Contacts of the helix formed by residues 101 - 122 (chain B) in PDB entry 3UYT
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 SER 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 1.3 77.6 - - - +
102B LEU* 1.3 65.2 + - - +
103B LYS* 3.5 7.5 + - - +
104B THR* 3.2 14.6 + - - -
105B VAL* 3.1 20.9 + - - +
289B ASP* 2.6 34.6 + - - -
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Residues in contact with LEU 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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101B SER* 1.3 71.9 - - - +
103B LYS* 1.3 59.3 + - - +
105B VAL* 3.2 5.5 + - + +
106B LEU* 2.8 45.5 + - + +
207B ASN* 4.9 7.2 - - - +
244B TYR* 6.1 0.7 - - + -
245B PRO* 4.0 33.7 - - + -
248B PHE* 4.0 20.0 - - + -
276B LEU* 4.9 2.2 - - + -
280B GLN* 3.8 34.5 - - + +
282B PHE* 4.7 6.1 - - + -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B SER* 3.3 7.2 + - - +
102B LEU* 1.3 79.1 - - - +
104B THR* 1.3 53.6 + - - +
106B LEU* 3.6 2.2 - - - +
107B LEU* 2.7 55.2 + - + +
277B PHE* 3.9 7.6 - - + -
282B PHE* 3.5 50.6 - - + -
283B SER* 3.7 20.0 + - - +
285B ASP* 3.2 27.0 + - - -
287B VAL* 4.0 15.5 + - - +
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Residues in contact with THR 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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100B PHE* 4.0 15.5 - - + -
101B SER* 3.2 12.3 + - - -
102B LEU 3.2 0.4 - - - -
103B LYS* 1.3 76.8 - - - +
105B VAL* 1.3 61.4 + - - +
107B LEU* 4.3 6.2 - - - +
108B LEU* 2.8 56.0 + - + +
287B VAL 4.8 0.7 + - - -
288B PHE* 3.6 8.8 - - + -
289B ASP* 2.9 36.5 + - - +
290B TRP* 3.7 23.3 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 3.8 20.2 - - + +
101B SER 3.1 17.5 + - - +
102B LEU* 3.6 8.1 - - + +
104B THR* 1.3 77.8 - - - +
106B LEU* 1.3 50.2 + - - +
108B LEU* 3.5 8.1 - - - +
109B ALA* 2.7 35.0 + - - +
203B LEU* 4.0 22.4 - - + +
206B PHE* 4.2 13.0 - - + -
207B ASN* 3.7 20.2 - - - +
248B PHE* 3.7 33.0 - - + -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 2.8 32.7 + - + +
103B LYS 3.8 1.1 - - - +
105B VAL* 1.3 74.1 - - - +
107B LEU* 1.3 65.6 + - - +
108B LEU 3.1 0.9 - - - -
109B ALA* 3.9 3.0 - - + +
110B ASP* 3.0 24.8 + - - +
248B PHE* 4.2 11.0 - - + -
273B PHE* 3.4 45.6 - - + +
276B LEU* 3.6 33.4 - - + -
277B PHE* 3.8 35.9 - - + +
282B PHE* 4.6 6.3 - - + -
284B TYR* 5.3 0.5 + - - -
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Residues in contact with LEU 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 LYS* 2.7 40.7 + - + +
104B THR* 3.7 1.3 - - - +
106B LEU* 1.3 73.3 - - - +
108B LEU* 1.3 64.3 + - - +
110B ASP* 3.5 10.6 + - - +
111B GLN* 3.5 20.0 + - - +
277B PHE* 3.4 29.8 - - + -
283B SER 4.6 3.1 - - - +
284B TYR* 3.8 17.2 - - + -
286B TYR* 4.3 14.6 - - + +
287B VAL 3.8 29.2 - - - +
288B PHE* 3.5 37.2 - - + -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 4.0 25.8 - - + -
100B PHE* 4.2 13.2 - - + -
104B THR* 2.8 43.9 + - + +
105B VAL* 3.5 6.7 - - - +
107B LEU* 1.3 76.8 - - - +
109B ALA* 1.3 60.7 + - - +
111B GLN* 3.1 3.8 + - - +
112B MET* 2.8 43.5 + - - +
136B MET* 4.1 2.5 - - - -
145B VAL* 3.7 26.7 - - + -
203B LEU* 5.6 0.4 - - + -
206B PHE* 4.5 5.8 - - + -
288B PHE* 3.8 15.3 - - + -
290B TRP* 3.9 17.5 - - + -
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Residues in contact with ALA 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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105B VAL* 2.7 21.4 + - + +
106B LEU* 3.3 10.1 + - + +
108B LEU* 1.3 73.7 - - - +
110B ASP* 1.3 62.1 + - - +
112B MET* 4.4 8.9 - - - -
113B ILE* 3.0 33.1 + - + +
199B LEU* 5.6 0.2 - - - -
203B LEU* 4.0 28.2 - - + +
273B PHE* 4.0 21.3 - - + -
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Residues in contact with ASP 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 LEU 3.0 16.1 + - - +
107B LEU 3.7 5.6 - - - +
108B LEU 3.2 0.2 - - - -
109B ALA* 1.3 78.0 - - - +
111B GLN* 1.3 65.0 + - + +
113B ILE* 5.3 0.9 - - - -
114B SER* 3.1 25.5 + - - -
270B ARG* 3.5 36.0 - - - +
273B PHE* 5.5 6.7 - - + +
274B ARG* 4.3 22.5 + - - +
284B TYR* 4.4 26.3 + - + +
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Residues in contact with GLN 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 LEU* 3.5 11.8 + - - +
108B LEU 3.1 5.7 + - - +
110B ASP* 1.3 84.1 - - - +
112B MET* 1.3 59.5 + - - +
113B ILE 3.3 0.4 - - - -
114B SER* 3.1 7.2 + - - -
115B ARG* 2.7 67.1 + - - +
143B ASN 3.2 20.8 + - - -
144B LEU* 3.5 5.7 - - - +
145B VAL* 2.8 41.7 + - + +
286B TYR* 4.5 11.8 - - + -
288B PHE* 3.9 13.5 - - - -
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Residues in contact with MET 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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89B LEU* 3.8 21.3 - - + -
108B LEU* 2.8 38.3 + - - +
109B ALA* 4.1 3.8 - - - +
111B GLN* 1.3 70.0 - - - +
113B ILE* 1.3 66.3 + - - +
115B ARG* 3.3 3.1 + - - +
116B ILE* 3.0 30.1 + - - +
134B PHE* 3.4 56.7 - - + -
145B VAL* 4.4 7.2 - - + -
199B LEU* 3.5 34.5 - - + -
202B VAL* 4.5 6.1 - - + -
203B LEU* 4.5 6.5 - - - -
206B PHE* 4.4 11.7 - - + -
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Residues in contact with ILE 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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109B ALA* 3.0 20.2 + - - +
110B ASP* 5.3 0.2 - - - -
112B MET* 1.3 76.7 - - - +
114B SER* 1.3 57.2 + - - +
116B ILE* 3.4 5.3 + - - +
117B GLU* 2.8 28.1 + - - +
196B LEU* 5.2 7.0 - - + -
199B LEU* 3.9 19.5 - - + -
251B TYR* 4.0 13.9 - - + +
266B TYR* 4.2 21.9 - - + +
269B LEU* 3.9 19.1 - - + +
270B ARG* 3.9 27.1 - - + +
273B PHE* 3.7 33.4 - - + -
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Residues in contact with SER 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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110B ASP* 3.1 17.0 + - - -
111B GLN* 3.1 10.4 + - - -
113B ILE* 1.3 81.3 - - - +
115B ARG* 1.3 72.8 + - - +
117B GLU* 3.7 3.3 - - - +
118B TYR* 2.9 29.6 + - - +
270B ARG* 3.3 27.7 + - - +
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Residues in contact with ARG 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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63B VAL* 3.5 37.5 + - - +
64B GLY* 3.3 14.9 - - - -
65B ILE* 4.9 3.5 - - + +
111B GLN* 2.7 66.5 + - - +
112B MET* 3.7 8.1 - - - +
113B ILE 3.3 0.4 - - - -
114B SER* 1.3 93.2 - - - +
116B ILE* 1.3 54.8 + - - +
118B TYR* 3.1 6.3 + - - +
119B ILE* 2.8 41.3 + - - +
134B PHE* 4.5 4.3 - - + -
144B LEU* 2.9 18.2 - - - +
145B VAL* 3.0 19.4 + - + +
147B ILE* 4.1 28.9 - - + +
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Residues in contact with ILE 116 (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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112B MET 3.0 22.4 + - - +
113B ILE* 3.7 4.7 - - - +
115B ARG* 1.3 73.7 - - - +
117B GLU* 1.3 59.2 + - - +
119B ILE* 3.2 9.0 + - + +
120B HIS* 2.8 63.6 + - + +
126B HIS* 6.3 1.3 - - + -
129B VAL* 4.4 16.4 - - + -
134B PHE* 4.7 3.6 - - + -
147B ILE* 4.7 13.2 - - + -
195B ASP* 4.2 16.8 - - + +
196B LEU* 3.8 18.2 - - + -
199B LEU* 3.8 32.3 - - + -
266B TYR* 4.5 0.4 - - + -
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Residues in contact with GLU 117 (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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113B ILE 2.8 14.4 + - - +
114B SER* 3.7 4.4 - - - +
116B ILE* 1.3 76.8 - - - +
118B TYR* 1.3 54.5 + - - +
120B HIS* 3.3 1.7 + - - +
121B SER* 2.7 35.9 + - - -
266B TYR* 3.3 56.4 - - + +
267B SER* 5.1 0.3 + - - -
270B ARG* 2.7 38.8 + - - -
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Residues in contact with TYR 118 (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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59B MET* 3.1 39.7 + - - -
60B GLN 3.5 7.1 + - - -
61B GLY 4.3 0.3 - - - -
62B GLY* 3.3 27.6 + - - -
63B VAL 5.3 4.7 - - - +
65B ILE* 4.0 23.1 - - + -
114B SER 2.9 19.1 + - - +
115B ARG* 3.4 6.7 - - - +
117B GLU* 1.3 75.9 - - - +
119B ILE* 1.3 67.1 + - - +
121B SER* 2.6 26.8 + - - -
122B LYS* 3.1 44.0 + - + +
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Residues in contact with ILE 119 (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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59B MET* 3.6 31.4 - - + +
65B ILE* 4.9 2.9 - - + -
115B ARG 2.8 18.4 + - - +
116B ILE* 3.5 10.1 - - + +
118B TYR* 1.3 75.5 - - - +
120B HIS* 1.3 61.4 + - + +
122B LYS* 2.9 23.0 + - - +
124B PHE* 3.4 31.2 + - + +
125B ILE* 4.5 6.1 - - - +
126B HIS* 4.4 9.9 - - + +
147B ILE* 3.2 43.1 - - + -
150B PHE* 3.9 21.8 - - + -
195B ASP* 5.6 0.2 - - - +
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Residues in contact with HIS 120 (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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116B ILE* 2.8 35.6 + - + +
117B GLU 3.5 3.8 - - - +
119B ILE* 1.3 75.8 - - + +
121B SER* 1.3 56.4 + - - +
122B LYS 2.8 5.2 - - - -
123B ASN* 2.8 18.9 + - - -
124B PHE 2.9 29.2 - - - -
125B ILE* 3.8 5.4 - - - +
156B TYR* 2.9 18.1 + - - +
157B ARG* 3.6 0.9 + - - -
192B ARG* 3.5 46.0 - - + +
195B ASP* 2.8 25.4 + - + -
196B LEU* 4.8 1.6 - - + -
266B TYR* 2.3 41.6 + + + +
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU* 2.7 21.8 + - - -
118B TYR* 2.6 30.5 + - - -
120B HIS* 1.3 72.4 - - - +
122B LYS* 1.3 67.6 + - - +
123B ASN* 3.3 3.0 + - - +
157B ARG* 3.3 20.1 + - - +
266B TYR* 5.9 0.2 - - - -
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Residues in contact with LYS 122 (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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58B MET* 3.6 27.4 + - + +
59B MET* 3.7 26.2 - - + -
60B GLN 5.5 0.6 + - - -
118B TYR* 3.2 47.2 + - + +
119B ILE 2.9 9.8 + - - +
120B HIS 2.8 1.4 - - - -
121B SER* 1.3 86.4 - - - +
123B ASN* 1.3 73.0 + - - +
124B PHE* 3.1 20.5 - - - -
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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