Contacts of the helix formed by residues 90 - 115 (chain B) in PDB entry 6QY3
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 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLN 4.0 6.8 + - - +
87B LEU* 3.3 16.4 + - - +
88B ASN 3.2 2.8 - - - +
89B ASP* 1.3 78.0 - - - +
91B PRO* 1.3 63.9 - - - +
92B GLU* 3.4 2.0 - - + +
93B VAL* 4.3 19.3 - - + +
94B ARG* 3.3 12.0 + - - +
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Residues in contact with PRO 91 (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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88B ASN 4.7 2.0 - - - +
89B ASP 3.9 3.6 - - - -
90B LYS* 1.3 72.0 - - - +
92B GLU* 1.3 58.0 + - - +
94B ARG* 3.5 5.7 + - + +
95B SER* 2.9 29.0 + - - -
19S ASN* 6.5 1.3 - - + -
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LYS* 3.4 1.3 - - + +
91B PRO* 1.3 76.3 - - - +
93B VAL* 1.3 60.8 + - - +
95B SER* 3.1 8.3 + - - -
96B GLU* 2.9 28.1 + - - +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 5.0 7.4 - - + +
90B LYS* 3.8 18.8 + - + +
91B PRO 3.5 0.2 - - - -
92B GLU* 1.3 78.8 - - - +
94B ARG* 1.3 58.8 + - - +
96B GLU* 3.3 6.3 + - - +
97B ILE* 2.9 30.5 + - - +
107C ILE* 6.3 2.5 - - + -
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Residues in contact with ARG 94 (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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87B LEU* 3.8 16.0 + - + +
88B ASN* 5.0 5.6 - - - +
90B LYS 3.3 17.3 + - - +
91B PRO* 3.8 5.6 - - + +
92B GLU 3.3 0.2 - - - -
93B VAL* 1.3 77.8 - - - +
95B SER* 1.3 56.4 + - - +
97B ILE* 3.9 5.5 - - - +
98B ASP* 2.9 29.5 + - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PRO 2.9 18.7 + - - -
92B GLU* 3.1 8.5 + - - -
94B ARG* 1.3 76.9 - - - +
96B GLU* 1.3 57.3 + - - +
98B ASP* 3.3 7.7 + - - +
99B SER* 2.9 27.8 + - - -
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Residues in contact with GLU 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 GLU 2.9 15.5 + - - +
93B VAL* 3.7 7.0 - - - +
95B SER* 1.3 75.0 - - - +
97B ILE* 1.3 63.6 + - - +
99B SER* 3.0 9.5 + - - -
100B LEU* 2.9 23.1 + - - +
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Residues in contact with ILE 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 VAL 2.9 17.4 + - - +
94B ARG* 3.9 6.5 - - - +
96B GLU* 1.3 76.0 - - - +
98B ASP* 1.3 58.5 + - - +
100B LEU* 3.4 6.3 + - - +
101B VAL* 2.9 31.0 + - - +
104C ILE* 6.4 2.7 - - + -
107C ILE* 6.1 5.2 - - + -
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Residues in contact with ASP 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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94B ARG 2.9 18.5 + - - +
95B SER* 3.5 8.5 - - - +
96B GLU 3.2 0.2 - - - -
97B ILE* 1.3 76.6 - - - +
99B SER* 1.3 55.6 + - - +
101B VAL* 3.8 4.7 - - - +
102B SER* 2.9 29.8 + - - -
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Residues in contact with SER 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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95B SER 2.9 13.4 + - - -
96B GLU* 3.0 11.6 + - - -
98B ASP* 1.3 74.1 - - - +
100B LEU* 1.3 66.5 + - - +
102B SER* 3.1 8.2 + - - -
103B LEU* 2.9 21.5 + - - +
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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 GLU 2.9 14.2 + - - +
97B ILE* 3.9 7.0 - - - +
99B SER* 1.3 75.8 - - - +
101B VAL* 1.3 63.0 + - - +
103B LEU* 3.0 9.4 + - - +
104B ILE* 2.9 23.7 + - - +
100C LEU* 5.1 21.8 - - + +
103C LEU* 5.9 4.3 - - + -
104C ILE* 5.4 9.9 - - + +
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Residues in contact with VAL 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 ILE 2.9 18.1 + - - +
98B ASP* 4.0 6.1 - - - +
100B LEU* 1.3 75.8 - - - +
102B SER* 1.3 57.6 + - - +
104B ILE* 3.5 6.6 + - - +
105B THR* 2.9 30.9 + - - -
124B ILE* 4.4 24.5 - - + +
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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
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98B ASP 2.9 19.4 + - - -
99B SER* 3.1 9.2 + - - -
101B VAL* 1.3 77.0 - - - +
103B LEU* 1.3 56.8 + - - +
105B THR* 3.4 6.5 + - - -
106B ASP* 2.9 28.1 + - - +
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Residues in contact with LEU 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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99B SER 2.9 12.4 + - - +
100B LEU* 3.0 11.0 + - - +
102B SER* 1.3 76.4 - - - +
104B ILE* 1.3 62.3 + - - +
106B ASP* 3.0 9.6 + - - +
107B ILE* 3.0 21.7 + - - +
100C LEU* 5.9 4.3 - - + -
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU 2.9 14.5 + - - +
101B VAL* 4.0 7.0 - - - +
103B LEU* 1.3 74.9 - - - +
105B THR* 1.3 57.3 + - - +
107B ILE* 3.2 7.9 + - - +
108B ILE* 2.9 31.9 + - - +
97C ILE* 6.4 2.9 - - + -
100C LEU* 5.5 9.0 - - + -
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Residues in contact with THR 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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101B VAL 2.9 19.0 + - - -
102B SER* 3.7 6.5 - - - -
104B ILE* 1.3 76.0 - - - +
106B ASP* 1.3 58.0 + - - +
108B ILE* 4.2 5.1 - - - +
109B MET* 2.9 31.4 + - - +
124B ILE* 5.8 9.2 - - - -
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Residues in contact with ASP 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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102B SER 2.9 14.7 + - - +
103B LEU* 3.0 12.5 + - - +
105B THR* 1.3 74.6 - - - +
107B ILE* 1.3 59.1 + - - +
109B MET* 3.3 5.8 + - - +
110B ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 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 LEU 3.0 12.4 + - - +
104B ILE* 3.2 10.0 + - - +
106B ASP* 1.3 77.0 - - - +
108B ILE* 1.3 63.1 + - - +
110B ALA* 3.1 8.8 + - - +
111B GLU* 2.9 22.9 + - - +
93C VAL* 6.2 4.9 - - + +
97C ILE* 6.2 4.9 - - + -
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Residues in contact with ILE 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 ILE 2.9 15.8 + - - +
105B THR* 4.2 5.8 - - - +
107B ILE* 1.3 77.1 - - - +
109B MET* 1.3 57.1 + - - +
111B GLU* 3.3 8.1 + - - +
112B CYS* 2.9 28.6 + - - +
130C ILE* 6.5 0.7 - - - -
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Residues in contact with MET 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 THR 2.9 21.7 + - - +
106B ASP* 3.6 6.5 - - - +
107B ILE 3.2 0.2 - - - -
108B ILE* 1.3 73.8 - - - +
110B ALA* 1.3 60.0 + - - +
112B CYS* 3.2 8.8 + - - +
113B ILE* 2.9 28.1 + - - +
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Residues in contact with ALA 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 ASP 2.9 14.0 + - - +
107B ILE* 3.1 10.1 + - - +
109B MET* 1.3 76.6 - - - +
111B GLU* 1.3 57.1 + - - +
113B ILE* 3.1 8.4 + - - +
114B GLU* 2.9 27.9 + - - +
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Residues in contact with GLU 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 ILE 2.9 12.3 + - - +
108B ILE* 3.6 11.4 - - - +
110B ALA* 1.3 77.0 - - - +
112B CYS* 1.3 60.3 + - - +
114B GLU* 3.5 14.4 + - - +
115B ASN* 3.6 11.6 + - - +
83C ILE* 5.5 13.4 - - + +
86C GLN* 5.4 15.1 - - + +
87C LEU* 5.8 6.7 - - + +
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Residues in contact with CYS 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 ILE 2.9 16.3 + - - +
109B MET* 3.5 8.7 - - - +
111B GLU* 1.3 73.8 - - - +
113B ILE* 1.3 64.7 + - - +
115B ASN* 3.3 21.9 + - - +
117B LEU 4.4 6.2 - - - +
119B ILE* 4.3 25.6 + - + +
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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 MET 2.9 16.1 + - - +
110B ALA* 3.1 8.5 + - - +
112B CYS* 1.3 76.3 - - - +
114B GLU* 1.3 60.7 + - - +
115B ASN 3.3 8.0 + - - +
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Residues in contact with GLU 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 ALA 2.9 15.4 + - - +
111B GLU* 3.7 10.5 - - - +
112B CYS 3.2 0.2 - - - -
113B ILE* 1.3 78.7 - - - +
115B ASN* 1.3 59.9 + - - +
116B GLU 3.9 0.5 + - - -
86C GLN* 6.6 0.2 - - + -
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Residues in contact with ASN 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 GLU 3.6 8.2 + - - +
112B CYS* 3.3 15.5 + - - +
113B ILE 3.2 9.9 - - - +
114B GLU* 1.3 81.8 - - - +
116B GLU* 1.3 64.0 + - - +
117B LEU* 3.4 16.7 - - + +
119B ILE* 6.1 1.3 - - + -
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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