Contacts of the helix formed by residues 110 - 132 (chain D) in PDB entry 1HYH
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 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D GLY* 1.3 70.4 - - - +
111D ARG* 1.3 53.3 + - - +
113D ALA* 3.0 7.3 + - - +
114D GLU* 2.7 58.5 + - - +
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Residues in contact with ARG 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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109D GLY 3.6 1.7 - - - +
110D ASP* 1.3 77.2 - - - +
112D PHE* 1.3 59.5 + - - +
114D GLU* 3.5 11.7 + - - +
115D LEU* 2.9 55.6 + - + +
321D ARG* 4.8 9.3 - - - +
324D GLU* 2.5 43.7 + - - -
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Residues in contact with PHE 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 GLY* 3.6 17.0 + - - +
110D ASP 3.3 0.4 - - - -
111D ARG* 1.3 77.2 - - + +
113D ALA* 1.3 72.7 + - - +
115D LEU* 3.2 9.5 + - + +
116D LYS* 2.9 56.2 + - + +
328D THR* 4.1 22.2 - - + -
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Residues in contact with ALA 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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109D GLY 2.8 22.1 + - - +
110D ASP* 3.2 7.2 - - - +
112D PHE* 1.3 78.2 - - - +
114D GLU* 1.3 63.8 + - + +
116D LYS* 3.0 8.6 + - - +
117D PHE* 2.9 46.3 + - + -
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Residues in contact with GLU 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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110D ASP* 2.7 49.5 + - - +
111D ARG* 3.7 8.9 - - - +
113D ALA* 1.3 71.2 - - + +
115D LEU* 1.3 65.2 + - + +
116D LYS 3.2 0.2 + - - -
117D PHE* 3.2 9.4 + - + +
118D THR* 2.8 31.0 + - - +
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Residues in contact with LEU 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 ARG* 2.9 51.5 + - + +
112D PHE* 3.5 11.9 - - + +
114D GLU* 1.3 76.1 - - + +
116D LYS* 1.3 53.2 + - - +
118D THR* 3.6 5.1 - - + -
119D SER* 2.8 36.6 + - - -
324D GLU* 3.6 36.3 - - + +
325D ILE* 4.0 25.4 - - + +
328D THR* 3.6 23.0 + - + +
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Residues in contact with LYS 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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112D PHE* 2.9 40.5 + - + +
113D ALA* 3.0 13.4 + - - +
115D LEU* 1.3 75.0 - - - +
117D PHE* 1.3 69.2 + - + +
119D SER* 3.1 7.8 + - - -
120D SER* 2.9 30.4 + - - -
328D THR* 2.9 33.0 + - - +
329D LEU* 4.4 8.8 + - - -
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Residues in contact with PHE 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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113D ALA* 2.9 41.5 + - + +
114D GLU* 3.9 7.9 - - + +
116D LYS* 1.3 84.8 - - + +
118D THR* 1.3 56.5 + - - +
120D SER* 3.4 6.7 + - - -
121D MET* 2.9 30.3 + - - +
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Residues in contact with THR 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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98D GLY 5.4 10.9 - - - -
114D GLU* 2.8 26.3 + - - +
115D LEU* 3.6 6.7 - - + -
117D PHE* 1.3 74.7 - - - +
119D SER* 1.4 66.8 + - - +
121D MET* 3.2 18.1 + - + +
122D VAL* 3.0 23.3 + - + +
148D ILE* 3.8 28.5 - - + -
325D ILE* 3.8 10.5 - - + -
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Residues in contact with SER 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 LEU 2.8 13.1 + - - -
116D LYS 3.1 11.4 + - - -
118D THR* 1.4 74.2 - - - +
120D SER* 1.3 61.9 + - - +
122D VAL* 3.3 2.6 + - - +
123D GLN* 3.0 23.7 + - - +
151D LEU* 4.2 15.1 - - - +
325D ILE* 3.9 16.4 - - - -
328D THR* 2.9 36.7 + - - -
329D LEU* 3.7 19.4 - - - +
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Residues in contact with SER 120 (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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116D LYS* 2.9 19.8 + - - -
117D PHE* 3.5 10.8 - - - -
118D THR 3.2 0.2 - - - -
119D SER* 1.3 78.6 + - - +
121D MET* 1.3 63.8 + - - +
123D GLN* 3.1 10.4 + - - +
124D SER* 2.9 32.1 + - - -
329D LEU* 5.3 1.6 - - - -
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Residues in contact with MET 121 (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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97D LEU* 3.9 38.1 - - + -
98D GLY* 4.3 20.6 - - - +
117D PHE 2.9 17.3 + - - +
118D THR* 3.6 12.3 - - + +
120D SER* 1.3 75.5 + - - +
122D VAL* 1.3 85.6 + - + +
124D SER* 3.3 6.0 + - - -
125D VAL* 3.0 24.9 + - - +
148D ILE* 6.0 1.3 - - + -
330D NAD 3.6 35.0 - - - +
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Residues in contact with VAL 122 (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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118D THR 3.0 17.1 + - - +
119D SER 3.8 4.7 - - - +
120D SER 3.3 0.2 - - - -
121D MET* 1.3 88.6 - - + +
123D GLN* 1.4 58.2 + - - +
125D VAL* 4.7 0.4 - - - -
126D GLY* 2.8 27.2 + - - -
148D ILE* 4.2 24.9 - - + -
151D LEU* 3.9 24.2 - - + +
152D PHE* 3.9 49.4 - - + +
155D VAL* 4.0 4.9 - - + +
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Residues in contact with GLN 123 (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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119D SER 3.0 13.2 + - - +
120D SER* 3.5 11.7 - - - +
122D VAL* 1.4 77.7 - - - +
124D SER* 1.3 61.2 + - - +
127D THR* 2.7 43.7 + - - +
155D VAL* 3.5 24.4 - - + +
329D LEU* 3.6 38.8 + - + +
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Residues in contact with SER 124 (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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120D SER* 2.9 23.1 + - - -
121D MET* 3.8 6.4 - - - -
123D GLN* 1.3 74.9 - - - +
125D VAL* 1.3 68.0 + - - +
127D THR* 3.8 3.5 - - - -
128D ASN* 2.9 36.7 + - - +
330D NAD 6.3 0.2 - - - -
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Residues in contact with VAL 125 (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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27D ILE* 4.1 26.7 - - + -
84D TRP* 4.0 16.0 - - + -
97D LEU* 3.5 27.1 - - + -
121D MET 3.0 17.0 + - - +
122D VAL 4.2 1.6 - - - +
124D SER* 1.3 75.0 - - - +
126D GLY* 1.3 59.1 + - - +
128D ASN* 3.2 4.2 + - - +
129D LEU* 2.8 31.4 + - + +
152D PHE* 3.8 23.3 - - + -
330D NAD 4.2 20.0 - - - +
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Residues in contact with GLY 126 (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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122D VAL 2.8 23.1 + - - -
123D GLN 4.1 0.2 - - - -
125D VAL* 1.3 75.6 - - - +
127D THR* 1.4 54.9 + - - +
129D LEU* 3.6 3.2 - - - +
130D LYS* 2.9 30.3 + - - +
152D PHE* 3.9 9.2 - - - -
155D VAL* 4.3 7.6 - - - -
156D THR* 3.7 23.6 - - - +
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Residues in contact with THR 127 (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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123D GLN* 2.7 34.2 + - - +
124D SER* 3.8 4.7 - - - -
126D GLY* 1.4 71.5 - - - +
128D ASN* 1.3 66.2 + - - +
130D LYS* 3.3 11.3 + - + +
131D GLU* 2.8 49.8 + - + +
155D VAL* 4.3 6.8 + - - +
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Residues in contact with ASN 128 (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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84D TRP* 3.8 43.5 - - + +
124D SER* 2.9 28.1 + - - +
125D VAL 3.7 3.1 - - - +
127D THR* 1.3 80.5 - - - +
129D LEU* 1.3 62.8 + - - +
131D GLU* 3.3 7.4 + - - +
132D SER* 3.0 24.3 + - - -
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Residues in contact with LEU 129 (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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27D ILE* 4.6 10.3 - - + -
84D TRP* 3.8 8.0 - - + -
87D LEU* 3.6 28.5 - - + -
93D VAL* 4.2 8.7 - - + -
125D VAL 2.8 17.4 + - - +
126D GLY* 3.6 4.7 - - - +
128D ASN* 1.3 77.2 - - - +
130D LYS* 1.3 60.1 + - - +
132D SER* 2.5 25.2 + - - -
134D PHE* 3.8 34.2 + - + +
138D LEU* 3.9 33.2 - - + -
152D PHE* 5.1 6.3 - - + -
156D THR* 4.8 3.4 - - + -
158D PHE* 4.1 17.3 - - + -
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Residues in contact with LYS 130 (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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126D GLY 2.9 18.3 + - - +
127D THR* 3.7 10.6 - - + +
129D LEU* 1.3 78.8 - - - +
131D GLU* 1.3 79.4 + - - +
132D SER 3.3 0.7 + - - -
133D GLY* 3.5 10.7 + - - -
134D PHE 4.7 1.7 + - - +
155D VAL 4.8 4.7 + - - +
156D THR* 3.6 30.5 - - - +
158D PHE* 3.9 20.9 - - + -
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Residues in contact with GLU 131 (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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127D THR* 2.8 38.8 + - + +
128D ASN* 3.8 9.0 - - - +
129D LEU 3.3 0.2 - - - -
130D LYS* 1.3 97.3 + - + +
132D SER* 1.3 61.8 + - - +
133D GLY* 3.3 1.4 + - - -
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Residues in contact with SER 132 (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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84D TRP* 3.2 32.8 - - - -
85D ALA* 4.4 7.2 - - - +
87D LEU* 4.0 7.2 - - - +
88D ALA* 3.5 17.7 - - - +
128D ASN 3.0 13.0 + - - -
129D LEU* 2.5 24.8 + - - -
131D GLU* 1.3 76.0 - - - +
133D GLY* 1.3 54.8 + - - +
134D PHE* 3.2 17.7 + - - +
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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
------------------------------------------------------------
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