Contacts of the helix formed by residues 106 - 119 (chain D) in PDB entry 4H3K
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 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D LEU* 3.7 37.2 - - + -
71D ASP* 4.0 20.2 - - - +
74D LEU* 4.2 22.4 - - + -
99D ALA* 3.7 21.3 - - + +
100D CYS* 4.2 5.8 - - - -
103D ASP* 2.9 27.0 + - + +
105D GLU* 1.3 74.8 - - - +
107D LEU* 1.3 64.4 + - - +
108D LEU 3.1 0.4 - - - -
109D LYS* 3.0 30.9 + - + +
110D LEU* 3.1 24.7 + - + +
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D CYS* 3.8 22.8 - - - -
104D ILE* 2.9 35.7 + - + +
106D LEU* 1.3 78.4 - - - +
108D LEU* 1.3 61.1 + - - +
110D LEU* 4.3 2.5 - - + +
111D ILE* 3.0 56.0 + - + +
114D LEU* 4.5 5.4 - - + -
133D MET* 6.5 0.4 - - + -
136D LEU* 4.4 20.9 - - + +
140D ALA* 3.8 22.2 - - + -
143D TRP* 4.7 2.5 - - + -
157D CYS* 3.6 16.6 - - - -
161D VAL* 3.9 13.2 - - + -
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D GLU* 3.1 30.2 + - + +
106D LEU 3.1 1.0 - - - -
107D LEU* 1.3 79.4 - - - +
109D LYS* 1.3 61.8 + - + +
111D ILE* 4.3 8.3 - - - +
143D TRP* 3.5 29.2 - - + -
151D SER* 5.4 2.2 - - - +
153D LEU* 3.9 35.0 - - + +
154D GLN* 3.7 26.7 - - + +
157D CYS* 3.7 15.2 - - + +
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Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ASP* 5.3 10.7 + - - +
74D LEU* 3.7 27.3 - - + +
75D ASP* 5.5 3.6 - - - -
105D GLU 4.9 1.6 - - - +
106D LEU* 3.0 32.1 + - + +
108D LEU* 1.3 80.5 - - + +
110D LEU* 1.3 61.9 + - + +
111D ILE 3.6 0.9 - - - -
112D ALA* 4.8 3.5 + - - +
113D ASN* 3.0 17.0 + - - -
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LEU* 4.4 24.7 - - + -
78D ILE* 3.8 32.5 - - + -
95D PHE* 5.6 0.2 - - + -
96D ILE* 4.1 31.1 - - + +
99D ALA* 4.6 4.9 - - + -
100D CYS* 4.0 20.9 - - - -
106D LEU* 3.1 27.8 + - + +
107D LEU* 3.3 2.4 + - - -
109D LYS* 1.3 85.0 - - + +
111D ILE* 1.3 65.2 + - - +
112D ALA 3.2 3.1 - - - -
113D ASN* 3.1 15.0 + - - +
114D LEU* 2.9 22.7 + - - +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU* 3.0 37.2 + - + +
108D LEU 4.3 9.0 - - - +
109D LYS 5.4 0.2 - - - -
110D LEU* 1.3 77.6 - - - +
112D ALA* 1.3 61.6 + - + +
114D LEU* 3.2 8.3 + - + +
115D ASN* 2.9 27.8 + - + +
133D MET* 4.8 2.9 - - + -
157D CYS* 4.2 13.7 - - + +
160D MET* 3.6 39.7 - - + -
161D VAL* 3.7 30.5 - - + +
164D MET* 4.2 20.6 - - - -
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Residues in contact with ALA 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LYS 4.8 2.8 + - - +
110D LEU 3.2 0.8 - - - +
111D ILE* 1.3 82.7 - - + +
113D ASN* 1.3 61.3 + - - +
115D ASN* 3.3 3.3 + - - +
116D MET* 2.8 30.7 + - - +
160D MET* 4.2 19.7 - - + -
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Residues in contact with ASN 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ILE* 3.5 16.0 - - + +
81D GLN* 2.8 32.4 + - - +
96D ILE* 4.4 13.0 - - + -
109D LYS 3.0 26.3 + - - -
110D LEU* 3.1 14.7 + - + +
112D ALA* 1.3 80.1 - - - +
114D LEU* 1.3 61.5 + - - +
116D MET* 3.1 13.0 - - - +
117D LEU* 3.0 27.9 + - + +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ILE* 4.3 17.9 - - + -
96D ILE* 3.9 24.2 - - + +
107D LEU* 4.5 12.3 - - + -
110D LEU 2.9 8.8 + - - +
111D ILE* 3.6 10.5 - - + +
113D ASN* 1.3 78.3 - - - +
115D ASN* 1.3 63.5 + - - +
117D LEU* 3.3 6.5 + - - +
118D LEU 3.0 17.8 + - - -
129D ALA* 4.6 10.3 - - + +
132D THR* 3.9 20.6 - - + -
133D MET* 3.5 29.8 - - - -
136D LEU* 3.7 23.3 - - + -
164D MET* 3.6 13.0 - - + +
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Residues in contact with ASN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ILE 2.9 17.2 + - - +
112D ALA* 3.9 6.7 - - - +
114D LEU* 1.3 75.5 - - - +
116D MET* 1.3 64.5 + - - +
118D LEU* 3.4 17.8 + - - +
119D ARG* 3.5 23.1 + - - +
160D MET* 4.4 20.1 + - + +
163D ALA* 5.9 1.4 - - - +
164D MET* 3.6 43.6 - - - +
167D ASP* 4.3 11.1 + - - +
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Residues in contact with MET 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLN* 4.2 29.6 - - + +
112D ALA 2.8 13.7 + - - +
113D ASN* 3.1 25.6 - - - +
114D LEU 3.2 0.4 - - - -
115D ASN* 1.3 78.8 - - - +
117D LEU* 1.3 70.4 + - + +
119D ARG* 2.9 31.3 + - - +
120D ASP* 3.4 1.9 + - - +
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLN* 4.4 27.1 - - + +
89D ARG* 4.4 10.1 - - + +
92D VAL* 4.5 11.7 - - + -
93D ILE* 3.7 30.1 - - + -
96D ILE* 4.3 18.8 - - + -
113D ASN 3.0 21.5 + - - +
114D LEU* 3.3 5.8 + - - +
116D MET* 1.3 81.8 - - - +
118D LEU* 1.3 61.0 + - - +
119D ARG 3.0 5.6 - - - -
120D ASP* 3.1 30.2 + - - +
125D VAL* 3.8 25.0 - - + +
126D VAL* 4.1 5.2 - - - -
129D ALA* 4.2 3.8 - - + -
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LEU 3.0 5.7 + - - -
115D ASN* 3.6 15.3 - - - +
116D MET 3.2 0.4 - - - -
117D LEU* 1.3 75.7 - - - +
119D ARG* 1.3 60.1 + - + +
120D ASP 3.4 0.7 - - - -
126D VAL* 3.4 27.1 - - + +
129D ALA* 3.8 19.0 - - + +
130D ILE* 3.6 32.1 - - + +
164D MET* 3.6 43.3 - - + -
167D ASP* 4.5 13.9 - - + +
168D ILE* 4.1 18.4 - - + -
171D LEU* 4.6 9.7 - - + +
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Residues in contact with ARG 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ASN* 3.5 20.9 + - - +
116D MET* 2.9 15.1 + - - +
118D LEU* 1.3 85.3 - - + +
120D ASP* 1.3 64.4 + - - +
121D GLU 3.7 0.2 + - - -
126D VAL* 4.6 0.7 - - - -
167D ASP* 4.2 19.8 + - - -
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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
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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