Contacts of the helix formed by residues 89 - 112 (chain A) in PDB entry 5ID6
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 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR* 3.1 2.4 - - - +
88A GLU* 1.3 78.1 - - - +
90A GLU* 1.3 61.2 + - - +
91A ASN* 3.1 15.0 + - - +
92A LYS* 3.2 50.2 - - + +
93A GLU* 3.9 2.8 + - - +
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Residues in contact with GLU 90 (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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80A LEU* 5.5 2.1 - - - +
86A ARG* 2.9 62.0 + - - +
87A THR 2.8 13.0 + - - +
88A GLU* 3.0 17.2 - - + +
89A LYS* 1.3 77.7 - - - +
91A ASN* 1.3 61.2 + - - +
92A LYS 3.1 0.4 - - - -
93A GLU* 3.2 23.9 - - - +
94A LEU* 3.9 1.9 + - - +
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Residues in contact with ASN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU 6.0 1.3 - - - +
85A THR* 3.9 28.0 + - - +
87A THR* 3.8 14.4 + - - +
89A LYS* 3.2 18.2 + - - +
90A GLU* 1.3 77.5 - - - +
92A LYS* 1.3 74.7 + - - +
93A GLU 3.2 0.2 - - - -
94A LEU* 2.9 22.7 + - + +
95A GLU* 2.9 44.7 + - - +
478A LYS* 5.8 1.4 - - - +
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LYS* 3.2 55.3 - - + +
91A ASN* 1.3 80.3 + - - +
93A GLU* 1.3 65.9 + - - +
95A GLU* 3.1 37.2 + - + +
96A ASN* 2.8 38.0 - - - +
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.2 25.2 - - + +
89A LYS 3.9 2.3 + - - +
90A GLU* 3.2 18.8 + - - +
92A LYS* 1.3 80.6 - - - +
94A LEU* 1.3 60.7 + - - +
96A ASN* 3.4 8.0 + - - +
97A LEU* 3.1 31.9 + - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 4.1 24.5 - - + +
80A LEU* 3.2 52.9 - - + +
81A PHE* 3.7 15.5 - - + +
90A GLU 3.9 0.6 + - - -
91A ASN* 2.9 32.2 + - + +
93A GLU* 1.3 75.9 - - - +
95A GLU* 1.3 76.7 + - + +
96A ASN 3.0 5.2 - - - -
97A LEU* 2.6 29.9 + - + +
98A GLU* 2.9 13.2 + - - +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 2.9 39.7 + - - +
92A LYS* 3.1 40.0 + - - +
94A LEU* 1.3 84.5 - - + +
96A ASN* 1.3 59.8 + - - +
98A GLU* 3.8 18.4 - - - +
99A ILE* 3.1 27.5 - - - +
478A LYS* 3.9 26.0 + - - -
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Residues in contact with ASN 96 (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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92A LYS* 2.8 38.2 + - - +
93A GLU* 3.7 10.0 - - - +
94A LEU 3.0 0.6 - - - -
95A GLU* 1.3 77.8 - - - +
97A LEU* 1.3 58.4 + - + +
98A GLU 3.3 0.4 - - - -
99A ILE* 3.8 10.1 + - - +
100A ASN* 2.4 40.4 + - - +
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Residues in contact with LEU 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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73A ASN* 3.2 26.2 + - - +
76A ASN* 3.9 27.6 - - + +
77A TYR* 4.2 16.2 - - + +
80A LEU* 4.0 21.5 - - + -
93A GLU* 3.1 29.1 + - - +
94A LEU* 2.6 21.0 + - - +
96A ASN* 1.3 74.5 - - + +
98A GLU* 1.3 64.7 + - - +
100A ASN* 3.3 11.0 + - - +
101A LEU* 3.2 22.7 + - - +
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Residues in contact with GLU 98 (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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77A TYR* 3.8 28.4 + - + +
94A LEU* 2.9 9.0 + - + +
95A GLU* 3.8 20.4 - - - +
96A ASN 3.3 0.4 - - - -
97A LEU* 1.3 76.4 - - - +
99A ILE* 1.3 61.8 + - - +
101A LEU* 2.6 34.5 + - - +
102A ARG* 3.0 30.5 + - - +
176A ILE* 4.4 16.2 - - + -
177A ASN* 3.1 16.6 + - - +
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Residues in contact with ILE 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 GLU 3.1 22.2 - - - +
96A ASN* 4.1 13.0 - - - +
97A LEU 3.4 0.2 - - - -
98A GLU* 1.3 80.2 - - - +
100A ASN* 1.3 60.1 + - - +
102A ARG* 3.3 43.5 + - + +
103A LYS* 2.9 39.3 + - + +
164A GLU* 5.3 5.1 - - + +
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Residues in contact with ASN 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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73A ASN* 2.9 24.5 + - - +
96A ASN* 2.4 28.3 + - - +
97A LEU* 3.3 10.6 + - - +
98A GLU 3.0 1.0 + - - -
99A ILE* 1.3 75.8 - - - +
101A LEU* 1.3 60.0 + - - +
103A LYS* 3.6 27.8 + - + +
104A GLU* 3.1 27.0 + - - +
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Residues in contact with LEU 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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71A LEU* 3.5 34.2 - - + +
73A ASN* 3.3 33.2 - - + +
74A LEU* 3.6 11.7 - - + +
77A TYR* 3.7 30.7 - - + -
97A LEU 3.2 25.0 + - - +
98A GLU* 2.6 18.5 + - - +
100A ASN* 1.3 73.4 - - - +
102A ARG* 1.3 59.3 + - - +
104A GLU* 3.4 5.6 + - - +
105A ILE* 3.3 25.5 + - - +
176A ILE* 3.7 28.7 - - + +
180A LEU* 5.0 2.7 - - + -
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Residues in contact with ARG 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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98A GLU* 3.0 34.8 + - - +
99A ILE* 3.3 38.6 + - - +
101A LEU* 1.3 72.8 - - - +
103A LYS* 1.3 65.1 - - - +
105A ILE* 3.2 2.6 + - - +
106A ALA* 3.0 25.3 + - - +
164A GLU* 3.2 29.1 + - + +
166A ALA* 3.2 27.3 - - - +
172A ALA* 3.8 20.4 - - + +
173A PHE* 4.0 20.6 - - - +
176A ILE* 4.1 12.6 - - + -
177A ASN* 3.1 28.9 - - - +
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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
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99A ILE* 2.9 30.9 + - + +
100A ASN* 3.6 28.2 + - + +
102A ARG* 1.3 78.0 - - - +
104A GLU* 1.3 55.1 + - - +
107A LYS* 3.1 31.8 + - - +
164A GLU* 3.2 38.6 - - - +
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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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69A ILE* 5.7 2.2 - - + +
70A LYS 3.6 8.7 - - - +
71A LEU* 4.2 15.9 - - + +
72A LYS* 3.1 30.3 + - - +
73A ASN* 3.5 30.2 + - - +
100A ASN 3.1 12.1 + - - +
101A LEU* 3.7 7.6 - - - +
102A ARG 3.2 0.4 - - - -
103A LYS* 1.3 78.6 - - - +
105A ILE* 1.3 61.7 + - - +
107A LYS* 4.2 4.0 - - - +
108A ALA* 3.3 22.9 + - - +
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Residues in contact with ILE 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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65A VAL* 5.2 0.2 - - - +
66A LEU* 5.2 10.5 - - + -
69A ILE* 5.5 4.3 - - + -
71A LEU* 4.4 17.9 - - + -
101A LEU 3.3 13.4 + - - +
102A ARG 3.2 8.1 + - - +
104A GLU* 1.3 77.7 - - - +
106A ALA* 1.3 67.2 + - - +
108A ALA* 3.1 14.8 + - - +
109A PHE* 3.2 38.5 + - + -
171A ILE* 5.1 1.8 - - + -
172A ALA* 3.5 24.9 - - + +
175A CYS* 3.6 34.3 - - + -
176A ILE* 4.0 14.1 - - + -
229A LEU* 5.3 3.6 - - + -
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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 ARG 3.0 7.6 + - - +
103A LYS 4.0 1.3 - - - +
105A ILE* 1.3 77.9 - - - +
107A LYS* 1.3 62.0 + - - +
109A PHE* 3.1 17.5 + - - +
110A LYS* 3.1 38.9 + - - +
162A PHE 3.3 21.1 - - - +
163A SER 4.1 3.6 - - - +
164A GLU* 3.4 29.2 - - + -
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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 LYS 3.1 16.4 + - - +
104A GLU* 4.4 3.6 - - - +
106A ALA* 1.3 80.1 - - - +
108A ALA* 1.3 54.5 + - - +
110A LYS* 3.9 16.6 - - + +
111A GLY* 2.6 48.6 + - - +
164A GLU* 5.4 1.3 - - - +
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Residues in contact with ALA 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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65A VAL* 3.3 15.9 - - + +
69A ILE* 3.8 35.0 - - + -
104A GLU 3.3 19.9 + - - +
105A ILE* 3.1 8.5 + - - +
107A LYS* 1.3 73.9 - - - +
109A PHE* 1.3 68.0 + - - +
111A GLY* 5.1 0.7 - - - -
112A ALA* 4.1 11.6 + - - +
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Residues in contact with PHE 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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61A PHE* 4.0 12.4 - + + -
62A ILE* 4.2 18.4 - - + -
65A VAL* 3.6 37.0 - - + +
66A LEU* 4.4 9.0 - - + -
105A ILE* 3.2 39.9 + - + -
106A ALA* 3.1 8.2 + - - +
108A ALA* 1.3 79.3 - - - +
110A LYS* 1.3 67.5 + - + +
112A ALA 3.4 13.7 - - - +
115A TYR* 3.6 13.6 - - + +
162A PHE* 3.4 48.5 - + + -
171A ILE* 3.9 33.2 - - + -
172A ALA 5.2 0.2 - - - -
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Residues in contact with LYS 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 47.0 + - - +
107A LYS* 3.9 17.3 - - + +
109A PHE* 1.3 81.6 - - + +
111A GLY* 1.3 65.4 + - - +
112A ALA 3.0 2.1 + - - -
114A GLY 3.6 13.7 - - - +
115A TYR* 3.5 41.6 - - + +
162A PHE* 4.3 10.9 + - + +
163A SER* 5.4 2.0 - - - +
164A GLU* 4.5 8.7 + - - +
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Residues in contact with GLY 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* 2.6 38.7 + - - +
108A ALA* 4.6 1.3 - - - -
109A PHE 3.4 0.4 - - - -
110A LYS* 1.3 72.8 - - - +
112A ALA* 1.3 62.4 + - - +
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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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61A PHE* 4.9 1.9 - - - -
65A VAL* 5.6 0.9 - - - +
108A ALA 4.1 8.6 + - - +
109A PHE 3.4 13.7 + - - +
110A LYS 3.0 1.2 + - - -
111A GLY* 1.3 79.7 - - - +
113A ALA* 1.3 74.3 + - + +
114A GLY 3.2 12.8 + - - +
115A TYR* 4.3 0.5 + - - +
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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