Contacts of the helix formed by residues 106 - 121 (chain A) in PDB entry 1HXK
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 ASP 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLN* 4.0 7.1 + - - -
102A TYR* 2.7 30.9 + - - +
104A GLN 3.6 0.8 - - - -
105A HIS* 1.3 85.1 - - - +
107A THR* 1.3 64.6 + - - +
108A LYS 3.4 2.2 - - - -
109A HIS* 3.1 10.2 + - - +
110A ILE* 3.0 26.5 + - + +
342A PHE* 3.8 30.7 - - + +
345A LYS* 2.9 33.8 + - + +
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Residues in contact with THR 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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91A ASN* 2.8 31.6 + - - +
102A TYR 3.0 13.5 + - - -
103A TYR* 3.9 12.1 - - + -
106A ASP* 1.3 73.6 - - - +
108A LYS* 1.3 62.2 + - - +
110A ILE* 3.2 4.0 + - - +
111A LEU* 3.0 28.9 + - + +
128A TRP* 4.0 10.8 - - + -
133A TYR* 3.7 38.5 - - + -
342A PHE* 3.5 12.3 - - - -
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Residues in contact with LYS 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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103A TYR* 2.9 59.4 + - + +
104A GLN* 2.8 43.9 + - - +
107A THR* 1.3 74.4 - - - +
109A HIS* 1.3 81.2 + - + +
112A SER* 3.0 29.6 + - - -
137A PHE* 3.4 12.6 - - + -
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Residues in contact with HIS 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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104A GLN 3.3 20.5 + - - -
105A HIS* 3.5 26.6 + - - -
106A ASP 3.1 5.8 + - - +
108A LYS* 1.3 97.1 - - + +
110A ILE* 1.3 60.9 + - - +
112A SER* 4.3 4.6 - - - -
113A ASN* 2.9 45.1 + - - +
345A LYS* 4.1 18.6 - - + -
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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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89A SER* 3.7 2.0 - - - +
91A ASN* 3.5 23.3 - - - +
106A ASP* 3.0 21.7 + - + +
107A THR* 3.5 6.5 - - - +
109A HIS* 1.3 77.5 - - - +
111A LEU* 1.3 59.1 + - - +
114A ALA* 2.9 29.8 + - - +
126A PHE* 4.2 9.0 - - + -
128A TRP* 3.8 25.6 - - + -
342A PHE* 3.6 25.1 - - + +
343A ARG 3.6 18.4 - - - +
344A PHE 3.5 18.3 - - - +
345A LYS* 3.6 20.6 - - + +
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Residues in contact with LEU 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 THR* 3.0 25.6 + - + +
110A ILE* 1.3 73.5 - - - +
112A SER* 1.3 64.6 + - - +
114A ALA* 3.6 5.0 - - + +
115A LEU* 3.1 22.9 + - - +
126A PHE* 5.0 5.4 - - + -
128A TRP* 3.7 50.9 - - + -
133A TYR 4.1 7.2 - - - +
134A PHE* 4.0 24.2 - - + -
137A PHE* 3.6 48.2 - - + -
149A MET* 4.2 5.1 - - + +
158A LEU* 5.9 2.5 - - + -
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Residues in contact with SER 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 LYS 3.0 20.4 + - - -
109A HIS* 3.3 7.4 + - - -
111A LEU* 1.3 76.0 - - - +
113A ASN* 1.3 65.0 + - - +
115A LEU* 3.4 7.3 + - - +
116A ARG* 3.2 49.2 + - - +
137A PHE* 3.5 17.1 - - - -
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Residues in contact with ASN 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 HIS* 2.9 22.8 + - - +
110A ILE 4.2 0.2 - - - +
112A SER* 1.3 76.6 + - - +
114A ALA* 1.3 60.2 + - - +
116A ARG* 3.7 23.8 + - - +
117A HIS* 2.9 38.3 + - - +
345A LYS 2.5 29.3 + - - +
346A GLN* 4.2 1.2 - - - +
347A ASN* 3.1 34.8 + - - +
350A TRP* 3.8 15.0 - - + +
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Residues in contact with ALA 114 (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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110A ILE 2.9 19.6 + - - +
111A LEU* 3.6 10.1 - - + +
113A ASN* 1.3 75.8 - - - +
115A LEU* 1.3 58.4 + - - +
118A LEU* 2.9 41.6 + - + +
126A PHE* 3.9 20.4 - - + -
149A MET* 6.0 1.3 - - + -
152A ILE* 5.0 0.4 - - + -
158A LEU* 5.7 1.3 - - + -
350A TRP* 3.3 29.1 - - + -
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Residues in contact with LEU 115 (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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111A LEU 3.1 13.6 + - - +
112A SER* 3.5 10.5 - - - +
114A ALA* 1.3 77.0 - - - +
116A ARG* 1.3 60.9 + - + +
118A LEU* 4.3 0.3 - - - +
119A HIS* 3.0 30.6 + - + +
137A PHE* 5.1 2.0 - - + -
141A LEU* 4.6 10.1 - - + -
145A LYS* 3.8 43.5 - - + +
148A GLN* 3.8 17.7 - - + +
149A MET* 3.6 46.4 - - + +
152A ILE* 3.7 17.9 - - + +
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Residues in contact with ARG 116 (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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112A SER* 3.2 33.5 + - - +
113A ASN* 3.7 22.5 + - - +
115A LEU* 1.3 80.1 - - + +
117A HIS* 1.3 61.9 + - + +
119A HIS* 3.3 5.2 + - - +
120A ASP* 3.0 40.6 + - - +
145A LYS* 5.2 17.6 - - - +
148A GLN* 5.8 2.7 - - - +
347A ASN* 4.9 10.1 - - - +
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Residues in contact with HIS 117 (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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113A ASN* 2.9 30.3 + - - +
114A ALA 4.3 0.2 - - - +
116A ARG* 1.3 73.8 - - + +
118A LEU* 1.3 61.3 + - - +
120A ASP* 3.5 1.7 + - - +
121A ASN* 2.9 44.9 + - - +
124A MET* 4.9 1.9 - - + +
347A ASN* 2.9 47.6 + - + -
350A TRP* 3.5 43.0 - + + +
351A ASP* 3.6 25.4 + - - -
354A ARG* 5.2 4.3 + - - +
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Residues in contact with LEU 118 (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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114A ALA* 2.9 34.3 + - + +
117A HIS* 1.3 70.1 - - - +
119A HIS* 1.3 67.0 + - - +
121A ASN 3.3 10.1 + - - +
124A MET* 3.5 44.6 - - + +
125A LYS* 4.0 10.5 - - - +
126A PHE* 3.9 21.1 - - + -
152A ILE* 3.9 15.7 - - + -
157A GLN* 2.8 31.1 + - + +
158A LEU* 3.9 30.5 - - + +
350A TRP* 4.3 7.2 - - + -
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Residues in contact with HIS 119 (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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115A LEU* 3.0 22.9 + - + +
116A ARG* 3.5 6.1 - - - +
117A HIS 3.3 0.2 - - - -
118A LEU* 1.3 79.9 - - - +
120A ASP* 1.3 80.7 + - - +
121A ASN 3.6 0.2 + - - -
122A PRO* 4.6 5.0 - - - +
148A GLN* 3.9 41.2 + - + +
151A SER* 5.3 2.9 - - - -
152A ILE* 4.2 16.5 - - + +
157A GLN* 4.9 2.4 + - - +
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Residues in contact with ASP 120 (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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116A ARG* 3.0 25.1 + - - +
117A HIS* 4.1 1.6 - - - +
119A HIS* 1.3 100.4 + - - +
121A ASN* 1.3 72.4 + - - +
122A PRO* 3.6 8.4 - - - +
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Residues in contact with ASN 121 (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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117A HIS* 2.9 32.0 + - - +
118A LEU 3.3 4.7 + - - +
120A ASP* 1.3 90.3 + - - +
122A PRO* 1.3 59.9 - - - +
123A GLU 3.2 2.5 - - - -
124A MET* 3.0 20.7 + - + +
157A GLN* 3.0 13.2 - - - +
354A ARG* 3.1 57.0 + - - +
358A GLU* 4.7 1.7 + - - +
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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