Contacts of the helix formed by residues 110 - 119 (chain A) in PDB entry 7ACN
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 GLU 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A GLY 3.5 0.4 + - - +
109A GLY* 1.3 68.4 - - - -
111A LYS* 1.3 87.5 + - + +
113A LEU* 3.3 9.1 + - - +
114A ARG* 2.8 76.0 + - - +
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Residues in contact with LYS 111 (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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107A LEU* 3.8 43.8 - - + +
108A GLY 3.4 6.0 + - - +
110A GLU* 1.3 99.1 + - + +
112A ASP* 1.4 64.8 + - - +
114A ARG* 3.3 18.6 + - - +
115A ARG* 3.1 23.8 + - - +
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Residues in contact with ASP 112 (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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103A ILE* 4.0 11.0 - - + +
104A GLU 3.3 21.3 - - - +
105A ALA* 3.4 7.4 - - - +
106A GLN* 2.9 20.1 + - - +
107A LEU* 2.8 23.9 + - - +
108A GLY* 2.8 38.8 + - - +
109A GLY 3.8 4.3 - - - +
111A LYS* 1.4 75.7 - - - +
113A LEU* 1.3 58.9 + - - +
115A ARG* 3.5 10.9 + - - +
116A ALA* 3.0 29.1 + - - +
417A LEU* 4.7 1.4 - - - +
418A ALA* 4.7 4.9 + - + +
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Residues in contact with LEU 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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103A ILE* 3.9 23.0 - - + +
109A GLY 3.1 13.5 + - - +
110A GLU* 3.6 11.7 - - - +
111A LYS 3.3 0.2 - - - -
112A ASP* 1.3 79.2 - - - +
114A ARG* 1.3 63.1 + - + +
116A ALA* 3.4 0.9 + - - +
117A LYS* 3.0 46.3 + - + +
141A PRO* 3.8 15.3 - - + +
142A GLY* 3.7 38.6 - - - +
418A ALA* 4.6 6.7 - - + -
514A GLN* 4.9 9.2 - - - +
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Residues in contact with ARG 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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110A GLU* 2.8 72.9 + - - +
111A LYS* 3.6 23.0 - - - +
113A LEU* 1.3 76.4 - - + +
115A ARG* 1.3 63.8 + - - +
117A LYS* 3.2 12.8 + - + +
118A ASP* 3.1 20.8 + - - +
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Residues in contact with ARG 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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104A GLU* 2.7 51.3 + - - +
106A GLN* 3.1 42.1 + - - +
107A LEU* 5.1 6.5 - - + -
111A LYS 3.1 13.1 + - - +
112A ASP* 3.7 9.5 + - - +
114A ARG* 1.3 77.2 - - - +
116A ALA* 1.4 61.1 + - - +
118A ASP* 3.1 7.1 + - - +
119A ILE* 2.8 59.8 + - + +
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU 4.0 0.7 - - - +
103A ILE* 3.7 36.8 - - + -
104A GLU 4.9 1.3 - - - +
112A ASP 3.0 18.7 + - - +
113A LEU* 3.8 4.3 - - + +
115A ARG* 1.4 75.6 - - - +
117A LYS* 1.3 57.7 + - - +
119A ILE* 4.4 4.0 - - - -
120A ASN* 2.8 49.7 + - - +
124A TYR* 3.5 4.6 - - + +
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Residues in contact with LYS 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 LEU* 3.0 40.8 + - + +
114A ARG* 3.2 12.1 + - + +
116A ALA* 1.3 75.5 - - - +
118A ASP* 1.3 63.0 + - - +
121A GLN* 3.4 24.6 + - - +
124A TYR* 3.9 9.5 - - + -
140A ARG* 6.1 1.3 - - - +
141A PRO* 3.9 37.7 + - + -
514A GLN* 5.6 2.8 + - - -
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Residues in contact with ASP 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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114A ARG 3.1 11.0 + - - +
115A ARG* 3.1 12.0 + - - +
117A LYS* 1.3 77.3 - - - +
119A ILE* 1.3 70.6 + - - +
120A ASN 3.2 0.7 + - - -
121A GLN* 3.3 14.3 + - - +
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Residues in contact with ILE 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 GLU* 6.4 0.2 - - + -
115A ARG* 2.8 62.0 + - + +
116A ALA* 4.1 4.5 - - - +
118A ASP* 1.3 79.3 - - - +
120A ASN* 1.4 73.3 + - - +
121A GLN 3.6 0.5 + - - -
122A GLU* 5.1 1.0 + - - +
537A ARG* 3.3 15.7 + - - +
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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
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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