Contacts of the helix formed by residues 101 - 122 (chain A) in PDB entry 3UYS
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PHE* 1.3 77.1 - - - +
102A LEU* 1.3 66.0 + - - +
103A LYS* 3.7 8.8 + - - +
104A THR 3.2 13.7 + - - -
105A VAL* 3.1 20.4 + - - +
207A ASN* 5.7 0.2 - - - -
289A ASP* 2.7 35.0 + - - -
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A SER* 1.3 73.8 - - - +
103A LYS* 1.3 63.4 + - - +
105A VAL* 3.1 7.1 + - + +
106A LEU* 3.0 43.7 + - + +
207A ASN* 4.9 4.7 - - - +
244A TYR* 6.2 1.1 - - + -
245A PRO* 4.0 22.2 - - + -
248A PHE* 3.8 28.0 - - + -
276A LEU* 4.5 2.0 - - + -
280A GLN* 3.9 36.8 - - + +
282A PHE* 3.9 8.3 - - + -
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 3.2 8.2 - - - +
102A LEU* 1.3 79.4 - - - +
104A THR* 1.3 57.1 + - - +
106A LEU* 3.4 3.1 + - - +
107A LEU* 2.9 46.6 + - + +
277A PHE* 4.1 1.1 - - + -
282A PHE* 3.5 47.4 - - + -
283A SER 3.6 17.6 + - - +
285A ASP* 2.7 42.8 + - - -
287A VAL* 4.0 16.3 + - - +
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Residues in contact with THR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PHE* 3.7 30.7 - - + -
101A SER* 3.2 14.0 + - - -
103A LYS* 1.3 77.3 - - - +
105A VAL* 1.3 64.9 + - - +
107A LEU* 3.4 8.7 + - - +
108A LEU* 3.0 32.9 + - + +
287A VAL 4.6 1.6 + - - -
288A PHE* 3.6 8.7 - - + -
289A ASP* 2.9 36.3 + - - +
290A TRP* 3.8 22.4 - - + -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 4.0 19.1 - - + +
101A SER 3.1 16.3 + - - +
102A LEU* 3.1 7.1 + - - +
104A THR* 1.3 75.9 - - - +
106A LEU* 1.3 53.4 + - - +
108A LEU* 3.3 7.6 + - - +
109A ALA* 2.6 37.5 + - - +
203A LEU* 3.6 33.8 - - + +
206A PHE* 4.3 11.4 - - + -
207A ASN* 3.4 20.2 - - - +
248A PHE* 3.8 24.9 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 3.0 37.5 + - + +
103A LYS 3.8 1.3 - - - +
105A VAL* 1.3 74.3 - - - +
107A LEU* 1.3 64.4 + - - +
109A ALA* 3.7 3.5 - - + +
110A ASP* 3.2 22.0 + - - +
248A PHE* 3.8 19.7 - - + -
273A PHE* 3.8 40.4 - - + +
276A LEU* 4.0 17.0 - - + -
277A PHE* 3.5 45.8 - - + +
282A PHE* 4.2 6.1 - - + -
284A TYR* 4.7 3.8 + - - -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 2.9 37.3 + - + +
104A THR* 3.7 2.0 - - - +
105A VAL 3.3 0.2 - - - -
106A LEU* 1.3 76.0 - - - +
108A LEU* 1.3 66.1 + - - +
110A ASP* 3.5 8.7 + - - +
111A GLN* 3.7 18.5 + - - +
277A PHE* 3.7 13.5 - - + -
283A SER 4.4 1.8 - - - +
284A TYR* 3.5 39.9 - - + -
286A TYR* 4.2 13.7 - - + +
287A VAL 3.9 27.1 - - - +
288A PHE* 3.5 34.5 - - + -
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 4.2 22.0 - - + -
100A PHE* 3.8 30.3 - - + -
104A THR* 3.0 32.1 + - + +
105A VAL* 3.6 4.3 - - - +
107A LEU* 1.3 75.3 - - - +
109A ALA* 1.3 66.4 + - - +
110A ASP 3.1 0.5 + - - -
111A GLN* 3.2 2.9 + - - +
112A MET* 3.0 39.5 + - - +
145A VAL* 3.9 21.5 - - + -
203A LEU* 5.3 1.6 - - + -
206A PHE* 4.3 8.5 - - + -
288A PHE* 3.6 21.8 - - + -
290A TRP* 3.7 16.6 - - + -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL 2.6 22.3 + - - +
106A LEU* 3.7 11.0 - - + +
108A LEU* 1.3 74.4 - - - +
110A ASP* 1.3 62.6 + - - +
112A MET* 4.2 4.2 - - - +
113A ILE* 3.0 31.0 + - - +
199A LEU* 5.6 0.4 - - - -
203A LEU* 3.6 33.6 - - + +
273A PHE* 4.0 19.7 - - + -
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Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU 3.2 13.3 + - - +
107A LEU 3.8 9.2 - - - +
108A LEU 3.1 1.0 + - - -
109A ALA* 1.3 78.0 - - - +
111A GLN* 1.3 69.6 + - + +
113A ILE* 3.5 1.1 + - - +
114A SER* 3.1 24.6 + - - -
270A ARG* 3.3 36.5 - - - +
273A PHE* 5.8 3.5 - - + +
274A ARG* 3.7 17.1 + - - -
284A TYR* 4.7 18.6 + - + +
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Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.7 10.4 + - - +
108A LEU 3.2 3.0 + - - +
110A ASP* 1.3 83.6 - - + +
112A MET* 1.3 60.3 + - - +
114A SER* 3.2 3.8 + - - -
115A ARG* 2.9 56.6 + - - +
143A ASN 3.2 21.2 + - - +
144A LEU* 3.5 5.3 - - - +
145A VAL* 2.6 53.2 + - + +
286A TYR* 5.1 12.9 - - + -
288A PHE* 3.9 13.5 - - - -
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Residues in contact with MET 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.6 17.3 - - + -
108A LEU* 3.0 39.3 + - - +
109A ALA 4.2 2.5 - - - +
111A GLN* 1.3 72.5 - - - +
113A ILE* 1.3 68.3 + - - +
115A ARG* 2.9 19.7 + - - +
116A ILE* 3.0 16.5 + - - +
134A PHE* 3.4 48.2 - - + -
145A VAL* 4.2 12.6 - - + -
199A LEU* 3.7 34.5 - - + -
202A VAL* 4.2 15.0 - - + -
203A LEU* 4.5 7.0 - - - -
206A PHE* 4.2 1.3 - - + -
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Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ALA* 3.0 19.9 + - - +
110A ASP 3.8 3.6 - - - +
112A MET* 1.3 77.5 - - - +
114A SER* 1.3 57.4 + - - +
116A ILE* 3.1 5.9 + - - +
117A GLU* 2.9 26.9 + - - +
196A LEU* 4.6 7.9 - - + -
199A LEU* 3.6 21.3 - - + -
251A TYR* 4.2 5.8 - - + +
266A TYR* 4.2 24.2 - - + +
269A LEU* 4.1 17.7 - - + -
270A ARG* 3.9 31.6 - - + +
273A PHE* 3.9 31.0 - - + -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP* 3.1 14.5 + - - -
111A GLN* 3.2 11.4 + - - -
112A MET 3.1 0.4 - - - -
113A ILE* 1.3 78.5 - - - +
115A ARG* 1.3 72.3 + - - +
117A GLU* 3.9 6.2 - - - +
118A TYR* 3.2 21.8 + - - +
270A ARG* 3.0 31.0 + - - +
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Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 3.1 41.8 + - - +
64A GLY* 3.1 21.0 - - - -
65A ILE* 5.1 1.7 - - - +
111A GLN* 2.9 60.3 + - - +
112A MET* 2.9 9.8 + - - +
114A SER* 1.3 91.4 + - - +
116A ILE* 1.3 62.2 + - - +
118A TYR* 3.2 6.3 + - - +
119A ILE* 3.0 34.1 + - - +
134A PHE* 4.7 5.4 - - + -
144A LEU* 4.5 5.7 - - - +
145A VAL* 2.6 31.0 + - + +
147A ILE* 4.4 26.2 - - + +
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Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A MET 3.0 9.9 + - - +
113A ILE 3.5 7.4 - - - +
115A ARG* 1.3 77.0 - - - +
117A GLU* 1.3 56.1 - - - +
119A ILE* 3.3 8.1 + - + +
120A HIS* 3.0 62.9 + - + +
126A HIS* 6.0 1.1 - - + -
129A VAL* 4.1 20.6 - - + -
134A PHE* 4.6 5.2 - - + -
147A ILE* 4.7 11.4 - - + -
195A ASP* 3.8 27.1 - - + +
196A LEU* 3.7 19.1 - - + -
199A LEU* 3.9 29.2 - - + -
266A TYR* 4.6 0.2 - - + -
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE 2.9 12.2 + - - +
114A SER* 3.9 5.1 - - - +
115A ARG 3.3 0.2 - - - -
116A ILE* 1.3 76.6 - - - +
118A TYR* 1.3 60.4 + - - +
120A HIS* 3.3 2.4 + - - +
121A SER* 2.8 30.2 + - - -
266A TYR* 3.3 52.7 + - + +
270A ARG* 2.9 37.2 + - - -
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Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A MET* 2.6 43.3 + - - -
60A GLN 3.6 3.1 + - - -
62A GLY* 3.4 23.3 + - - -
63A VAL 5.0 8.1 - - - +
65A ILE* 3.5 28.9 - - + -
114A SER 3.2 15.5 + - - +
115A ARG* 3.2 10.3 + - - +
117A GLU* 1.3 75.8 - - - +
119A ILE* 1.3 68.9 + - - +
121A SER* 2.8 29.4 + - - -
122A LYS* 3.1 39.0 + - - +
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A MET* 3.7 22.7 - - + +
65A ILE* 4.4 7.4 - - + -
115A ARG 3.0 13.2 + - - +
116A ILE* 3.3 8.0 + - - +
118A TYR* 1.3 76.4 - - - +
120A HIS* 1.3 67.0 + - + +
122A LYS* 3.0 13.2 + - - +
124A PHE* 3.0 38.1 + - + +
125A ILE* 4.2 9.6 - - - +
126A HIS* 4.3 5.8 - - + +
147A ILE* 3.2 39.0 - - + -
150A PHE* 3.3 34.5 - - + -
195A ASP* 5.2 0.2 - - - +
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Residues in contact with HIS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 3.0 40.9 + - + +
117A GLU 3.6 2.7 - - - +
119A ILE* 1.3 74.9 - - + +
121A SER* 1.3 61.3 + - - +
122A LYS 3.0 5.6 - - - -
123A ASN 3.0 9.4 + - - -
124A PHE 3.2 18.2 - - - -
125A ILE* 3.9 3.8 - - - -
156A TYR* 2.7 22.3 + - - -
157A ARG* 3.7 1.9 + - - -
192A ARG* 3.2 54.2 - - + +
195A ASP* 2.8 26.7 + - + -
196A LEU* 4.8 0.9 - - + -
266A TYR* 2.6 33.4 + + + +
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 2.8 20.0 + - - -
118A TYR* 2.8 26.4 + - - -
120A HIS* 1.3 76.4 - - - +
122A LYS* 1.3 66.3 + - - +
123A ASN* 3.3 2.5 + - - +
157A ARG* 3.6 18.0 + - - +
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Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A MET* 3.9 23.7 + - + +
59A MET* 3.7 20.0 - - + -
60A GLN 5.5 1.1 + - - -
118A TYR* 3.1 48.6 + - + +
119A ILE 3.0 8.8 + - - +
120A HIS 3.0 1.8 - - - -
121A SER* 1.3 86.1 - - - +
123A ASN* 1.3 72.1 + - - +
124A PHE* 3.3 20.0 - - + -
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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