - - - +
106B ALA 2.9 17.9 + - - +
107B LYS* 3.7 25.8 + - - +
109B THR* 1.3 77.0 + - - +
111B HIS* 1.3 59.6 + - - +
113B GLY* 3.0 3.0 + - - +
114B TYR* 2.9 57.2 + - + -
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Residues in contact with HIS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 3.4 31.4 - - + +
78B GLU* 5.8 3.6 - - - -
81B SER* 3.1 32.3 + - - -
107B LYS* 2.8 16.0 + - + +
108B ILE* 3.3 10.5 - - + +
110B GLU* 1.3 76.5 - - - +
112B TRP* 1.3 80.1 + + - +
114B TYR* 3.2 16.2 + - - +
115B LYS* 3.4 35.2 + - + +
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Residues in contact with TRP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASN* 3.7 2.2 - - - +
80B MSE 3.4 24.5 - - + -
81B SER* 2.9 27.9 + - - +
83B GLY* 4.7 0.9 - - - -
108B ILE* 3.0 41.1 + - + -
109B THR* 3.7 13.9 - - + +
110B GLU 3.3 0.2 - - - -
111B HIS* 1.3 85.7 - + - +
113B GLY* 1.3 63.0 + - - +
115B LYS* 3.0 11.8 + - + +
117B ILE* 2.9 52.2 + - + +
121B ARG* 3.5 36.8 - - + +
124B SER* 2.9 28.7 - - - -
125B LEU* 4.3 6.7 - - + -
84D PHE* 3.8 25.1 - + + -
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASN* 3.2 21.7 - - - +
41B ILE* 3.3 17.3 - - - +
42B VAL* 3.7 13.9 - - - +
109B THR 2.9 12.8 + - - -
110B GLU 3.0 5.3 + - - -
112B TRP* 1.3 78.0 - - - +
114B TYR* 1.3 57.0 + - - +
116B LYS* 2.9 26.2 + - - +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.7 43.8 - - + +
48A THR* 3.4 34.4 - - + +
55A LYS* 5.9 2.6 - - - -
58A MSE 4.5 12.5 - - + +
41B ILE* 3.8 22.3 - - + +
110B GLU* 2.9 49.8 + - + +
111B HIS* 3.2 12.1 + - - +
113B GLY* 1.3 75.0 - - - +
115B LYS* 1.3 61.1 + - + +
116B LYS* 3.3 2.1 + - - +
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B SER* 3.7 17.8 + - - -
82B GLU* 5.0 7.3 + - - -
111B HIS* 3.6 35.7 + - + +
112B TRP* 3.0 10.4 + - + +
114B TYR* 1.3 77.2 - - + +
116B LYS* 1.3 70.1 + - - +
117B ILE* 3.3 31.2 + - + +
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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
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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