Contacts of the helix formed by residues 110 - 132 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLY* 1.3 68.7 - - - -
111C ARG* 1.3 60.6 + - - +
113C ALA* 3.5 8.3 - - - +
114C GLU* 2.8 38.4 + - + +
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Residues in contact with ARG 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLY 3.3 3.7 - - - +
110C ASP* 1.3 76.5 - - - +
112C PHE* 1.3 63.5 + - - +
114C GLU* 3.3 10.3 + - - +
115C LEU* 3.0 47.7 + - - +
324C GLU* 2.7 44.3 + - - -
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Residues in contact with PHE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLY* 3.1 21.8 + - - +
111C ARG* 1.3 78.5 - - - +
113C ALA* 1.3 69.0 + - - +
115C LEU* 3.2 12.0 + - + +
116C LYS* 2.9 51.3 + - + +
328C THR* 4.2 20.9 - - + -
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLY 2.7 17.8 + - - +
110C ASP* 3.2 13.4 + - - +
112C PHE* 1.3 76.0 - - - +
114C GLU* 1.3 64.2 + - + +
116C LYS* 3.0 8.7 + - - +
117C PHE* 2.8 48.2 + - + -
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Residues in contact with GLU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASP* 2.8 28.6 + - + +
111C ARG* 3.5 9.6 - - - +
113C ALA* 1.3 72.6 - - + +
115C LEU* 1.3 63.2 + - + +
117C PHE* 3.4 6.9 + - - +
118C THR* 2.8 32.1 + - - +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ARG* 3.0 47.1 + - - +
112C PHE* 3.2 14.1 + - + +
114C GLU* 1.3 77.2 - - + +
116C LYS* 1.3 65.1 + - - +
118C THR* 3.3 4.8 + - - +
119C SER* 3.0 26.9 + - - -
324C GLU* 3.8 33.4 - - + +
325C ILE* 4.1 23.2 - - + +
328C THR* 3.6 21.8 + - + +
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Residues in contact with LYS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C PHE* 2.9 35.0 + - + +
113C ALA* 3.4 11.2 - - - +
115C LEU* 1.3 77.7 - - - +
117C PHE* 1.3 65.9 + - + +
119C SER* 3.0 19.1 + - - -
120C SER* 3.0 17.2 + - - -
327C ASP 5.4 0.2 + - - -
328C THR* 2.7 39.5 + - - +
329C LEU* 4.3 9.5 + - - -
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Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ALA* 2.8 41.4 + - + +
114C GLU* 3.9 7.2 - - + +
116C LYS* 1.3 83.4 - - + +
118C THR* 1.3 58.1 + - - +
120C SER* 3.6 8.7 - - - -
121C MET* 3.0 28.1 + - - +
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Residues in contact with THR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLY* 4.9 13.3 + - - +
114C GLU* 2.8 23.9 + - - +
115C LEU* 3.8 4.7 - - - -
117C PHE* 1.3 71.7 - - - +
119C SER* 1.3 65.2 + - - +
121C MET* 3.2 21.4 + - + +
122C VAL* 3.0 27.4 + - + +
143C ASN 6.1 0.4 - - - +
148C ILE* 3.8 29.8 - - + -
325C ILE* 4.3 9.6 - - + -
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Residues in contact with SER 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C LEU 3.0 7.1 + - - -
116C LYS 3.0 13.0 + - - -
118C THR* 1.3 72.5 - - - +
120C SER* 1.3 64.9 + - - +
122C VAL* 3.8 1.2 - - - +
123C GLN* 3.0 25.6 + - - +
151C LEU* 4.0 14.1 - - - -
325C ILE* 4.0 15.4 - - - +
328C THR* 2.8 35.1 + - - -
329C LEU* 3.7 21.9 - - - +
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Residues in contact with SER 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LYS* 3.0 19.0 + - - -
117C PHE* 3.6 12.1 - - - -
119C SER* 1.3 78.2 + - - +
121C MET* 1.3 62.3 + - - +
123C GLN* 3.1 10.3 + - - +
124C SER* 2.9 32.4 + - - -
329C LEU* 5.5 0.2 - - - -
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Residues in contact with MET 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LEU* 3.7 41.3 - - + -
98C GLY* 4.0 16.4 - - - +
117C PHE 3.0 14.9 + - - +
118C THR* 3.2 25.5 + - + +
120C SER* 1.3 77.2 - - - +
122C VAL* 1.3 72.6 + - + +
123C GLN 3.3 0.2 + - - -
124C SER* 3.3 5.8 + - - -
125C VAL* 3.0 25.3 + - - +
148C ILE* 6.4 0.7 - - + -
330C NAD 3.5 37.7 - - - +
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Residues in contact with VAL 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C THR 3.0 16.6 + - - +
119C SER 3.8 4.5 - - - +
121C MET* 1.3 89.4 - - + +
123C GLN* 1.3 56.9 + - - +
126C GLY* 2.9 27.4 + - - -
148C ILE* 4.4 15.9 - - + -
151C LEU* 3.9 36.6 - - + +
152C PHE* 4.0 49.0 - - + +
155C VAL* 3.7 4.9 - - + +
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Residues in contact with GLN 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C SER 3.0 18.2 + - - +
120C SER* 3.4 8.0 - - - +
122C VAL* 1.3 77.7 - - - +
124C SER* 1.3 58.2 + - - +
127C THR* 2.8 43.3 + - - +
155C VAL* 3.5 21.6 - - + +
329C LEU* 3.7 43.9 + - + +
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Residues in contact with SER 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C SER* 2.9 21.1 + - - -
121C MET* 3.8 6.2 - - - -
123C GLN* 1.3 74.8 - - - +
125C VAL* 1.3 67.8 + - - +
127C THR* 3.4 4.3 + - - -
128C ASN* 3.0 37.9 + - - +
330C NAD 6.1 1.1 - - - -
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 4.0 32.8 - - + -
84C TRP* 3.9 16.7 - - + -
97C LEU* 3.5 24.7 - - + -
121C MET 3.0 16.8 + - - +
122C VAL 4.4 1.1 - - - +
124C SER* 1.3 82.3 - - - +
126C GLY* 1.3 57.7 + - - +
128C ASN* 3.4 1.8 + - - +
129C LEU* 2.8 31.0 + - + +
152C PHE* 4.0 21.1 - - + -
330C NAD 4.0 20.6 - - + +
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Residues in contact with GLY 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C VAL 2.9 20.6 + - - -
123C GLN 3.9 0.4 - - - -
125C VAL* 1.3 78.8 - - - +
127C THR* 1.3 54.5 + - - +
129C LEU* 3.6 3.5 - - - +
130C LYS* 2.9 29.5 + - - +
152C PHE* 4.1 8.2 - - - -
155C VAL* 4.2 5.8 - - - -
156C THR* 3.4 27.2 - - - +
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Residues in contact with THR 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLN* 2.8 30.2 + - - +
124C SER* 3.9 4.5 - - - -
125C VAL 3.3 0.2 - - - -
126C GLY* 1.3 72.4 - - - +
128C ASN* 1.3 66.4 + - - +
130C LYS* 3.2 17.9 + - - +
131C GLU* 2.8 51.5 + - + +
155C VAL* 4.3 9.9 + - - +
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Residues in contact with ASN 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C TRP* 3.8 45.8 - - + +
124C SER* 3.0 30.1 + - - +
125C VAL 3.8 1.6 - - - +
127C THR* 1.3 80.1 - - - +
129C LEU* 1.3 60.7 + - - +
131C GLU* 3.4 8.5 + - - +
132C SER* 3.0 23.6 + - - -
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 4.4 10.5 - - + -
84C TRP* 3.8 7.3 - - + -
87C LEU* 3.7 27.6 - - + -
93C VAL* 4.3 11.0 - - + -
125C VAL 2.8 18.4 + - - +
126C GLY 3.6 5.4 - - - +
128C ASN* 1.3 76.7 - - - +
130C LYS* 1.3 60.1 + - - +
132C SER* 2.5 24.5 + - - -
134C PHE* 3.9 32.7 + - + +
138C LEU* 3.8 37.5 - - + -
152C PHE* 5.1 6.5 - - + -
156C THR* 4.9 3.8 - - + -
158C PHE* 4.2 12.3 - - + -
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Residues in contact with LYS 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C GLY 2.9 17.6 + - - +
127C THR* 3.4 15.9 + - - +
129C LEU* 1.3 75.1 - - - +
131C GLU* 1.3 81.5 + - - +
132C SER 3.3 1.0 + - - -
133C GLY* 3.3 13.2 + - - -
134C PHE 4.6 1.9 + - - +
155C VAL 4.3 11.7 - - - -
156C THR* 3.3 27.6 - - - +
158C PHE* 3.9 21.6 - - + -
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Residues in contact with GLU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C THR* 2.8 36.9 + - + +
128C ASN* 3.8 9.2 - - - +
129C LEU 3.3 0.2 - - - -
130C LYS* 1.3 97.9 + - + +
132C SER* 1.3 59.3 + - - +
133C GLY* 3.3 1.0 + - - -
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Residues in contact with SER 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C TRP* 3.1 32.5 - - - -
85C ALA* 4.5 7.4 - - - +
87C LEU* 4.0 8.9 - - - +
88C ALA* 3.5 20.0 - - - +
128C ASN 3.0 12.7 + - - -
129C LEU* 2.5 23.3 + - - -
131C GLU* 1.3 76.3 - - - +
133C GLY* 1.3 56.7 + - - +
134C PHE* 3.2 15.6 + - - +
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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
------------------------------------------------------------
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