Contacts of the helix formed by residues 109 - 126 (chain A) in PDB entry 1HIK
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 LEU 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A CYS 4.4 0.2 - - - +
25A THR* 3.9 19.5 + - + +
27A LEU 2.8 17.5 + - - +
28A THR* 4.4 0.2 - - - +
29A VAL* 3.9 23.1 - - + -
52A LEU* 4.0 22.9 - - + -
55A PHE* 3.8 37.0 - - + -
79A LEU* 4.2 21.5 - - + -
83A LEU* 4.2 5.4 - - + -
107A SER 3.5 1.8 + - - -
108A THR* 1.3 69.4 - - - +
110A GLU* 1.3 52.6 + - - +
112A PHE* 3.0 9.5 + - + +
113A LEU* 2.8 57.7 + - + +
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Residues in contact with GLU 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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18A THR* 5.2 2.4 - - - +
21A LYS* 3.3 33.1 - - - +
25A THR* 3.2 28.1 + - - +
26A GLU* 4.2 17.6 - - - +
108A THR* 3.8 8.6 + - - +
109A LEU* 1.3 79.8 - - - +
111A ASN* 1.3 79.0 + - - +
113A LEU* 3.4 9.6 + - - +
114A GLU* 3.2 22.6 + - + +
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Residues in contact with ASN 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 SER* 5.2 5.8 - - - -
108A THR* 3.3 26.4 + - - +
110A GLU* 1.3 96.8 + - - +
112A PHE* 1.3 61.3 + - - +
114A GLU* 2.8 44.4 - - - +
115A ARG* 3.3 8.5 + - - +
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Residues in contact with PHE 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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29A VAL* 3.4 24.5 - - + -
30A THR 3.8 11.2 - - - -
31A ASP* 4.6 6.7 - - - -
32A ILE* 3.5 31.6 - - + -
33A PHE* 3.8 22.9 - + - -
48A ALA* 4.3 4.0 - - + -
51A VAL* 3.6 24.5 - - + -
52A LEU* 3.8 37.0 - - + -
107A SER* 4.6 6.7 - - - -
108A THR 3.0 13.7 + - - +
109A LEU* 3.0 10.1 + - + +
111A ASN* 1.3 76.0 - - - +
113A LEU* 1.3 64.0 + - + +
115A ARG* 3.1 7.7 + - - +
116A LEU* 3.0 33.2 + - + +
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Residues in contact with LEU 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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14A LEU* 4.3 9.3 - - + +
17A LEU* 4.4 28.3 - - + +
18A THR* 4.2 15.9 - - + +
25A THR* 5.7 3.6 - - + -
52A LEU* 4.5 17.9 - - + -
79A LEU* 5.5 2.0 - - + -
83A LEU* 4.6 8.7 - - + -
86A LEU* 4.0 27.1 - - + -
109A LEU* 2.8 44.4 + - + +
110A GLU* 3.8 8.3 - - - +
112A PHE* 1.3 73.4 - - + +
114A GLU* 1.3 60.5 + - - +
116A LEU* 3.4 9.4 + - + +
117A LYS* 2.9 28.8 + - - +
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Residues in contact with GLU 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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18A THR* 4.3 10.0 - - + +
110A GLU* 3.2 13.3 + - + +
111A ASN* 2.8 45.8 - - - +
112A PHE 3.2 0.2 - - - -
113A LEU* 1.3 77.2 - - - +
115A ARG* 1.3 69.7 + - - +
117A LYS* 3.2 11.9 - - + +
118A THR* 3.2 26.5 + - - +
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Residues in contact with ARG 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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31A ASP* 5.4 0.9 - - - -
33A PHE* 3.3 44.6 + - + +
111A ASN 3.3 10.9 + - - +
112A PHE* 3.1 9.7 + - - +
114A GLU* 1.3 86.9 + - - +
116A LEU* 1.3 64.0 + - - +
118A THR* 3.4 22.5 + - - +
119A ILE* 3.1 36.6 + - + +
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Residues in contact with LEU 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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10A ILE* 5.2 0.4 - - + -
14A LEU* 4.2 9.2 - - + -
33A PHE* 4.0 21.9 - - + -
45A PHE* 5.9 0.4 - - + -
48A ALA* 4.6 7.2 - - + -
52A LEU* 4.0 17.0 - - + -
86A LEU* 3.9 28.5 - - + -
90A LEU* 4.1 13.7 - - + -
112A PHE* 3.0 19.6 + - + +
113A LEU* 3.6 12.1 - - + +
114A GLU 3.4 0.2 - - - -
115A ARG* 1.3 72.7 - - - +
117A LYS* 1.3 59.3 + - - +
119A ILE* 3.2 6.8 + - + -
120A MET* 2.9 65.5 + - + +
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Residues in contact with LYS 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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11A ILE* 5.3 4.4 - - + +
14A LEU* 3.8 25.5 - - + +
15A ASN* 3.3 31.1 + - - +
18A THR* 2.8 38.9 + - + -
113A LEU 2.9 17.7 + - - +
114A GLU* 3.2 9.2 - - - +
116A LEU* 1.3 76.6 - - - +
118A THR* 1.3 60.7 + - - +
120A MET* 3.4 2.6 + - - +
121A ARG* 3.1 27.0 + - + +
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Residues in contact with THR 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 GLU* 3.2 13.9 + - - +
115A ARG* 3.6 26.5 + - - +
116A LEU 3.2 0.4 - - - -
117A LYS* 1.3 76.0 - - - +
119A ILE* 1.3 68.1 + - + +
121A ARG* 3.1 9.1 + - - +
122A GLU* 3.1 21.7 + - + +
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Residues in contact with ILE 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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33A PHE* 3.7 35.0 - - + -
44A THR* 5.4 7.6 - - + -
45A PHE* 4.7 9.6 - - + -
115A ARG* 3.1 34.9 + - + +
116A LEU* 3.7 8.5 - - + +
118A THR* 1.3 78.8 - - + +
120A MET* 1.3 80.4 + - + +
122A GLU* 3.1 11.8 - - + +
123A LYS* 3.1 23.3 + - + +
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Residues in contact with MET 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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7A LEU* 3.7 26.7 - - + +
10A ILE* 3.8 22.9 - - + -
11A ILE* 3.9 21.5 - - + +
14A LEU* 3.8 6.3 - - + -
45A PHE* 3.4 37.5 - - + -
90A LEU* 3.7 17.7 - - + -
116A LEU* 2.9 39.1 + - + +
117A LYS 3.7 4.9 - - - +
119A ILE* 1.3 80.8 - - + +
121A ARG* 1.3 60.0 + - - +
123A LYS* 3.3 8.0 + - - +
124A TYR* 2.9 26.5 + - - +
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Residues in contact with ARG 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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8A GLN* 3.3 14.3 + - - +
11A ILE* 3.2 36.3 - - + +
117A LYS* 3.1 16.7 + - + +
118A THR* 3.1 9.8 + - - +
120A MET* 1.3 74.0 - - - +
122A GLU* 1.3 59.1 + - - +
124A TYR* 3.2 46.0 - - - +
125A SER* 2.9 33.2 + - - -
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Residues in contact with GLU 122 (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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118A THR* 3.1 12.4 + - + +
119A ILE* 3.1 15.5 - - + +
120A MET 3.2 0.2 - - - -
121A ARG* 1.3 73.3 - - - +
123A LYS* 1.3 66.1 + - - +
125A SER* 3.3 6.3 + - - -
126A LYS* 3.0 62.9 + - - +
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Residues in contact with LYS 123 (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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2A LYS* 3.6 38.7 - - - +
7A LEU* 4.0 16.2 - - + -
41A GLU* 3.2 42.7 + - - +
45A PHE* 4.5 11.4 - - + -
119A ILE* 3.1 12.6 + - + +
120A MET* 3.4 13.2 - - - +
122A GLU* 1.3 78.3 - - - +
124A TYR* 1.3 62.6 + - - +
126A LYS* 3.1 28.6 + - - +
127A CYS* 3.0 29.8 + - - -
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Residues in contact with TYR 124 (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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7A LEU* 4.1 20.8 - - + +
8A GLN* 3.5 22.0 + - + +
11A ILE* 3.9 9.2 - - + -
120A MET 2.9 12.1 + - - +
121A ARG* 3.2 53.2 - - - +
122A GLU 3.3 0.2 - - - -
123A LYS* 1.3 76.3 - - - +
125A SER* 1.3 59.9 + - - +
127A CYS* 3.0 22.3 + - + +
128A SER* 3.2 25.1 + - - -
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Residues in contact with SER 125 (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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121A ARG* 2.9 19.2 + - - -
122A GLU* 3.8 7.4 - - - -
124A TYR* 1.3 78.5 - - - +
126A LYS* 1.3 58.5 + - - +
127A CYS 3.1 0.2 - - - -
128A SER* 3.1 6.4 + - - -
129A SER* 3.1 43.5 + - - +
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Residues in contact with LYS 126 (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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3A CYS* 5.1 0.9 - - - -
41A GLU* 5.1 1.8 + - - -
122A GLU* 3.0 54.9 + - - +
123A LYS* 3.1 30.6 + - + +
125A SER* 1.3 76.2 - - - +
127A CYS* 1.3 61.4 + - - +
128A SER 3.3 0.6 + - - -
129A SER* 4.7 5.9 - - - +
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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