Contacts of the helix formed by residues 106 - 113 (chain L) in PDB entry 2AAZ
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 SER 106 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102L ASP 3.0 16.2 + - - -
103L GLY* 3.2 13.2 + - - -
104L ASN 3.5 0.2 - - - -
105L GLY* 1.3 82.0 - - - +
107L LYS* 1.3 64.7 + - - +
108L GLU* 3.7 9.2 + - - +
109L PHE* 3.1 16.8 + - - +
110L LEU* 3.0 21.7 + - - +
120L GLU* 3.8 12.1 - - - -
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Residues in contact with LYS 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I ASN* 3.1 26.2 + - - +
105L GLY 4.6 0.2 - - - -
106L SER* 1.3 73.5 - - - +
108L GLU* 1.3 62.5 + - - +
110L LEU* 4.0 5.3 - - + +
111L GLU* 3.1 62.6 + - - +
115L LEU 4.9 0.2 + - - -
116L GLY* 2.9 26.3 + - - -
118L ARG 3.2 17.8 + - - +
119L ARG* 4.5 1.1 - - - +
120L GLU* 3.2 43.5 + - + +
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Residues in contact with GLU 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L SER* 3.0 9.0 - - - +
107L LYS* 1.3 78.2 - - - +
109L PHE* 1.3 65.1 + - - +
111L GLU* 3.6 6.1 + - - +
112L LYS* 3.1 26.0 + - + +
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Residues in contact with PHE 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L ARG* 4.3 11.2 - - - -
103L GLY 3.5 10.1 - - - +
104L ASN* 3.2 42.4 - - - +
106L SER* 3.1 18.9 + - - +
108L GLU* 1.3 76.6 - - - +
110L LEU* 1.3 66.6 + - - +
112L LYS* 2.9 41.8 + - + +
113L VAL* 3.0 36.6 + - + +
183L ALA* 3.2 26.7 - - + -
184L LEU* 4.6 1.8 - - + -
317L ALA* 3.7 33.4 - - + -
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Residues in contact with LEU 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104L ASN 3.7 16.8 - - - +
105L GLY* 3.4 21.8 - - - +
106L SER 3.0 17.0 + - - +
107L LYS* 4.0 5.8 - - - +
109L PHE* 1.3 77.2 - - + +
111L GLU* 1.3 56.5 + - + +
113L VAL* 3.2 12.4 + - - +
115L LEU* 2.7 54.8 + - + +
118L ARG* 4.4 10.5 - - + +
119L ARG 3.7 23.3 - - - +
120L GLU* 4.1 4.3 - - - -
121L GLY 4.1 1.8 - - - +
122L ASP 4.0 19.7 - - - +
183L ALA* 3.9 17.7 - - + -
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Residues in contact with GLU 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I ASN 5.0 0.3 - - - +
163I ASN* 3.5 22.9 + - - +
107L LYS* 3.1 55.4 + - - +
108L GLU* 3.9 5.3 - - - +
110L LEU* 1.3 77.1 - - - +
112L LYS* 1.3 63.0 + - - +
114L GLY* 3.3 11.6 + - - -
116L GLY* 3.6 17.9 - - - +
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Residues in contact with LYS 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J LYS* 3.7 27.9 - - + +
113J VAL* 5.2 2.1 - - - +
40L ARG* 6.0 0.6 + - - +
41L THR* 5.8 2.4 + - - +
108L GLU* 3.1 20.1 + - + +
109L PHE* 2.9 38.8 + - + +
111L GLU* 1.3 80.4 - - - +
113L VAL* 1.3 59.2 + - + +
114L GLY 3.3 2.3 + - - -
317L ALA* 4.5 16.6 + - - +
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Residues in contact with VAL 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J LYS 5.2 2.9 - - - +
113J VAL* 5.7 6.4 - - - +
109L PHE* 3.0 46.0 + - + +
110L LEU* 3.2 17.0 - - - +
112L LYS* 1.3 80.5 - - + +
114L GLY* 1.3 58.5 + - - +
115L LEU* 3.7 26.8 - - + +
180L PRO 5.4 1.9 - - - +
182L MET 5.3 1.3 - - - +
183L ALA* 4.6 7.0 - - - +
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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