Contacts of the helix formed by residues 112 - 121 (chain B) in PDB entry 5HKE
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 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 3.7 12.8 - - - +
110B CYS 3.6 0.8 - - - -
111B SER* 1.3 90.0 + - - +
113B VAL* 1.3 64.8 + - - +
114B ASN* 3.4 9.8 + - - +
115B GLU* 3.0 30.1 + - - +
116B ALA* 3.1 19.9 + - - +
145B ASP* 3.5 15.0 - - + +
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Residues in contact with VAL 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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73B LEU* 4.0 4.5 - - + -
112B ASP* 1.3 72.9 - - - +
114B ASN* 1.4 58.2 + - - +
116B ALA* 3.2 7.2 + - - +
117B ARG* 2.8 30.9 + - - +
143B ILE* 4.1 7.6 - - + +
144B ALA* 3.9 8.7 - - - -
145B ASP* 2.9 40.8 + - + +
148B LYS* 3.5 40.4 - - + +
150B ILE* 3.7 33.2 - - + +
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Residues in contact with ASN 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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112B ASP* 3.3 10.8 + - - +
113B VAL* 1.4 75.8 - - - +
115B GLU* 1.3 63.6 + - + +
117B ARG* 3.3 21.0 + - - +
118B ASN* 3.0 32.9 + - - +
148B LYS* 2.9 33.7 + - - +
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Residues in contact with GLU 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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49B LYS* 5.1 0.7 - - - -
109B GLN 4.0 5.4 - - - +
110B CYS* 3.5 21.7 - - + -
111B SER* 2.8 40.7 + - - -
112B ASP* 3.0 20.4 + - - +
114B ASN* 1.3 75.1 - - + +
116B ALA* 1.3 66.9 + - - +
118B ASN* 3.3 9.6 + - - +
119B LEU* 3.0 19.1 + - - +
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Residues in contact with ALA 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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73B LEU* 4.3 3.8 - - + -
106B ILE* 3.8 23.2 - - + +
110B CYS* 3.7 11.1 - - - -
112B ASP 3.1 13.0 + - - +
113B VAL 3.4 8.1 - - - +
115B GLU* 1.3 78.0 - - - +
117B ARG* 1.3 52.2 + - - +
119B LEU* 3.2 2.4 + - - +
120B VAL* 2.8 40.7 + - - +
143B ILE* 3.9 26.7 - - + -
150B ILE* 4.8 1.1 - - + -
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Residues in contact with ARG 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 VAL* 2.8 17.9 + - - +
114B ASN* 3.5 31.8 + - - +
116B ALA* 1.3 71.7 - - - +
118B ASN* 1.3 65.6 + - - +
120B VAL* 3.2 7.5 + - - +
121B GLU* 2.9 53.8 + - - +
148B LYS* 4.0 12.9 - - - +
150B ILE* 4.0 30.7 - - + +
161B ILE* 3.8 24.2 + - + +
163B ASP* 3.1 32.3 + - - +
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Residues in contact with ASN 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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114B ASN* 3.0 22.1 + - - +
115B GLU* 3.7 8.9 - - - +
116B ALA 3.3 0.2 - - - -
117B ARG* 1.3 84.7 + - - +
119B LEU* 1.3 61.0 + - - +
121B GLU* 3.3 28.9 + - - +
122B LYS* 3.0 30.4 + - - +
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Residues in contact with LEU 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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95B ASP* 3.9 14.1 - - - +
105B TRP* 3.6 53.8 - - + +
106B ILE* 3.8 11.4 - - + -
109B GLN* 3.7 12.3 - - + +
110B CYS* 3.7 18.2 - - - -
115B GLU 3.0 15.9 + - - +
116B ALA 3.8 2.9 - - - +
118B ASN* 1.3 74.0 - - - +
120B VAL* 1.3 67.7 + - - +
122B LYS* 3.0 29.6 + - + +
123B ILE* 3.6 7.5 + - - +
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Residues in contact with VAL 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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102B PHE* 3.9 14.8 - - + -
106B ILE* 3.8 17.3 - - + -
116B ALA 2.8 23.4 + - - +
117B ARG* 3.6 5.8 - - - +
119B LEU* 1.3 77.4 - - - +
121B GLU* 1.3 61.1 + - - +
122B LYS 3.1 1.4 + - - -
123B ILE* 3.1 27.8 + - + +
143B ILE* 4.5 5.8 - - + -
150B ILE* 5.6 0.2 - - + -
152B VAL* 3.9 28.5 - - + -
159B VAL* 3.7 21.3 - - + +
161B ILE* 3.6 20.6 - - + -
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Residues in contact with GLU 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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94B LYS* 3.0 22.4 + - - -
117B ARG* 2.9 42.0 + - - +
118B ASN* 3.5 19.7 - - - +
119B LEU 3.3 0.4 - - - -
120B VAL* 1.3 74.7 - - - +
122B LYS* 1.3 57.7 + - + +
123B ILE 3.5 0.2 - - - -
159B VAL* 5.4 2.7 - - - -
161B ILE* 3.8 13.8 - - + +
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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