Contacts of the helix formed by residues 90 - 115 (chain c) 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 c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86c GLN 3.8 5.9 + - - +
87c LEU* 3.1 18.8 + - - +
88c ASN 3.2 2.6 - - - +
89c ASP* 1.3 79.3 - - + +
91c PRO* 1.3 64.5 - - - +
92c GLU* 3.3 1.8 - - + +
93c VAL* 4.2 18.8 - - + +
94c ARG* 3.4 10.9 + - - +
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Residues in contact with PRO 91 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88c ASN 4.7 3.1 - - - +
89c ASP 4.0 2.6 - - - -
90c LYS* 1.3 73.0 - - - +
92c GLU* 1.3 58.2 + - - +
94c ARG* 3.6 5.5 + - + +
95c SER* 2.9 29.5 + - - -
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Residues in contact with GLU 92 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90c LYS* 3.3 1.7 - - + +
91c PRO* 1.3 76.4 - - - +
93c VAL* 1.3 61.8 + - - +
95c SER* 3.2 7.8 + - - -
96c GLU* 2.9 28.1 + - - +
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Residues in contact with VAL 93 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107b ILE* 6.2 3.8 - - + -
87c LEU* 5.3 3.8 - - + +
90c LYS* 3.7 19.6 + - + +
91c PRO 3.4 0.6 - - - -
92c GLU* 1.3 78.2 - - - +
94c ARG* 1.3 58.5 + - - +
96c GLU* 3.2 8.5 + - - +
97c ILE* 2.9 27.8 + - - +
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Residues in contact with ARG 94 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87c LEU* 3.7 19.2 + - + +
88c ASN* 5.2 3.6 - - - -
90c LYS 3.4 15.7 + - - +
91c PRO* 3.9 4.9 - - + +
92c GLU 3.3 0.4 - - - -
93c VAL* 1.3 77.6 - - - +
95c SER* 1.3 58.7 + - - +
97c ILE* 3.3 8.5 + - - +
98c ASP* 2.9 27.5 + - - +
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Residues in contact with SER 95 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91c PRO 2.9 20.0 + - - -
92c GLU* 3.4 8.7 - - - -
94c ARG* 1.3 74.8 - - - +
96c GLU* 1.3 60.1 + - - +
98c ASP* 3.2 8.5 + - - +
99c SER* 2.9 27.4 + - - -
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Residues in contact with GLU 96 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92c GLU 2.9 12.9 + - - +
93c VAL* 3.6 10.5 - - - +
95c SER* 1.3 75.2 - - - +
97c ILE* 1.3 57.7 + - - +
99c SER* 3.2 8.7 + - - -
100c LEU* 2.9 28.8 + - - +
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Residues in contact with ILE 97 (chain c).
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* 6.4 3.4 - - + -
107b ILE* 6.2 4.7 - - + -
93c VAL 2.9 16.9 + - - +
94c ARG* 3.6 9.4 - - - +
95c SER 3.3 0.2 - - - -
96c GLU* 1.3 75.9 - - - +
98c ASP* 1.3 59.0 + - - +
100c LEU* 3.5 5.3 + - - +
101c VAL* 2.9 30.8 + - - +
126c LEU* 6.4 2.0 - - + -
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Residues in contact with ASP 98 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94c ARG 2.9 13.8 + - - +
95c SER* 3.2 11.4 + - - +
97c ILE* 1.3 77.7 - - - +
99c SER* 1.3 56.1 + - - +
101c VAL* 3.8 5.9 - - - +
102c SER* 2.9 28.6 + - - -
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Residues in contact with SER 99 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95c SER 2.9 13.6 + - - -
96c GLU* 3.2 11.9 + - - -
98c ASP* 1.3 74.1 - - - +
100c LEU* 1.3 60.4 + - - +
102c SER* 3.1 9.2 + - - -
103c LEU* 2.9 26.9 + - - +
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Residues in contact with LEU 100 (chain c).
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* 5.1 21.8 - - + +
103b LEU* 5.9 4.3 - - + -
104b ILE* 5.5 9.9 - - + +
96c GLU 2.9 15.6 + - - +
97c ILE* 4.0 6.3 - - - +
99c SER* 1.3 76.2 - - - +
101c VAL* 1.3 57.3 + - - +
103c LEU* 3.1 8.5 + - - +
104c ILE* 2.9 30.1 + - - +
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Residues in contact with VAL 101 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97c ILE 2.9 19.0 + - - +
98c ASP* 3.9 6.3 - - - +
100c LEU* 1.3 76.9 - - - +
102c SER* 1.3 58.3 + - - +
104c ILE* 3.9 6.0 - - - +
105c THR* 2.9 30.7 + - - -
124c ILE* 5.1 21.6 - - + +
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Residues in contact with SER 102 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98c ASP 2.9 18.8 + - - -
99c SER* 3.1 8.9 + - - -
101c VAL* 1.3 75.2 - - - +
103c LEU* 1.3 59.1 + - - +
105c THR* 3.8 5.4 - - - -
106c ASP* 2.9 28.9 + - - +
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Residues in contact with LEU 103 (chain c).
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* 5.9 5.4 - - + -
99c SER 2.9 12.0 + - - +
100c LEU* 3.1 10.7 + - - +
102c SER* 1.3 74.5 - - - +
104c ILE* 1.3 60.0 + - - +
106c ASP* 3.1 7.6 + - - +
107c ILE* 2.9 28.1 + - - +
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Residues in contact with ILE 104 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97b ILE* 6.4 2.9 - - + -
100b LEU* 5.4 10.0 - - + +
100c LEU 2.9 16.7 + - - +
101c VAL* 4.0 6.3 - - - +
103c LEU* 1.3 75.4 - - - +
105c THR* 1.3 57.3 + - - +
107c ILE* 3.2 6.5 + - - +
108c ILE* 2.9 32.0 + - - +
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Residues in contact with THR 105 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101c VAL 2.9 19.4 + - - -
102c SER* 3.8 7.0 - - - -
104c ILE* 1.3 76.3 - - - +
106c ASP* 1.3 57.1 + - - +
108c ILE* 4.6 4.0 - - - +
109c MET* 2.9 31.5 + - - +
123c GLU* 6.5 1.1 - - - -
124c ILE* 6.0 6.5 - - - -
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Residues in contact with ASP 106 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102c SER 2.9 18.5 + - - +
103c LEU* 3.1 8.3 + - - +
105c THR* 1.3 74.9 - - - +
107c ILE* 1.3 60.0 + - - +
109c MET* 3.7 5.0 - - - +
110c ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 107 (chain c).
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* 6.3 2.9 - - + -
97b ILE* 6.1 5.2 - - + -
103c LEU 2.9 14.4 + - - +
104c ILE* 3.7 6.7 - - - +
106c ASP* 1.3 78.0 - - - +
108c ILE* 1.3 58.0 + - - +
110c ALA* 3.1 7.7 + - - +
111c GLU* 2.9 27.2 + - - +
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Residues in contact with ILE 108 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130b ILE* 6.5 1.8 - - + -
104c ILE 2.9 16.8 + - - +
105c THR* 4.4 3.8 - - - +
107c ILE* 1.3 75.8 - - - +
109c MET* 1.3 58.4 + - - +
111c GLU* 3.4 7.9 + - - +
112c CYS* 2.9 28.1 + - - +
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Residues in contact with MET 109 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105c THR 2.9 22.6 + - - +
106c ASP* 3.7 6.3 - - - +
108c ILE* 1.3 75.4 - - - +
110c ALA* 1.3 59.5 + - - +
112c CYS* 3.2 7.8 + - - +
113c ILE* 2.9 28.2 + - - +
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Residues in contact with ALA 110 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106c ASP 2.9 18.9 + - - +
107c ILE* 3.5 7.0 - - - +
109c MET* 1.3 76.9 - - - +
111c GLU* 1.3 55.7 + - - +
113c ILE* 3.2 8.3 + - - +
114c GLU* 2.9 27.6 + - - +
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Residues in contact with GLU 111 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83b ILE* 5.7 6.3 - - + +
86b GLN* 5.7 11.1 - - + +
87b LEU* 5.7 9.6 - - + +
107c ILE 2.9 15.6 + - - +
108c ILE* 3.8 8.5 - - - +
110c ALA* 1.3 76.0 - - - +
112c CYS* 1.3 61.9 + - - +
114c GLU* 3.3 15.6 + - - +
115c ASN* 3.4 12.1 + - - +
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Residues in contact with CYS 112 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108c ILE 2.9 17.2 + - - +
109c MET* 3.5 9.0 - - - +
110c ALA 3.2 0.2 - - - -
111c GLU* 1.3 75.6 - - - +
113c ILE* 1.3 64.4 + - - +
115c ASN* 3.3 22.1 + - - +
117c LEU 4.2 7.3 - - - +
119c ILE* 4.1 25.1 - - + +
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Residues in contact with ILE 113 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109c MET 2.9 16.9 + - - +
110c ALA* 3.2 8.0 + - - +
112c CYS* 1.3 75.7 - - - +
114c GLU* 1.3 61.9 + - - +
115c ASN 3.4 7.5 + - - +
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Residues in contact with GLU 114 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110c ALA 2.9 13.4 + - - +
111c GLU* 3.6 13.5 - - - +
112c CYS 3.2 0.6 - - - -
113c ILE* 1.3 79.2 - - - +
115c ASN* 1.3 60.6 + - - +
116c GLU* 3.8 0.9 + - - -
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Residues in contact with ASN 115 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111c GLU 3.4 8.2 + - - +
112c CYS* 3.3 18.2 + - - +
113c ILE 3.2 11.1 - - - +
114c GLU* 1.3 81.5 - - - +
116c GLU* 1.3 64.1 + - - +
117c LEU* 3.3 14.8 + - + +
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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