Contacts of the helix formed by residues 91 - 113 (chain B) in PDB entry 3D0O
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 THR 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLN* 3.7 4.8 + - - +
89B GLY 4.7 4.5 - - - +
90B GLU* 1.3 77.6 - - - +
92B ARG* 1.3 65.9 + - - +
93B LEU* 3.4 11.7 + - - +
94B ASP* 2.9 41.0 + - - +
95B LEU* 2.9 10.2 + - - +
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Residues in contact with ARG 92 (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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86B GLN* 3.9 19.1 - - - +
91B THR* 1.3 73.8 - - - +
93B LEU* 1.3 62.6 + - - +
95B LEU* 3.1 11.2 + - + +
96B VAL* 3.0 28.8 + - + +
178B GLU* 4.8 10.9 + - - -
181B ASP* 3.2 35.7 + - - +
305B THR* 5.9 4.8 - - - +
309B ILE* 5.5 19.8 - - + +
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Residues in contact with LEU 93 (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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91B THR* 3.0 10.9 + - - +
92B ARG* 1.3 79.0 - - - +
94B ASP* 1.3 64.4 + - - +
96B VAL* 3.3 8.9 + - + -
97B SER* 2.9 31.8 + - - +
309B ILE* 3.9 10.7 - - + +
312B GLU* 3.2 58.1 - - + +
313B ALA* 3.8 20.9 - - + +
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLY 4.0 3.5 - - - +
90B GLU* 3.5 24.9 - - + +
91B THR* 2.9 42.9 + - - +
93B LEU* 1.3 78.5 - - - +
95B LEU* 1.3 56.6 + - - +
97B SER* 3.2 6.8 + - - -
98B LYS* 3.0 30.8 + - - +
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Residues in contact with LEU 95 (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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84B ALA 3.3 27.1 - - - +
85B ALA* 3.8 1.6 - - - -
86B GLN* 3.5 47.8 - - + +
90B GLU* 4.4 4.9 + - - +
91B THR 2.9 11.1 + - - +
92B ARG* 3.1 14.3 + - + +
94B ASP* 1.3 73.5 - - - +
96B VAL* 1.3 67.1 + - + +
98B LYS* 3.6 6.5 + - - +
99B ASN* 2.9 40.7 + - - +
124B ASN 5.2 3.4 - - - +
125B PRO* 4.5 19.2 - - + +
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Residues in contact with VAL 96 (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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92B ARG* 3.0 18.4 + - + +
93B LEU* 3.3 10.1 + - + +
95B LEU* 1.3 77.2 - - + +
97B SER* 1.3 57.8 + - - +
99B ASN* 3.3 3.4 + - - +
100B LEU* 2.8 51.4 + - + +
125B PRO* 4.1 25.8 - - + -
128B ILE* 3.9 18.2 - - + -
129B LEU* 5.1 1.0 - - - +
309B ILE* 3.8 29.8 - - + -
310B MET* 5.8 0.2 - - - -
313B ALA* 4.2 14.6 - - + -
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Residues in contact with SER 97 (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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93B LEU* 2.9 28.7 + - - +
94B ASP* 3.8 7.4 - - - -
96B VAL* 1.3 75.7 - - - +
98B LYS* 1.3 62.8 + - - +
100B LEU* 3.4 11.1 + - - +
101B LYS* 3.1 45.0 + - - +
313B ALA* 4.6 10.0 - - - +
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Residues in contact with LYS 98 (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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84B ALA* 3.7 22.8 - - + +
85B ALA 2.6 29.4 + - - -
87B LYS* 4.0 10.7 - - - +
90B GLU* 2.8 36.9 + - - +
94B ASP 3.0 13.9 + - - +
95B LEU* 3.7 12.6 - - - +
96B VAL 3.3 0.2 - - - -
97B SER* 1.3 77.8 - - - +
99B ASN* 1.3 60.5 + - - +
101B LYS* 3.6 10.7 + - - +
102B ILE* 3.3 28.3 + - + +
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Residues in contact with ASN 99 (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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83B GLY* 3.3 12.7 - - - -
84B ALA* 2.7 51.1 + - - +
95B LEU* 2.9 30.5 + - - +
96B VAL 4.1 1.8 - - - +
98B LYS* 1.3 75.7 - - - +
100B LEU* 1.3 61.2 + - - +
102B ILE* 3.3 4.4 + - - +
103B PHE* 2.8 34.8 + - + +
123B THR* 4.2 5.9 - - - +
124B ASN 4.3 10.6 - - - +
125B PRO* 4.7 2.2 - - + +
129B LEU* 3.8 23.8 - - + -
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Residues in contact with LEU 100 (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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96B VAL* 2.8 39.8 + - + +
97B SER* 3.6 8.7 - - - +
99B ASN* 1.3 77.9 - - - +
101B LYS* 1.3 57.4 + - + +
103B PHE* 3.4 1.7 + - - +
104B LYS* 2.9 30.5 + - - +
128B ILE* 4.5 10.1 - - + -
129B LEU* 4.1 11.2 - - + +
132B ALA* 3.4 32.3 - - + -
136B PHE* 3.6 15.4 - - + -
313B ALA* 3.9 19.3 - - + -
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Residues in contact with LYS 101 (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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97B SER* 3.1 37.6 + - - +
98B LYS* 3.8 8.7 - - - +
99B ASN 3.3 0.2 - - - -
100B LEU* 1.3 77.5 - - + +
102B ILE* 1.3 64.0 + - + +
104B LYS* 3.3 7.9 + - - +
105B SER* 3.3 20.6 + - - -
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Residues in contact with ILE 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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82B ALA* 5.3 0.9 - - + -
83B GLY* 4.1 15.9 - - - +
84B ALA* 3.9 33.9 - - + +
98B LYS* 3.3 18.4 + - + +
99B ASN* 3.3 9.8 + - - +
101B LYS* 1.3 78.7 - - + +
103B PHE* 1.3 61.7 + - + +
105B SER* 3.2 8.4 + - - -
106B ILE* 2.9 47.7 + - + +
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Residues in contact with PHE 103 (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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80B ILE* 3.5 31.0 - - + -
82B ALA 3.5 21.3 - - - -
83B GLY* 5.2 0.4 - - - -
99B ASN* 2.8 25.6 + - + +
100B LEU 3.9 3.4 - - - +
102B ILE* 1.3 75.8 - - + +
104B LYS* 1.3 65.8 + - - +
106B ILE* 4.4 7.0 - - + +
107B VAL* 2.9 37.5 + - + +
121B VAL* 4.3 9.0 - - + -
123B THR* 3.5 28.3 - - + -
129B LEU* 3.8 34.1 - - + -
132B ALA* 5.2 1.1 - - + -
133B THR* 3.2 27.8 - - - -
136B PHE* 3.9 11.7 - - + -
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Residues in contact with LYS 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 LEU 2.9 18.4 + - - +
101B LYS* 3.7 8.5 - - - +
102B ILE 3.3 0.4 - - - -
103B PHE* 1.3 75.3 - - - +
105B SER* 1.3 58.1 + - - +
107B VAL* 4.5 0.5 - - - +
108B GLY* 3.0 27.4 + - - -
136B PHE* 3.5 46.9 + - + +
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Residues in contact with SER 105 (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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69B TYR* 5.5 1.0 + - - -
101B LYS 3.3 8.1 + - - -
102B ILE* 3.2 10.3 + - - -
104B LYS* 1.3 78.4 - - - +
106B ILE* 1.3 67.1 + - - +
108B GLY* 3.3 2.1 + - - -
109B GLU* 3.0 33.9 + - - +
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Residues in contact with ILE 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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12B ILE* 3.8 32.8 - - + -
69B TYR* 3.4 24.0 - - - +
80B ILE* 3.9 28.3 - - + -
82B ALA* 4.0 23.8 - - + +
102B ILE* 2.9 43.2 + - + +
103B PHE* 4.1 8.3 - - + +
105B SER* 1.3 72.5 - - - +
107B VAL* 1.3 65.1 + - - +
109B GLU* 3.2 3.6 + - - +
110B VAL* 2.9 23.6 + - + +
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Residues in contact with VAL 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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80B ILE* 4.3 15.0 - - + -
103B PHE* 2.9 29.2 + - + +
106B ILE* 1.3 73.0 - - - +
108B GLY* 1.3 56.8 + - - +
110B VAL* 3.2 5.9 + - - +
111B MET* 2.8 34.9 + - + +
119B PHE* 4.3 6.5 - - + -
133B THR* 3.9 33.0 - - + +
136B PHE* 3.8 18.4 - - + +
137B SER* 3.8 35.0 - - - +
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Residues in contact with GLY 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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104B LYS* 3.0 22.2 + - - -
105B SER* 3.6 1.6 - - - -
107B VAL* 1.3 77.7 - - - +
109B GLU* 1.3 61.7 + - - +
111B MET* 3.4 4.3 + - - +
112B ALA* 3.1 23.9 + - - +
136B PHE* 5.8 0.4 - - - +
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Residues in contact with GLU 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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69B TYR* 3.5 49.8 - - + +
105B SER* 3.0 29.1 + - - +
106B ILE 3.7 2.7 - - - +
108B GLY* 1.3 76.7 - - - +
110B VAL* 1.3 64.8 + - - +
112B ALA* 3.4 10.3 + - - +
113B SER* 3.3 17.3 + - - -
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Residues in contact with VAL 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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12B ILE* 3.5 30.5 - - + -
69B TYR* 4.0 9.9 - - + -
72B CYS* 4.1 11.2 - - + -
78B VAL* 4.2 9.9 - - + -
106B ILE* 2.9 21.7 + - + +
107B VAL 3.6 4.3 - - - +
109B GLU* 1.3 74.3 - - - +
111B MET* 1.3 64.8 + - - +
113B SER* 2.6 28.1 + - - -
115B PHE* 3.4 27.1 - - + +
119B PHE* 3.5 30.7 - - + -
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Residues in contact with MET 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 VAL* 2.8 32.3 + - + +
108B GLY* 4.1 4.3 - - - +
110B VAL* 1.3 76.8 - - - +
112B ALA* 1.3 56.9 + - - +
114B LYS* 3.0 21.1 + - - +
115B PHE* 3.9 26.8 + - - +
116B ASP* 6.1 0.2 - - - +
119B PHE* 3.9 27.8 - - - -
136B PHE 5.0 1.8 - - - +
137B SER* 3.6 26.7 - - - +
139B LEU* 4.1 19.5 - - + -
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Residues in contact with ALA 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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108B GLY 3.1 18.0 + - - +
109B GLU* 3.7 12.6 - - - +
110B VAL 3.1 0.4 - - - -
111B MET* 1.3 77.3 - - - +
113B SER* 1.3 61.5 + - - +
114B LYS* 3.1 11.4 + - - +
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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
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69B TYR 3.4 23.3 - - - -
70B SER* 4.1 10.8 - - - +
72B CYS* 3.4 16.3 - - - +
73B HIS* 3.1 26.3 - - - +
109B GLU 3.3 7.4 + - - -
110B VAL 2.6 20.6 + - - -
112B ALA* 1.3 76.3 - - - +
114B LYS* 1.3 65.5 + - - +
115B PHE 3.3 7.4 + - - -
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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
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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