Contacts of the helix formed by residues 94 - 115 (chain B) in PDB entry 1RX0
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 CYS 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B MET* 3.8 11.7 - - + +
42B MET* 4.0 24.7 - - + -
45B TRP* 4.2 17.0 - - + -
90B LEU 3.3 3.6 + - - -
91B ALA 3.7 2.2 - - - -
93B GLY* 1.3 79.0 - - - +
95B THR* 1.3 67.3 + - - +
96B SER* 3.8 10.8 - - - -
97B THR* 3.1 36.3 - - - +
98B THR* 2.8 28.4 + - - -
218B SER* 4.3 3.1 - - - -
364B GLN* 4.1 4.0 - - - -
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET* 5.0 2.2 - - - -
91B ALA* 3.0 23.4 + - - +
94B CYS* 1.3 71.1 - - - +
96B SER* 1.3 59.8 + - - +
98B THR* 3.4 1.7 + - - -
99B ALA* 2.9 29.0 + - - +
261B CYS* 3.9 16.0 - - + +
265B ALA* 3.5 23.0 - - + +
365B TYR* 3.7 9.1 - - - -
368B ASP* 3.9 21.5 + - + -
369B SER 4.7 0.7 - - - +
372B HIS* 3.5 33.9 - - + +
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B CYS* 3.3 7.3 - - - -
95B THR* 1.3 79.3 - - - +
97B THR* 1.3 61.9 + - - +
99B ALA* 3.2 1.9 + - - +
100B TYR 3.1 5.5 + - - -
216B TRP* 3.1 46.1 + - - -
217B ASN 4.4 1.1 - - - -
218B SER* 2.7 23.6 + - - -
219B GLN* 2.8 26.7 + - - +
364B GLN* 4.4 3.4 - - - -
368B ASP* 3.2 18.1 + - - -
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Residues in contact with THR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B MET* 4.2 9.0 - - + -
45B TRP* 3.5 12.7 - - + -
52B PRO* 3.8 21.3 - - + +
55B VAL* 6.2 0.9 - - + -
56B MET* 4.0 20.4 - - + -
94B CYS* 3.1 24.6 - - - -
96B SER* 1.3 74.3 - - - +
98B THR* 1.3 64.5 + - - +
100B TYR* 3.2 7.7 + - - +
101B ILE* 3.0 28.8 + - + +
218B SER* 2.8 23.1 + - - +
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B MET* 3.5 4.5 - - - +
87B PHE* 3.4 39.0 - - + +
90B LEU* 3.1 33.0 + - + +
91B ALA* 3.8 6.3 - - - +
94B CYS 2.8 23.3 + - - -
95B THR 3.8 3.1 - - - -
97B THR* 1.3 76.6 - - - +
99B ALA* 1.3 63.2 + - - +
101B ILE* 3.1 11.0 + - + +
102B SER* 2.9 21.8 + - - -
261B CYS* 3.7 12.8 - - - -
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B THR 2.9 17.9 + - - +
96B SER 3.4 5.2 - - - +
97B THR 3.2 0.2 - - - -
98B THR* 1.3 77.2 - - - +
100B TYR* 1.3 61.4 + - - +
102B SER* 3.2 6.2 + - - -
103B ILE* 3.1 25.4 + - - +
216B TRP* 3.3 37.4 - - + +
219B GLN* 3.9 0.9 - - - +
258B ILE* 5.7 2.5 - - + -
261B CYS* 3.9 16.7 - - - -
372B HIS* 4.5 3.6 - - - +
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 3.5 29.4 - + + -
56B MET* 3.7 20.2 - - - -
96B SER 3.1 7.5 + - - +
97B THR* 3.2 9.1 + - - +
99B ALA* 1.3 75.0 - - - +
101B ILE* 1.3 67.5 + - - +
103B ILE* 3.0 9.8 + - + +
104B HIS* 2.8 33.0 + - + +
130B MET* 4.7 1.6 - - + -
133B PHE* 3.3 32.8 - + - +
134B ALA 2.7 31.0 + - - -
171B SER* 4.0 23.1 - - - -
172B GLY* 4.1 6.3 - - - -
176B SER* 3.5 3.2 + - - -
219B GLN* 3.4 34.2 - - + +
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B MET* 4.9 7.9 - - + -
56B MET* 4.3 23.1 - - + -
59B ALA* 4.7 15.3 - - + -
64B PHE* 3.5 16.4 - - + +
87B PHE* 4.2 12.1 - - + -
90B LEU* 4.7 13.9 - - + -
97B THR* 3.0 32.8 + - + +
98B THR* 3.1 14.6 + - + +
100B TYR* 1.3 78.1 - - - +
102B SER* 1.3 57.4 + - - +
104B HIS* 3.3 5.9 + - - +
105B ASN* 2.8 50.5 + - - +
130B MET* 4.4 11.2 - - + -
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 4.4 2.1 + - - -
87B PHE* 3.4 26.3 - - - -
98B THR 2.9 12.7 + - - -
99B ALA* 3.4 13.5 - - - -
100B TYR 3.1 0.2 - - - -
101B ILE* 1.3 77.3 - - - +
103B ILE* 1.3 56.2 + - - +
105B ASN* 3.2 2.9 + - - +
106B MET* 2.9 28.6 + - - +
254B GLY* 5.6 1.9 - - - -
257B ASN* 3.2 31.1 + - - +
258B ILE* 4.9 0.8 + - - -
261B CYS* 4.9 4.5 - - - -
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ALA 3.1 14.7 + - - +
100B TYR* 3.0 18.0 + - + +
102B SER* 1.3 73.9 - - - +
104B HIS* 1.3 67.7 + - - +
106B MET* 3.1 12.9 + - + +
107B CYS* 3.1 22.3 + - - -
134B ALA 5.0 1.3 - - - +
135B SER* 5.1 0.7 - - - -
136B TYR* 4.2 30.3 - - + +
171B SER* 3.8 28.5 - - - +
216B TRP* 4.0 20.6 - - + -
219B GLN* 4.2 2.9 - - - +
376B GLU* 5.0 10.8 - - - +
399B FAD 4.4 11.9 - - + +
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Residues in contact with HIS 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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65B GLY 3.4 18.0 + - - -
100B TYR* 2.8 27.4 + - + +
101B ILE 3.4 7.6 - - - +
103B ILE* 1.3 78.3 - - - +
105B ASN* 1.3 63.4 + - - +
107B CYS* 3.2 5.9 + - - +
108B ALA* 3.1 20.0 + - + +
127B LEU* 2.8 42.3 + - + +
130B MET* 3.5 26.1 - - + +
132B LYS 3.4 14.3 + - - -
133B PHE* 3.7 6.1 - + - -
134B ALA* 3.1 42.2 + - + +
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE 3.1 22.0 + - - -
65B GLY* 3.4 10.9 + - - -
66B GLY* 3.3 6.1 - - - -
67B VAL* 2.8 33.4 + - - +
68B TYR* 3.8 19.7 + - + -
69B ILE* 4.1 4.0 - - - +
87B PHE* 4.1 10.7 - - + -
101B ILE* 2.8 35.2 + - - +
102B SER* 3.4 8.1 - - - +
104B HIS* 1.3 79.5 + - - +
106B MET* 1.3 56.9 + - - +
108B ALA* 3.2 5.9 + - - +
109B TRP* 2.9 27.9 + - - +
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Residues in contact with MET 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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68B TYR* 3.4 15.2 + - - +
102B SER 2.9 13.1 + - - +
103B ILE* 3.1 14.3 + - + +
105B ASN* 1.3 76.1 - - - +
107B CYS* 1.3 62.9 + - - +
109B TRP* 3.1 6.9 + - + +
110B MET* 2.9 35.9 + - + +
136B TYR* 3.4 52.5 - - + -
250B GLY* 3.7 34.3 - - - +
251B LEU* 6.3 0.4 - - - -
254B GLY* 4.8 6.7 - - - +
376B GLU* 4.8 17.9 - - - +
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Residues in contact with CYS 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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103B ILE 3.1 18.3 + - - -
104B HIS 3.2 7.4 + - - +
106B MET* 1.3 75.5 - - - +
108B ALA* 1.3 64.0 + - - +
110B MET* 3.2 10.1 + - - +
111B ILE* 3.2 27.2 + - - +
127B LEU* 5.3 0.4 - - + -
134B ALA* 3.6 20.6 - - + -
135B SER* 3.5 36.1 - - - -
136B TYR* 3.5 17.3 - - - -
180B VAL* 3.7 19.0 - - + +
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Residues in contact with ALA 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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65B GLY 5.0 5.4 - - - +
69B ILE* 3.4 19.0 - - + +
104B HIS* 3.1 10.1 + - + +
105B ASN* 3.2 10.5 + - - +
107B CYS* 1.3 78.4 - - - +
109B TRP* 1.3 58.4 + - - +
111B ILE* 3.3 4.5 + - - +
112B ASP* 2.9 30.3 + - - +
124B CYS* 3.8 7.5 - - - -
127B LEU* 3.9 33.1 - - + +
128B CYS* 5.3 2.5 - - - -
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Residues in contact with TRP 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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68B TYR* 3.3 50.1 + + + -
69B ILE* 3.2 11.8 - - + +
80B ARG* 3.5 26.6 - - - +
105B ASN 2.9 8.7 + - - +
106B MET* 3.1 11.9 + - + +
108B ALA* 1.3 75.8 - - - +
110B MET* 1.3 72.0 + - + +
112B ASP* 4.2 3.4 - - - -
113B SER* 2.8 58.5 + - - -
114B PHE* 3.9 26.5 - + - -
249B ARG* 3.9 24.9 - - + -
250B GLY* 3.9 25.1 - - - -
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Residues in contact with MET 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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106B MET* 2.9 29.0 + - + +
107B CYS* 3.2 8.5 + - - +
109B TRP* 1.3 88.8 - - + +
111B ILE* 1.3 59.4 + - + +
114B PHE* 3.0 38.0 + - - +
136B TYR* 3.6 46.2 - - + +
180B VAL* 4.1 16.2 - - + -
182B MET* 4.4 0.4 - - + -
195B CYS* 5.4 2.5 - - - -
237B ILE* 3.8 3.6 - - + +
246B ILE* 3.5 43.3 - - + +
247B ALA* 4.1 2.2 - - - +
250B GLY* 3.9 16.4 - - - -
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Residues in contact with ILE 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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107B CYS 3.2 13.8 + - - +
108B ALA 3.7 5.8 - - - +
109B TRP 3.2 0.2 - - - -
110B MET* 1.3 79.3 - - + +
112B ASP* 1.3 57.9 + - - +
115B GLY* 2.8 28.8 + - - +
119B GLN* 3.9 23.8 - - + +
120B ARG* 3.7 3.3 - - - +
123B PHE* 3.8 25.6 - - + -
124B CYS* 3.8 15.7 - - - -
127B LEU* 4.3 14.6 - - + -
178B ILE* 4.4 9.0 - - + -
180B VAL* 4.5 8.7 - - + -
197B VAL* 4.0 19.5 - - + -
237B ILE* 4.2 23.3 - - + -
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Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR 4.6 1.7 - - - +
69B ILE* 3.7 16.5 - - + +
70B GLN* 3.0 37.4 + - - +
73B VAL* 4.0 1.9 - - - +
108B ALA 2.9 18.2 + - - +
109B TRP* 3.8 4.3 - - - +
111B ILE* 1.3 77.3 - - - +
113B SER* 1.3 64.8 + - - +
115B GLY 4.5 0.3 + - - +
120B ARG* 2.6 58.1 + - - +
124B CYS* 3.7 14.8 - - - -
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TRP* 2.8 57.6 + - - -
112B ASP* 1.3 76.6 + - - +
114B PHE* 1.3 79.1 + - - +
115B GLY 5.1 0.8 - - - +
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TRP* 3.9 29.6 - + - -
110B MET* 3.0 20.0 + - - +
113B SER* 1.3 88.0 - - - +
115B GLY* 1.3 64.9 + - - +
237B ILE* 3.6 13.0 - - + -
238B GLY* 3.6 18.2 + - - +
242B GLN* 3.3 20.7 + - - +
245B LEU* 3.8 27.4 - - + -
246B ILE* 3.8 32.3 - - + -
249B ARG* 4.2 16.8 - - + -
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Residues in contact with GLY 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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111B ILE 2.8 19.6 + - - -
112B ASP 4.6 0.7 - - - +
113B SER 5.1 0.5 - - - +
114B PHE* 1.3 82.4 - - - +
116B ASN* 1.3 65.9 + - - +
117B GLU* 5.1 0.7 - - - +
119B GLN* 3.3 15.7 - - - -
120B ARG* 3.8 13.3 - - - -
237B ILE* 3.9 10.0 - - - +
238B GLY 4.9 0.4 - - - -
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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