Contacts of the helix formed by residues 112 - 123 (chain B) in PDB entry 3HAD
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B GLU 4.1 0.2 + - - -
111B ASN* 1.3 72.8 + - - +
113B LYS* 1.3 63.8 + - - +
115B LYS* 3.3 1.4 + - - -
116B ASN* 2.8 40.0 + - - +
139B LEU* 3.3 47.2 - - + +
140B GLN* 5.5 2.5 - - + +
143B SER* 4.0 23.1 - - - +
144B ILE* 3.7 28.5 - - + -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASN* 2.9 11.9 + - - +
112B LEU* 1.3 79.0 - - - +
114B VAL* 1.3 61.7 + - + +
116B ASN* 3.5 5.5 - - - +
117B GLU* 2.9 36.8 + - + +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ILE* 3.8 10.8 - - + -
109B VAL* 4.1 13.5 - - + -
111B ASN* 3.2 32.7 + - + +
113B LYS* 1.3 79.7 - - + +
115B LYS* 1.3 64.3 + - - +
117B GLU* 3.4 12.2 + - - +
118B LEU* 2.9 22.2 + - - +
750B NAD 3.8 26.2 - - - +
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU* 3.1 27.4 + - - +
108B ILE* 3.2 24.5 + - + -
109B VAL 2.7 27.3 + - - -
110B GLU* 3.3 14.3 + - - +
111B ASN 2.9 15.5 + - - +
112B LEU* 3.6 4.5 - - - +
114B VAL* 1.3 75.8 - - - +
116B ASN* 1.3 63.3 + - - +
118B LEU* 3.0 5.7 + - - +
119B PHE* 2.8 35.3 + - + -
136B THR* 3.7 10.3 - - - -
139B LEU* 3.6 20.2 - - + -
144B ILE* 3.8 17.9 - - + -
750B NAD 3.1 24.9 + - - -
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Residues in contact with ASN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 2.8 31.9 + - - +
113B LYS* 3.5 5.4 - - - +
115B LYS* 1.3 71.1 - - - +
117B GLU* 1.3 64.3 + - - +
118B LEU 3.1 0.2 + - - -
119B PHE* 3.2 0.9 + - - +
120B LYS* 2.7 29.9 + - - +
143B SER 3.1 28.0 + - - +
144B ILE* 3.4 26.7 - - - +
147B ALA* 3.8 19.8 - - + +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS* 2.9 27.1 + - + +
114B VAL* 3.7 11.7 - - - +
116B ASN* 1.3 71.7 - - - +
118B LEU* 1.3 66.2 + - - +
120B LYS* 3.7 8.7 - - - +
121B ARG* 3.0 32.6 + - + +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.9 29.2 - - + -
94B ALA* 4.6 9.4 - - + -
106B GLU* 4.2 13.9 - - + -
108B ILE* 3.6 26.9 - - + -
114B VAL 2.9 13.8 + - - +
115B LYS 3.0 10.1 + - - +
117B GLU* 1.3 79.6 - - - +
119B PHE* 1.3 61.8 + - + +
121B ARG* 3.3 7.8 + - + +
122B LEU* 3.0 50.9 + - + +
750B NAD 4.8 12.8 - - - +
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 6.1 0.2 - - + -
104B VAL* 4.5 12.3 - - + -
106B GLU* 3.3 48.2 - - + -
115B LYS* 2.8 25.4 + - + +
116B ASN 4.1 1.6 - - - +
118B LEU* 1.3 75.6 - - + +
120B LYS* 1.3 60.6 + - - +
122B LEU* 3.9 6.9 - - + +
123B ASP* 2.8 32.6 + - - +
132B PHE* 3.2 46.1 - + + -
133B ALA 3.7 14.8 - - - -
134B SER* 4.9 1.1 - - - -
144B ILE* 3.9 19.5 - - + +
148B THR* 3.6 14.2 - - + +
154B PHE* 3.4 20.9 - + + -
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ASN 2.7 24.2 + - - +
117B GLU* 3.7 8.3 - - - +
119B PHE* 1.3 74.0 - - - +
121B ARG* 1.3 63.5 + - - +
123B ASP* 3.6 11.5 + - - +
124B LYS* 3.6 28.7 - - - +
147B ALA* 3.3 28.7 + - + +
148B THR* 4.0 2.2 - - - +
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ASP* 4.6 7.1 + - - -
95B ALA* 2.8 38.2 - - - +
117B GLU* 3.0 26.5 + - + +
118B LEU* 3.5 7.2 - - - +
120B LYS* 1.3 77.6 - - - +
122B LEU* 1.3 64.9 + - + +
124B LYS* 3.2 19.6 + - + +
125B ARG* 3.3 47.9 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.3 31.4 - - + -
94B ALA* 3.7 22.7 - - + -
95B ALA* 3.7 12.6 - - + +
98B VAL* 3.7 26.7 - - + -
104B VAL* 4.2 13.7 - - + -
118B LEU* 3.0 31.6 + - + +
119B PHE* 3.9 10.8 - - + +
121B ARG* 1.3 74.2 - - + +
123B ASP* 1.3 65.3 + - - +
124B LYS 3.0 2.5 - - - -
125B ARG* 2.9 14.3 + - - +
126B ALA* 2.9 16.5 + - - +
132B PHE* 3.8 11.4 - - + -
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Residues in contact with ASP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B PHE 2.8 20.2 + - - +
120B LYS 3.6 8.5 - - - +
121B ARG 3.2 0.4 - - - -
122B LEU* 1.3 72.8 - - - +
124B LYS* 1.3 61.8 + - + +
125B ARG 3.5 0.2 + - - -
126B ALA 4.1 1.2 + - - +
132B PHE* 3.7 10.3 - - + -
148B THR* 3.4 20.6 - - + -
149B THR* 2.9 36.3 + - - +
150B ARG* 2.9 46.8 + - - +
153B ARG* 4.8 0.9 + - - -
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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