Contacts of the helix formed by residues 112 - 119 (chain A) in PDB entry 3SA0
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 ASP* 1.3 70.8 - - - +
113A TYR* 1.3 65.8 + - - +
115A LEU* 4.2 5.6 - - + -
116A LEU* 2.9 48.3 + - + +
121A LEU* 4.3 6.7 - - + -
129A PHE* 4.0 31.2 - - + -
133A ILE* 5.1 1.8 - - + -
152A PRO* 3.3 18.1 + - + +
155A LEU* 2.9 38.4 + - + +
157A LEU* 4.0 13.8 - - + +
163A LEU* 5.5 2.7 - - + -
217A ILE* 3.8 19.5 - - + -
221A MET* 4.1 13.9 - - + -
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Residues in contact with TYR 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 ASP* 3.0 9.3 + - - +
112A LEU* 1.3 78.4 - - - +
114A LYS* 1.3 76.2 - - + +
116A LEU* 3.8 3.5 - - - +
117A LYS* 3.2 62.6 + - + +
152A PRO* 3.3 19.4 + - + +
153A SER* 3.7 27.4 - - - +
192A TRP* 6.0 6.3 - + - -
193A TYR* 5.9 1.1 - - - -
220A GLU* 5.3 7.4 - - - -
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Residues in contact with LYS 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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31A ILE* 5.3 4.0 - - - +
109A GLU 5.1 1.3 + - - -
110A THR* 3.5 31.0 - - - +
111A ASP* 2.9 39.3 + - - +
113A TYR* 1.3 88.6 - - + +
115A LEU* 1.3 64.6 + - - +
117A LYS* 3.4 17.2 + - - +
118A THR* 3.8 9.7 + - - +
156A LEU* 6.2 0.4 - - - +
361A NRA 3.9 28.3 + - - -
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Residues in contact with LEU 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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110A THR* 4.2 12.8 + - + +
111A ASP 3.0 15.8 + - - +
112A LEU* 3.8 9.4 - - + +
113A TYR 3.2 0.2 - - - -
114A LYS* 1.3 78.3 - - - +
116A LEU* 1.3 57.0 + - - +
118A THR 3.1 2.8 + - - -
119A GLN* 2.8 59.9 + - + +
121A LEU* 4.7 7.6 - - + -
129A PHE* 4.1 22.2 - - + -
157A LEU* 3.5 26.7 - - + -
161A CME 4.2 23.6 - - + +
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Residues in contact with LEU 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 43.0 + - + +
113A TYR* 3.3 4.2 + - - +
115A LEU* 1.3 73.8 - - - +
117A LYS* 1.3 66.3 + - - +
119A GLN 4.3 0.2 + - - -
121A LEU* 3.7 33.0 - - + -
152A PRO* 4.4 7.0 - - + -
220A GLU* 3.9 39.0 - - + +
221A MET* 4.1 13.9 - - + +
224A ASN* 3.0 51.3 + - - +
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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 TYR* 3.2 59.3 + - + +
114A LYS* 3.6 11.7 - - - +
115A LEU 3.2 0.6 - - - -
116A LEU* 1.3 80.3 - - - +
118A THR* 1.3 66.7 + - + +
220A GLU* 6.1 0.7 - - - -
224A ASN 6.0 1.8 - - - +
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Residues in contact with THR 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 LYS 3.8 7.6 + - - +
115A LEU* 3.1 3.1 + - - -
116A LEU 4.7 0.2 - - - -
117A LYS* 1.3 92.9 - - + +
119A GLN* 1.3 86.2 + - - +
120A HIS 4.3 0.9 + - - -
224A ASN* 5.4 0.2 - - - -
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Residues in contact with GLN 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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115A LEU* 2.8 42.4 + - + +
116A LEU 4.3 0.6 + - - -
117A LYS 4.0 0.4 - - - -
118A THR* 1.3 107.0 + - - +
120A HIS* 1.3 68.3 + - - +
121A LEU* 3.5 9.1 - - + +
224A ASN* 2.9 20.5 + - - -
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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