Contacts of the helix formed by residues 112 - 122 (chain A) in PDB entry 2HDH
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ASN* 1.3 71.4 + - - +
113A LYS* 1.3 66.7 + - - +
115A LYS* 3.2 2.9 + - - +
116A ASN* 2.9 53.0 + - - +
139A LEU* 3.9 29.5 - - + +
143A SER* 4.0 24.7 - - - +
144A ILE* 3.8 20.4 - - + -
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Residues in contact with LYS 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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111A ASN* 2.9 14.4 + - - +
112A LEU* 1.3 76.9 - - - +
114A VAL* 1.3 65.4 + - + +
116A ASN* 3.4 5.8 + - - +
117A GLU* 3.0 33.7 + - + +
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Residues in contact with VAL 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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108A ILE* 3.8 20.6 - - + -
109A VAL* 4.0 16.4 - - + -
111A ASN* 2.9 33.8 + - + +
113A LYS* 1.3 78.8 - - + +
115A LYS* 1.3 63.4 + - - +
117A GLU* 3.3 11.5 + - - +
118A LEU* 3.0 20.8 + - - +
350A NAD 3.8 18.6 - - - +
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Residues in contact with LYS 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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106A GLU* 3.1 33.3 + - - +
108A ILE* 3.2 18.4 + - + -
109A VAL 2.7 30.2 + - - +
110A GLU* 3.2 18.0 + - - +
111A ASN 3.1 8.6 + - - +
112A LEU 3.6 5.8 - - - +
114A VAL* 1.3 76.2 - - - +
116A ASN* 1.3 60.1 + - - +
118A LEU* 3.0 9.6 + - - +
119A PHE* 2.9 35.6 + - + -
136A THR* 3.8 23.3 - - - -
139A LEU* 3.4 23.6 - - + -
144A ILE* 3.6 23.3 - - + -
350A NAD 3.2 0.8 + - - -
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Residues in contact with ASN 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 LEU* 2.9 36.6 + - - +
113A LYS* 3.8 5.8 - - - +
115A LYS* 1.3 74.2 - - - +
117A GLU* 1.3 58.6 + - - +
119A PHE* 4.6 0.4 - - - +
120A LYS* 2.8 33.5 + - - +
143A SER 3.1 18.7 + - - -
144A ILE* 3.1 25.7 - - - +
146A ASN 5.5 0.2 - - - -
147A ALA* 3.5 24.4 - - + +
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Residues in contact with GLU 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 LYS* 3.0 28.3 + - + +
114A VAL* 3.6 10.9 - - - +
116A ASN* 1.3 75.8 - - - +
118A LEU* 1.3 65.2 + - - +
120A LYS* 3.5 9.1 + - + +
121A ARG* 3.3 21.5 + - + +
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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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21A ILE* 4.0 28.9 - - + -
94A ALA* 5.3 2.7 - - + -
106A GLU* 3.9 29.4 - - + -
108A ILE* 3.9 15.9 - - + -
114A VAL 3.0 14.5 + - - +
115A LYS* 3.2 9.6 - - - +
117A GLU* 1.3 80.6 - - - +
119A PHE* 1.3 62.5 + - + +
121A ARG* 3.3 5.6 + - - +
122A LEU* 3.0 48.6 + - + +
350A NAD 4.8 12.8 - - - +
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Residues in contact with PHE 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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104A VAL* 4.1 15.7 - - + -
106A GLU* 3.4 46.2 - - + -
115A LYS* 2.9 29.3 + - + +
116A ASN 4.3 1.6 - - - +
118A LEU* 1.3 75.3 - - + +
120A LYS* 1.3 66.1 + - - +
122A LEU* 4.3 10.3 - - + +
123A ASP* 3.0 24.9 + - - +
132A PHE* 3.4 43.7 - + + -
133A ALA 3.8 11.7 - - - -
134A SER* 4.7 0.4 - - - -
144A ILE* 3.6 20.6 - - + +
147A ALA* 5.0 0.2 - - + -
148A THR* 3.5 18.4 - - + +
154A PHE* 3.7 18.2 - + + -
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Residues in contact with LYS 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 ASN 2.8 23.6 + - - +
117A GLU* 3.8 8.7 - - + +
119A PHE* 1.3 74.4 - - - +
121A ARG* 1.3 61.9 + - - +
123A ASP* 3.5 13.5 - - - +
124A LYS* 3.9 27.5 - - - +
147A ALA* 3.5 27.7 + - + +
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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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93A ASP* 3.0 40.6 + - - -
95A ALA* 3.2 16.9 - - - +
117A GLU* 3.3 13.4 + - + +
118A LEU* 3.3 6.4 + - - +
120A LYS* 1.3 78.1 - - - +
122A LEU* 1.3 68.2 + - + +
123A ASP 3.1 2.0 - - - -
124A LYS* 3.2 23.4 + - + +
125A ARG* 3.4 39.2 - - - +
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Residues in contact with LEU 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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21A ILE* 3.4 31.0 - - + -
94A ALA* 3.7 10.3 - - + -
95A ALA* 3.5 36.6 - - + +
98A VAL* 4.1 11.8 - - + +
104A VAL* 4.2 14.1 - - + -
118A LEU* 3.0 34.9 + - + +
119A PHE* 4.1 9.9 - - + +
121A ARG* 1.3 79.4 - - + +
123A ASP* 1.3 67.2 + - - +
125A ARG* 2.9 15.9 + - - +
126A ALA* 3.0 15.6 + - - +
132A PHE* 3.8 12.8 - - + -
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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