Contacts of the helix formed by residues 106 - 113 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102G ASP 3.0 15.7 + - - -
103G GLY* 3.3 12.7 + - - -
104G ASN 3.5 0.2 - - - -
105G GLY* 1.3 81.1 - - - +
107G LYS* 1.3 64.2 + - - +
108G GLU* 3.8 7.5 + - - +
109G PHE* 3.2 15.1 + - - +
110G LEU* 3.0 21.0 + - - +
120G GLU* 3.7 14.6 - - - -
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Residues in contact with LYS 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G GLY 3.8 1.0 + - - -
106G SER* 1.3 72.3 - - - +
108G GLU* 1.3 55.5 + - - +
110G LEU* 4.4 6.1 - - + -
111G GLU* 2.7 81.9 + - + +
116G GLY* 3.1 27.4 + - - -
117G HIS 5.1 0.4 - - - -
118G ARG 3.1 21.2 + - - +
119G ARG* 4.7 3.4 - - - +
120G GLU* 3.3 27.7 + - + +
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Residues in contact with GLU 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G SER* 3.2 7.7 + - - +
107G LYS* 1.3 79.0 - - - +
109G PHE* 1.3 59.9 + - - +
111G GLU* 3.9 5.9 - - - +
112G LYS* 2.9 46.1 + - + +
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Residues in contact with PHE 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G ARG* 4.1 12.1 - - - -
103G GLY 3.5 20.6 - - - +
104G ASN* 3.3 41.3 - - - +
106G SER* 3.2 10.6 + - - +
108G GLU* 1.3 81.6 - - - +
110G LEU* 1.3 63.5 + - - +
112G LYS* 2.9 34.9 + - + +
113G VAL* 3.0 42.0 + - + +
183G ALA* 3.3 27.4 - - + -
184G LEU* 4.5 2.9 - - + -
317G ALA* 3.5 34.1 - - + -
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Residues in contact with LEU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ASN 3.7 16.4 - - - +
105G GLY* 3.4 22.7 - - - +
106G SER 3.0 16.3 + - - +
107G LYS* 3.7 7.6 - - + +
109G PHE* 1.3 75.6 - - - +
111G GLU* 1.3 56.3 + - - +
113G VAL* 3.2 12.0 + - - +
115G LEU* 2.7 54.5 + - + +
118G ARG* 4.4 9.0 - - + +
119G ARG 3.6 23.6 - - - +
120G GLU* 4.2 4.0 - - - -
121G GLY 4.1 1.6 - - - +
122G ASP 4.0 19.7 - - - +
183G ALA* 3.9 19.1 - - + -
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Residues in contact with GLU 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G LYS* 2.7 66.5 + - + +
108G GLU* 4.1 5.1 - - - +
110G LEU* 1.3 72.5 - - - +
112G LYS* 1.3 62.2 + - - +
114G GLY* 3.2 12.3 + - - -
116G GLY* 3.6 18.6 - - - +
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Residues in contact with LYS 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G ARG* 5.9 1.2 + - - +
41G THR* 5.7 3.2 + - - +
108G GLU* 2.9 35.0 + - + +
109G PHE* 3.0 30.4 - - + +
111G GLU* 1.3 79.5 - - - +
113G VAL* 1.3 60.3 + - + +
114G GLY 3.6 2.1 + - - -
317G ALA* 4.6 15.0 + - - +
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Residues in contact with VAL 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G PHE* 3.0 46.2 + - + +
110G LEU* 3.2 15.7 - - - +
112G LYS* 1.3 80.8 - - + +
114G GLY* 1.3 59.2 + - - +
115G LEU* 3.7 27.4 - - + +
180G PRO 5.3 1.9 - - - +
182G MET 5.3 1.1 - - - +
183G ALA* 4.5 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