Contacts of the helix formed by residues 106 - 113 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102P ASP 3.0 15.1 + - - -
103P GLY* 3.2 13.5 + - - -
105P GLY* 1.3 81.7 - - - +
107P LYS* 1.3 65.7 + - - +
108P GLU* 3.7 8.8 + - - +
109P PHE* 3.1 16.3 + - - +
110P LEU* 3.0 22.2 + - - +
120P GLU* 3.8 13.0 - - - -
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Residues in contact with LYS 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P GLY 4.6 0.2 - - - -
106P SER* 1.3 73.1 - - - +
108P GLU* 1.3 61.9 + - - +
110P LEU* 4.1 5.5 - - + +
111P GLU* 3.1 65.2 + - - +
116P GLY* 2.9 26.4 + - - -
118P ARG 3.1 23.0 + - - +
119P ARG* 4.4 2.0 - - - +
120P GLU* 3.3 39.4 + - + +
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Residues in contact with GLU 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P SER* 3.0 8.9 - - - +
107P LYS* 1.3 80.2 - - - +
109P PHE* 1.3 61.7 + - - +
111P GLU* 4.0 5.3 - - - +
112P LYS* 3.1 26.1 + - + +
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Residues in contact with PHE 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P ARG* 4.3 11.7 - - - -
103P GLY 3.5 8.3 - - - +
104P ASN* 3.2 45.8 - - + +
106P SER* 3.1 17.8 + - - +
108P GLU* 1.3 78.4 - - - +
110P LEU* 1.3 66.1 + - - +
112P LYS* 2.9 37.2 + - + +
113P VAL* 3.0 39.6 + - + +
183P ALA* 3.2 26.5 - - + -
184P LEU* 4.6 2.5 - - + -
317P ALA* 3.6 34.3 - - + -
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Residues in contact with LEU 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P ASN 3.8 16.4 - - - +
105P GLY* 3.5 22.4 - - - +
106P SER 3.0 16.5 + - - +
107P LYS* 4.1 5.4 - - + +
109P PHE* 1.3 77.4 - - + +
111P GLU* 1.3 56.9 + - + +
113P VAL* 3.1 12.7 + - - +
115P LEU* 2.7 54.5 + - + +
116P GLY* 5.2 0.2 - - - -
118P ARG* 4.4 9.9 - - + +
119P ARG 3.7 24.0 - - - +
120P GLU* 4.2 4.5 - - - -
121P GLY 4.2 1.1 - - - +
122P ASP 4.0 20.0 - - - +
183P ALA* 3.9 17.9 - - + -
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Residues in contact with GLU 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P LYS* 3.1 48.2 + - - +
108P GLU* 4.0 4.2 - - - +
110P LEU* 1.3 76.9 - - - +
112P LYS* 1.3 62.4 + - - +
114P GLY* 3.3 11.4 + - - -
116P GLY* 3.6 28.3 - - - +
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Residues in contact with LYS 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P ARG* 6.0 0.4 - - - +
41P THR* 5.8 2.2 + - - +
108P GLU* 3.1 19.7 + - + +
109P PHE* 2.9 37.0 + - + +
111P GLU* 1.3 79.8 - - - +
113P VAL* 1.3 58.3 + - + +
114P GLY 3.3 2.1 + - - -
317P ALA* 4.5 16.4 + - - +
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Residues in contact with VAL 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P PHE* 3.0 46.3 + - + +
110P LEU* 3.2 16.2 - - - +
112P LYS* 1.3 81.0 - - + +
114P GLY* 1.3 58.2 + - - +
115P LEU* 3.7 27.9 - - + +
180P PRO 5.4 1.7 - - - +
182P MET 5.3 1.1 - - - +
183P ALA* 4.6 6.3 - - - +
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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