Contacts of the helix formed by residues 91 - 116 (chain A) in PDB entry 3ORY
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 LYS 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TYR* 4.0 6.7 - - + -
84A ASP* 2.8 40.8 + - - +
86A LYS* 4.5 8.3 - - + -
87A PRO 3.7 13.5 - - - +
88A PRO* 3.3 11.4 + - + +
89A GLU 3.5 0.8 - - - -
90A LEU* 1.3 75.6 - - - +
92A ALA* 1.3 63.7 + - - +
93A ARG 3.4 2.2 - - - -
94A GLU* 3.3 39.7 + - + +
95A ILE* 3.1 25.5 + - - +
156A GLU* 4.1 12.5 - - - +
240A ASP* 2.9 28.5 + - - +
354A PO4 4.2 13.2 + - - -
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 3.5 6.6 + - - +
91A LYS* 1.3 72.9 - - - +
93A ARG* 1.3 63.1 + - - +
95A ILE* 3.4 8.7 + - - +
96A GLU* 3.0 24.3 + - - +
240A ASP* 3.5 28.5 + - + +
243A PRO* 3.7 17.3 - - + +
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Residues in contact with ARG 93 (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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-1A ASP* 4.8 1.0 + - - -
1A MET 4.9 0.4 - - - +
2A GLY* 2.9 43.3 + - - -
3A VAL* 4.8 2.7 - - + +
4A ASP 5.3 1.4 - - - +
92A ALA* 1.3 73.8 - - - +
94A GLU* 1.3 61.9 + - + +
96A GLU* 3.2 9.6 + - - -
97A ARG* 2.8 63.0 + - + +
179A ASP* 5.8 0.9 - - - +
237A LEU* 3.1 33.7 + - - +
238A GLY* 3.2 24.5 + - - +
239A THR* 3.9 1.8 - - - -
240A ASP* 2.9 32.5 + - - +
243A PRO* 2.7 39.6 + - - -
244A ASP 4.6 1.2 - - - -
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.3 33.8 - - + +
33A TYR* 3.3 24.0 - - - +
37A TYR* 3.3 30.0 + - + +
88A PRO* 4.1 5.6 - - - +
91A LYS* 3.3 36.4 + - + +
93A ARG* 1.3 77.7 - - - +
95A ILE* 1.3 60.0 + - + +
97A ARG* 4.4 0.4 - - - -
98A ARG* 3.0 25.5 + - - +
240A ASP* 4.4 0.6 + - - -
354A PO4 2.4 36.7 + - - +
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 5.8 2.5 - - - +
88A PRO 4.2 7.0 - - - +
89A GLU* 3.0 35.7 - - - +
90A LEU* 4.5 1.3 - - - -
91A LYS 3.1 24.8 + - - +
92A ALA* 3.8 6.3 - - - +
93A ARG 3.2 0.2 - - - -
94A GLU* 1.3 75.7 - - + +
96A GLU* 1.3 61.6 + - - +
98A ARG* 3.4 10.7 + - - +
99A LYS* 3.0 30.0 + - + +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA 3.0 18.1 + - - +
93A ARG* 3.3 9.3 + - - +
95A ILE* 1.3 75.8 - - - +
97A ARG* 1.3 103.7 + - - +
99A LYS* 3.4 6.7 + - + +
100A ALA* 3.0 30.8 + - - +
243A PRO* 3.2 25.8 - - + +
244A ASP* 3.3 30.6 - - - +
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Residues in contact with ARG 97 (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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-1A ASP* 3.2 41.1 + - - +
1A MET* 3.7 29.8 - - + -
2A GLY 3.8 0.4 - - - +
93A ARG* 2.8 55.6 + - - +
94A GLU 3.7 4.7 - - - +
96A GLU* 1.3 106.7 + - - +
98A ARG* 1.3 65.7 + - - +
100A ALA* 3.2 16.8 + - - +
101A VAL* 3.0 30.2 + - - +
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.3 12.4 - - + +
37A TYR* 5.0 8.7 - - + +
94A GLU 3.0 17.8 + - - +
95A ILE* 3.7 10.3 + - - +
96A GLU 3.4 0.2 - - - -
97A ARG* 1.3 76.7 - - - +
99A LYS* 1.3 65.2 + - - +
101A VAL* 3.3 6.8 + - - +
102A LYS* 3.0 60.5 + - + +
127A MET* 5.7 1.6 - - - +
128A SER* 3.2 36.4 + - - -
129A ALA 4.0 9.8 + - - +
130A LYS* 3.4 51.3 - - - +
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Residues in contact with LYS 99 (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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95A ILE* 3.0 20.9 + - + +
96A GLU* 3.7 7.2 - - - +
98A ARG* 1.3 78.9 - - - +
100A ALA* 1.3 56.8 + - - +
102A LYS* 3.4 12.8 + - + +
103A GLU* 3.0 53.5 + - + +
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Residues in contact with ALA 100 (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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96A GLU* 3.0 22.3 + - - +
97A ARG* 3.2 24.7 + - - +
99A LYS* 1.3 77.2 - - - +
101A VAL* 1.3 62.2 + - + +
103A GLU* 3.4 9.6 + - - +
104A GLU* 3.1 24.4 + - - +
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Residues in contact with VAL 101 (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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-2A VAL* 5.5 16.8 - - + -
-1A ASP* 5.0 11.9 - - + +
1A MET* 6.2 2.2 - - - -
97A ARG* 3.0 21.2 + - - +
98A ARG* 3.3 6.3 + - - +
100A ALA* 1.3 75.0 - - + +
102A LYS* 1.3 54.5 + - - +
104A GLU* 3.3 7.1 + - - +
105A ALA* 2.8 38.4 + - + +
128A SER* 3.6 20.0 - - - +
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ARG* 3.0 63.8 + - - +
99A LYS* 3.6 9.4 - - - +
101A VAL* 1.3 77.2 - - - +
103A GLU* 1.3 57.5 + - + +
105A ALA* 3.5 6.5 + - - +
106A ALA* 2.9 31.1 + - - +
128A SER* 3.7 22.7 + - - +
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Residues in contact with GLU 103 (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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99A LYS* 3.0 55.6 + - + +
100A ALA* 3.8 7.8 - - - +
101A VAL 3.4 0.2 - - - -
102A LYS* 1.3 76.5 - - + +
104A GLU* 1.3 61.5 + - - +
106A ALA* 3.5 6.7 + - - +
107A LYS* 3.2 22.3 + - - +
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Residues in contact with GLU 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 ALA 3.1 17.5 + - - +
101A VAL* 3.6 6.3 - - - +
103A GLU* 1.3 75.3 - - - +
105A ALA* 1.3 65.0 + - - +
107A LYS* 3.3 25.6 + - - +
108A LYS* 3.1 53.5 + - + +
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Residues in contact with ALA 105 (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 VAL* 2.8 26.0 + - + +
102A LYS* 3.8 6.7 - - - +
104A GLU* 1.3 72.4 - - - +
106A ALA* 1.3 52.5 + - - +
108A LYS* 4.5 5.2 - - - -
109A TYR* 2.8 35.5 + - - +
124A TYR* 3.6 29.8 - - + +
126A MET 5.2 6.1 - - - +
128A SER* 5.9 0.9 - - - +
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Residues in contact with ALA 106 (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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102A LYS 2.9 18.8 + - - +
103A GLU* 3.7 7.4 - - - +
104A GLU 3.3 0.2 - - - -
105A ALA* 1.3 73.5 - - - +
107A LYS* 1.3 64.8 + - - +
109A TYR* 3.5 7.8 + - - +
110A GLU* 3.1 24.0 + - - +
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Residues in contact with LYS 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 GLU 3.2 11.1 + - - +
104A GLU* 3.3 35.2 + - - +
106A ALA* 1.3 78.2 - - - +
108A LYS* 1.3 64.0 + - - +
110A GLU* 3.3 10.3 + - - +
111A GLU* 3.1 54.4 + - + +
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Residues in contact with LYS 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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104A GLU* 3.1 41.0 + - + +
105A ALA* 3.8 1.3 - - - +
107A LYS* 1.3 82.6 - - - +
109A TYR* 1.3 65.0 + - - +
111A GLU* 3.4 24.9 + - - +
112A ALA* 3.0 24.4 + - - +
124A TYR* 3.4 55.9 - - + -
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Residues in contact with TYR 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 ALA 2.8 20.9 + - - +
106A ALA* 3.8 7.6 - - - +
107A LYS 3.4 0.2 - - - -
108A LYS* 1.3 72.7 - - - +
110A GLU* 1.3 61.2 + - - +
112A ALA* 3.3 4.7 + - - +
113A VAL* 3.0 49.6 + - + +
121A ALA* 3.3 41.5 - - + +
124A TYR* 3.6 13.4 - - + +
125A ALA* 3.7 20.0 - - + -
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Residues in contact with GLU 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 ALA 3.1 17.9 + - - +
107A LYS* 3.5 8.9 - - - +
108A LYS 3.3 0.2 - - - -
109A TYR* 1.3 82.5 - - + +
111A GLU* 1.3 58.9 + - + +
113A VAL* 3.4 6.3 + - - +
114A GLN* 3.0 39.3 + - + +
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Residues in contact with GLU 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 LYS* 3.1 39.2 + - + +
108A LYS* 3.5 39.3 + - - +
109A TYR 3.3 0.4 - - - -
110A GLU* 1.3 79.3 - - + +
112A ALA* 1.3 57.2 + - - +
114A GLN* 3.4 9.9 + - - +
115A SER* 2.9 31.8 + - - -
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Residues in contact with ALA 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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108A LYS 3.0 17.3 + - - +
109A TYR* 3.6 4.5 - - - +
111A GLU* 1.3 74.5 - - - +
113A VAL* 1.3 59.5 + - - +
115A SER* 3.3 7.1 + - - -
116A GLY 2.9 8.3 + - - -
117A ASP* 2.9 31.5 + - + +
120A LEU* 3.8 19.3 - - + +
121A ALA* 3.6 30.3 - - - +
124A TYR* 4.6 1.1 - - + -
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Residues in contact with VAL 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 TYR* 3.0 56.6 + - + +
110A GLU* 3.8 6.5 - - - +
112A ALA* 1.3 74.4 - - - +
114A GLN* 1.3 64.6 + - - +
116A GLY* 3.3 12.1 + - - -
121A ALA* 4.7 7.2 - - + -
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Residues in contact with GLN 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 GLU* 3.0 28.6 + - + +
111A GLU* 3.7 9.5 - - - +
113A VAL* 1.3 79.5 - - - +
115A SER* 1.3 58.9 + - - +
116A GLY 3.7 0.2 + - - -
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU 2.9 16.4 + - - -
112A ALA* 3.3 10.9 + - - -
114A GLN* 1.3 76.2 - - - +
116A GLY* 1.3 60.1 + - - +
117A ASP* 3.6 15.1 - - - +
120A LEU* 5.6 1.2 - - - +
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Residues in contact with GLY 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 ALA 2.9 5.4 + - - -
113A VAL* 3.3 11.4 + - - -
114A GLN 3.3 0.6 - - - -
115A SER* 1.3 80.5 - - - +
117A ASP* 1.3 59.4 + - - +
118A LEU* 3.6 5.2 + - - +
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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