Contacts of the helix formed by residues 95 - 113 (chain A) in PDB entry 5JJ2
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 ASN 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ILE* 3.8 0.4 - - - +
94A THR* 1.3 76.0 + - - +
96A LYS* 1.3 64.9 + - - +
97A GLU* 2.9 33.5 + - - +
98A ILE* 3.0 22.5 + - + +
99A ILE* 3.2 12.7 + - - +
254A GLU* 2.8 36.7 + - - +
255A GLU* 3.0 17.1 + - - +
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Residues in contact with LYS 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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94A THR 3.2 9.5 + - - +
95A ASN* 1.3 74.3 + - - +
97A GLU* 1.3 57.9 + - - +
99A ILE* 3.9 14.5 - - + +
100A LYS* 2.9 57.6 + - - +
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Residues in contact with GLU 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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95A ASN* 2.9 23.0 + - - +
96A LYS* 1.3 78.0 - - - +
98A ILE* 1.3 60.3 + - - +
100A LYS* 4.1 3.9 - - - +
101A GLY* 3.1 19.2 + - - -
251A ARG 4.5 5.0 - - - +
252A PHE 3.6 20.9 - - - +
253A GLY* 4.0 10.2 - - - -
254A GLU 5.0 0.2 + - - -
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Residues in contact with ILE 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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93A ILE* 3.9 10.8 - - + -
95A ASN* 3.0 19.1 + - + +
97A GLU* 1.3 75.2 - - - +
99A ILE* 1.3 66.4 + - - +
101A GLY* 3.2 1.7 + - - -
102A ILE* 2.9 28.7 + - + +
126A PHE* 6.1 0.2 - - + -
168A PHE* 3.8 17.5 - - + -
220A LEU* 3.7 28.5 - - + -
252A PHE* 3.6 26.8 - - + +
253A GLY* 3.7 17.3 - - - +
254A GLU 3.7 30.1 - - - +
255A GLU* 4.0 9.4 - - + +
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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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93A ILE* 3.8 33.2 - - + +
94A THR* 4.2 6.3 - - - +
95A ASN 3.2 19.4 + - - +
96A LYS* 3.9 16.6 - - + +
98A ILE* 1.3 76.6 - - - +
100A LYS* 1.3 65.2 + - + +
102A ILE 3.4 0.2 + - - -
103A LYS* 3.1 36.3 + - + +
123A ASP* 4.2 13.5 - - + +
126A PHE* 3.8 28.9 - - + -
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Residues in contact with LYS 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 LYS* 2.9 45.3 + - - +
97A GLU* 4.1 3.6 - - - +
99A ILE* 1.3 78.4 - - + +
101A GLY* 1.3 63.4 + - - +
103A LYS* 3.3 12.7 + - + +
104A ILE* 3.0 36.6 + - + +
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Residues in contact with GLY 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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97A GLU 3.1 16.7 + - - -
98A ILE 3.7 2.5 - - - -
100A LYS* 1.3 77.9 - - - +
102A ILE* 1.3 61.2 + - - +
104A ILE* 3.3 12.3 + - - +
105A LEU 3.0 18.0 + - - -
247A PHE* 5.0 1.7 - - - -
250A HIS* 5.3 5.8 - - - -
252A PHE* 3.6 24.1 - - - -
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Residues in contact with ILE 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 ILE* 2.9 32.5 + - + +
101A GLY* 1.3 71.5 - - - +
103A LYS* 1.3 60.6 + - - +
105A LEU* 3.2 7.2 + - + +
106A GLN* 2.9 29.3 + - - +
126A PHE* 3.4 33.7 - - + -
181A VAL* 3.5 35.0 - - + -
220A LEU* 4.3 18.6 - - + -
222A PHE* 3.7 26.0 - - + -
252A PHE* 3.8 14.8 - - + -
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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* 3.1 27.9 + - + +
100A LYS* 3.3 13.9 + - + +
102A ILE* 1.3 76.2 - - - +
104A ILE* 1.3 57.8 + - + +
106A GLN* 3.3 16.7 + - - +
107A ASN* 2.9 42.1 + - - +
123A ASP* 3.0 45.7 + - + +
126A PHE* 4.4 1.6 - - + -
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Residues in contact with ILE 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 LYS* 3.0 29.1 + - + +
101A GLY* 3.6 9.9 - - - +
102A ILE 3.3 0.2 - - - -
103A LYS* 1.3 74.4 - - + +
105A LEU* 1.3 60.3 + - - +
107A ASN* 3.2 8.6 + - - +
108A ALA* 2.9 29.7 + - + +
247A PHE* 4.2 18.8 - - + -
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Residues in contact with LEU 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 GLY 3.0 13.1 + - - +
102A ILE* 3.2 11.0 + - + +
104A ILE* 1.3 76.3 - - - +
106A GLN* 1.3 62.2 + - - +
108A ALA* 3.2 2.8 + - - +
109A ILE* 3.1 46.0 + - + +
171A ILE* 4.2 3.8 - - + -
181A VAL* 4.1 7.0 - - + -
222A PHE* 3.7 37.7 - - + -
244A TYR* 4.0 13.9 - - + -
247A PHE* 3.6 38.6 - - + -
252A PHE* 4.1 22.0 - - + -
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Residues in contact with GLN 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 ILE* 2.9 17.3 + - - +
103A LYS* 3.5 20.7 - - - +
105A LEU* 1.3 75.8 - - - +
107A ASN* 1.3 61.6 + - - +
109A ILE* 3.2 6.3 + - - +
110A ILE* 3.0 32.9 + - + +
120A MET* 3.7 31.5 - - + +
121A VAL 3.0 27.1 + - - +
123A ASP* 5.4 1.6 + - - +
126A PHE* 3.9 20.7 - - - -
222A PHE* 2.9 35.7 + - + +
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Residues in contact with ASN 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* 2.9 31.4 + - - +
104A ILE* 3.7 8.2 - - - +
106A GLN* 1.3 78.1 - - - +
108A ALA* 1.3 58.4 + - - +
110A ILE* 3.4 17.7 + - - +
111A GLN* 3.0 28.4 + - - +
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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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104A ILE* 2.9 17.9 + - + +
105A LEU 3.2 5.1 + - - +
107A ASN* 1.3 77.7 - - - +
109A ILE* 1.3 61.6 + - + +
111A GLN* 3.6 12.8 + - - +
112A GLN* 3.0 25.2 + - - +
243A LEU 5.7 0.7 - - - +
247A PHE* 3.8 25.4 - - + -
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Residues in contact with ILE 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 LEU* 3.1 27.4 + - + +
106A GLN* 3.2 7.2 + - - +
108A ALA* 1.3 76.1 - - + +
110A ILE* 1.3 64.6 + - - +
112A GLN* 3.0 20.0 + - - +
113A ASP* 3.1 10.7 + - - +
116A LEU* 3.7 23.3 - - + -
120A MET* 3.6 19.7 - - + -
222A PHE* 3.7 31.2 - - + -
223A MET* 4.3 9.2 - - - -
239A ILE* 6.3 0.2 - - + -
243A LEU* 3.9 30.1 - - + +
244A TYR* 4.4 10.8 - - + -
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Residues in contact with ILE 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 GLN* 3.0 22.3 + - + +
107A ASN* 3.4 19.9 + - - +
109A ILE* 1.3 75.4 - - - +
111A GLN* 1.3 64.0 + - - +
113A ASP 3.1 26.0 - - - -
114A GLU* 3.1 17.0 + - + +
116A LEU* 5.1 0.2 - - - -
117A ALA* 3.8 42.4 - - + +
120A MET* 4.0 18.6 - - + -
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Residues in contact with GLN 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 ASN 3.0 16.9 + - - +
108A ALA* 3.7 9.6 - - - +
109A ILE 3.2 0.4 - - - -
110A ILE* 1.3 77.6 - - - +
112A GLN* 1.3 62.9 + - + +
114A GLU 5.1 0.7 + - - -
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Residues in contact with GLN 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 ALA* 3.0 25.1 + - - +
109A ILE* 3.0 8.6 + - - +
111A GLN* 1.3 82.0 - - + +
113A ASP* 1.3 60.1 + - - +
114A GLU 4.2 0.2 - - - -
242A ASP 4.2 4.5 - - - +
243A LEU* 2.9 54.6 + - + +
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Residues in contact with ASP 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 ILE 3.1 4.8 + - - -
110A ILE* 3.1 9.4 + - - +
112A GLN* 1.3 79.6 - - - +
114A GLU* 1.3 64.3 + - - +
115A ARG* 3.0 52.0 + - - +
116A LEU* 3.0 42.7 + - + +
236A VAL* 4.0 9.0 - - - +
243A LEU* 4.7 6.7 - - + -
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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