Contacts of the helix formed by residues 91 - 111 (chain D) in PDB entry 1J1J
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 TRP 91 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 4.0 19.1 - - + -
28D VAL* 3.8 15.0 - - + -
75D LEU* 4.0 14.1 - - + -
79D PHE* 3.5 38.8 - + - -
84D TYR* 3.1 56.7 + + - -
87D PHE* 3.6 25.6 - - + -
88D HIS* 3.0 28.8 + + - -
90D HIS* 1.3 76.6 - - - +
92D ARG* 1.3 68.5 + - - +
93D PHE 3.3 2.9 - - - -
94D VAL* 3.4 14.4 - - + +
95D LEU* 2.9 36.0 + - + +
133D PHE* 3.4 18.6 - + - -
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Residues in contact with ARG 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D HIS* 3.0 46.4 + - + +
89D GLU* 2.9 47.3 + - - +
90D HIS 3.6 1.6 - - - -
91D TRP* 1.3 78.0 - - - +
93D PHE* 1.3 66.3 + - - +
95D LEU* 3.6 2.6 - - - +
96D GLN* 3.1 51.7 + - - +
139D ASP* 3.7 2.9 - - - +
190D SER* 4.8 14.6 + - - -
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Residues in contact with PHE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLU* 3.3 34.8 - - + +
89D GLU 4.9 1.4 + - - -
90D HIS 5.3 1.7 + - - +
91D TRP 3.3 1.2 - - - -
92D ARG* 1.3 82.1 - - - +
94D VAL* 1.3 63.4 + - + +
96D GLN* 3.3 8.7 + - - +
97D ARG* 3.0 67.6 + - + +
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL* 4.5 8.3 - - + -
31D LEU* 3.9 24.9 - - + +
32D GLU* 3.8 42.8 + - + +
35D ALA* 4.1 10.5 - - + -
72D LEU* 6.2 1.6 - - + -
91D TRP* 3.4 25.0 + - + +
93D PHE* 1.3 78.4 - - + +
95D LEU* 1.3 65.1 + - + +
97D ARG* 3.3 7.7 + - + +
98D LEU* 2.8 46.3 + - + +
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Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LEU* 5.8 3.8 - - + -
84D TYR* 3.6 24.0 - - - +
91D TRP* 2.9 30.2 + - + +
92D ARG* 3.6 5.2 - - - +
93D PHE 3.2 0.2 - - - -
94D VAL* 1.3 78.8 - - + +
96D GLN* 1.3 58.4 + - - +
98D LEU* 3.3 7.4 + - + +
99D VAL* 3.0 32.7 + - + +
123D LEU* 3.7 28.5 - - + -
125D ILE* 5.3 3.1 - - + -
133D PHE* 4.7 10.5 - - + -
134D HIS 4.2 5.8 - - - +
135D LEU* 4.0 25.4 - - + -
139D ASP* 3.6 20.0 - - - +
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Residues in contact with GLN 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ARG* 3.1 33.8 + - - +
93D PHE* 3.7 7.6 - - - +
94D VAL 3.2 0.2 - - - -
95D LEU* 1.3 74.5 - - - +
97D ARG* 1.3 66.7 + - - +
99D VAL* 3.3 4.4 + - - +
100D PHE* 3.1 18.0 + - - +
138D GLU* 4.4 1.0 + - - +
139D ASP* 2.9 46.8 + - + +
142D SER* 3.3 27.2 + - - -
143D GLY* 3.6 8.9 - - - +
146D ILE* 4.4 8.2 - - + +
194D ARG* 3.4 23.5 + - - +
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Residues in contact with ARG 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ALA* 4.8 11.9 - - + +
36D ARG* 6.1 2.8 - - - +
39D LEU* 4.2 20.2 - - - +
93D PHE* 3.0 59.5 + - + +
94D VAL* 3.7 7.6 - - + +
96D GLN* 1.3 78.3 - - - +
98D LEU* 1.3 58.0 + - - +
100D PHE* 3.1 32.1 + - - +
101D LEU* 2.8 43.7 + - + +
146D ILE* 4.1 21.8 - - - +
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 4.3 11.2 - - + +
35D ALA* 4.2 19.5 - - + +
38D ILE* 4.8 0.9 - - + -
65D PHE* 3.9 16.3 - - + -
68D VAL* 3.9 42.0 - - + -
72D LEU* 4.9 7.4 - - + -
94D VAL* 2.8 43.0 + - + +
95D LEU* 3.7 9.0 - - + +
96D GLN 3.2 0.2 - - - -
97D ARG* 1.3 75.3 - - - +
99D VAL* 1.3 65.7 + - - +
101D LEU* 3.8 7.5 - - + +
102D ALA* 3.0 25.6 + - - +
119D VAL* 5.2 0.7 - - - -
123D LEU* 3.9 21.6 - - + +
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D LEU* 3.0 22.9 + - + +
96D GLN 3.5 7.0 - - - +
97D ARG 3.2 0.2 - - - -
98D LEU* 1.3 75.1 - - - +
100D PHE* 1.3 59.0 + - - +
102D ALA* 3.3 1.9 + - - +
103D ALA* 2.8 31.2 + - + +
119D VAL* 4.2 17.7 - - + +
123D LEU* 5.3 0.2 - - - +
135D LEU* 3.8 36.3 - - + -
139D ASP 3.9 8.5 - - - +
140D TYR* 3.6 38.8 - - + +
143D GLY* 3.8 9.4 - - - -
144D VAL* 4.4 2.2 - - + +
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Residues in contact with PHE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 3.8 26.0 - - + -
96D GLN 3.1 12.5 + - - +
97D ARG* 3.1 29.8 + - - +
99D VAL* 1.3 76.5 - - - +
101D LEU* 1.3 60.2 + - + +
103D ALA* 3.2 4.5 + - - +
104D PHE* 2.7 48.8 + + + +
143D GLY* 3.6 18.3 - - - +
146D ILE* 3.5 22.9 - - + -
147D LEU* 3.5 24.7 - - + -
150D GLU* 3.5 47.3 - - + -
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ALA* 3.6 39.0 - - + +
38D ILE* 4.1 10.3 - - + -
39D LEU* 3.8 43.3 - - + +
42D LEU* 3.9 13.9 - - + +
65D PHE* 3.8 15.9 - - + -
97D ARG* 2.8 30.9 + - + +
98D LEU* 3.8 7.9 - - + +
100D PHE* 1.3 82.7 - - + +
102D ALA* 1.3 58.0 + - - +
104D PHE* 3.2 5.0 + - + +
105D VAL* 2.9 33.4 + - - +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D PHE* 3.6 17.6 - - + -
98D LEU 3.0 17.4 + - - +
99D VAL 3.7 3.1 - - - +
101D LEU* 1.3 75.6 - - - +
103D ALA* 1.3 63.4 + - - +
105D VAL* 3.3 6.9 + - - +
106D VAL* 3.0 26.3 + - - +
114D VAL* 4.1 2.2 - - - -
119D VAL* 4.4 19.3 - - + -
122D ILE* 4.0 26.3 - - + +
123D LEU* 5.6 0.4 - - + -
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL* 2.8 21.9 + - + +
100D PHE* 3.6 5.8 - - - +
102D ALA* 1.3 78.7 - - - +
104D PHE* 1.3 56.5 + - - +
107D TYR* 2.9 30.8 + - - +
112D THR 4.8 0.3 - - - +
113D LEU* 4.9 12.1 - - + -
114D VAL* 3.0 24.2 - - + +
119D VAL* 5.1 0.9 - - + +
140D TYR* 6.5 1.3 - - + -
143D GLY 5.4 0.9 - - - +
144D VAL* 5.6 3.6 - - + -
147D LEU* 4.3 18.5 - - + +
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Residues in contact with PHE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 5.7 1.1 - - + -
42D LEU* 4.0 42.0 - - + -
43D GLN* 5.1 1.3 - - + -
45D VAL* 5.0 3.4 - - + -
46D HIS* 4.6 6.5 - - - -
100D PHE* 2.7 34.7 + + + +
101D LEU* 3.2 8.5 + - + +
103D ALA* 1.3 72.9 - - - +
105D VAL* 1.3 64.2 + - - +
107D TYR* 3.5 1.3 + - + -
108D LEU* 3.0 52.1 + - + +
147D LEU* 3.7 19.7 - - + +
150D GLU* 3.7 32.5 - - + -
151D LEU* 3.9 18.4 - - + -
154D LEU* 4.4 10.1 - - + -
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 3.8 20.9 - - + -
58D CYS* 3.9 16.1 - - + +
61D ALA* 3.9 18.6 - - + -
62D ARG* 3.9 21.3 - - + +
65D PHE* 4.3 12.1 - - + -
101D LEU 2.9 18.9 + - - +
102D ALA* 3.5 8.7 - - - +
103D ALA 3.3 0.2 - - - -
104D PHE* 1.3 75.3 - - - +
106D VAL* 1.3 63.1 + - + +
108D LEU* 3.2 6.0 + - - +
109D GLU* 3.0 50.1 + - - +
122D ILE* 6.1 1.1 - - + -
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Residues in contact with VAL 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ARG* 3.9 21.3 - - - +
102D ALA 3.0 9.4 + - - +
105D VAL* 1.3 76.5 - - + +
107D TYR* 1.3 52.3 + - - +
109D GLU* 3.3 7.1 + - - +
110D THR* 2.7 45.3 + - + +
112D THR* 3.6 27.6 - - + +
114D VAL* 3.2 47.1 - - + +
122D ILE* 4.3 7.2 - - + -
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Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ALA 2.9 17.2 + - - +
104D PHE* 3.9 5.6 - - + +
106D VAL* 1.3 76.8 - - - +
108D LEU* 1.3 69.1 + - + +
111D GLU* 2.5 74.2 + - + +
112D THR 3.6 14.8 + - - +
147D LEU* 4.8 7.0 - - + -
151D LEU* 3.9 31.4 - - + -
154D LEU* 5.2 1.6 - - + -
166D ARG* 5.0 9.5 + - + +
169D HIS* 3.9 6.1 + - - +
170D ILE* 3.6 36.9 + - + +
173D PHE* 3.5 37.6 - + + +
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 4.3 13.9 - - + -
45D VAL* 4.0 29.2 - - + -
54D ILE* 3.6 28.1 - - + +
58D CYS* 3.6 20.0 - - - -
104D PHE* 3.0 52.5 + - + +
105D VAL 3.2 4.5 + - - +
107D TYR* 1.3 83.1 - - + +
109D GLU* 1.3 61.5 + - - +
111D GLU* 4.8 3.1 + - - +
154D LEU* 4.1 17.9 - - + -
166D ARG* 5.0 14.5 + - - +
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 5.1 2.0 - - + -
55D PRO* 6.1 1.1 - - + -
58D CYS* 3.7 22.2 - - + +
59D LEU* 5.2 3.3 + - - +
62D ARG* 2.8 44.8 + - - -
105D VAL* 3.0 30.1 + - - +
106D VAL* 3.7 8.8 - - - +
108D LEU* 1.3 79.3 - - - +
110D THR* 1.3 71.5 + - + +
111D GLU* 5.6 0.4 - - - -
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Residues in contact with THR 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D VAL* 2.7 24.4 + - + +
109D GLU* 1.3 91.8 - - + +
111D GLU* 1.3 70.2 + - - +
112D THR* 2.8 37.9 + - + +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D TYR* 2.5 59.0 + - + +
108D LEU 5.1 4.0 - - - +
109D GLU 5.6 0.4 - - - -
110D THR* 1.3 75.5 + - - +
112D THR* 1.3 57.1 + - - +
166D ARG* 5.1 15.5 + - - +
169D HIS* 3.1 43.9 + - + +
173D PHE* 4.4 5.5 - - - -
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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
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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