Contacts of the helix formed by residues 113 - 120 (chain Q) in PDB entry 2X17
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 ASP 113 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N TYR* 5.5 1.4 + - - -
2Q LEU* 3.8 11.4 - - - +
3Q SER 5.4 0.7 + - - -
6Q MET* 3.7 18.4 - - + +
60Q TYR* 4.7 0.2 + - - -
64Q ARG* 5.0 4.9 + - - -
108Q ALA* 2.8 25.9 + - - +
111Q GLU* 3.2 13.6 - - + +
112Q LYS* 1.3 70.9 - - - +
114Q TYR* 1.3 62.4 + - - +
115Q SER* 3.8 8.7 + - - -
116Q THR* 2.8 33.2 + - - -
117Q ARG* 3.2 21.5 + - - +
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Residues in contact with TYR 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N TYR* 3.6 54.7 - + + -
105N ALA* 4.0 13.0 - - + -
106N ALA* 3.4 20.1 - - + +
109N GLU* 3.0 36.5 + - - -
117N ARG* 3.7 19.4 + - - -
124N ILE* 3.6 11.6 - - + +
112Q LYS* 3.3 37.7 + - + +
113Q ASP* 1.3 70.9 + - - +
115Q SER* 1.3 59.0 + - - +
117Q ARG* 3.7 7.5 - - + +
118Q ALA* 2.8 32.1 + - - +
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Residues in contact with SER 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N TYR* 2.6 31.2 + - - -
124N ILE* 3.8 12.1 + - - +
125N ASN* 4.9 1.4 - - - +
128N VAL* 3.8 22.4 - - - +
60Q TYR* 3.1 16.5 + - - -
64Q ARG* 3.6 17.6 + - - -
113Q ASP* 3.3 4.9 + - - -
114Q TYR* 1.3 78.3 - - - +
116Q THR* 1.3 57.9 + - - +
118Q ALA* 3.4 3.2 + - - +
119Q PHE* 3.0 26.0 + - - +
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Residues in contact with THR 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q LEU* 3.6 8.7 - - - +
6Q MET* 3.8 23.3 - - + -
10Q LEU* 3.9 23.1 - - + -
60Q TYR* 2.9 21.8 + - + -
108Q ALA* 4.3 4.0 - - + -
113Q ASP* 2.8 30.8 + - - -
114Q TYR 3.4 0.2 - - - -
115Q SER* 1.3 73.6 - - - +
117Q ARG* 1.3 62.6 + - - +
119Q PHE* 3.3 2.3 + - + +
120Q LEU* 3.0 42.0 + - + +
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Residues in contact with ARG 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L TYR* 3.4 25.5 + - - +
117L ARG* 5.4 8.3 - - - +
118L ALA* 5.9 0.6 - - - +
117N ARG* 5.3 9.6 - - - +
121N GLU* 4.9 0.8 + - - +
105Q ALA* 3.7 33.2 - - - +
108Q ALA* 3.9 10.2 - - + +
109Q GLU* 3.1 30.1 + - + +
113Q ASP 3.2 17.6 + - - +
114Q TYR* 3.7 10.5 - - + +
116Q THR* 1.3 77.8 - - - +
118Q ALA* 1.3 59.3 + - - +
120Q LEU* 3.6 3.9 + - - +
121Q GLU* 2.8 39.2 + - - +
124Q ILE* 3.4 19.1 - - - +
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Residues in contact with ALA 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N ARG* 5.7 1.3 - - - +
121N GLU* 3.7 30.3 - - - +
124N ILE* 3.8 16.2 - - + -
125N ASN* 3.4 28.4 + - - +
114Q TYR 2.8 17.9 + - - +
115Q SER 3.8 3.1 - - - +
117Q ARG* 1.3 73.9 - - - +
119Q PHE* 1.3 64.0 + - - +
121Q GLU* 3.4 15.4 - - - +
122Q TRP 4.5 1.0 + - - -
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Residues in contact with PHE 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125N ASN* 4.2 4.9 + - - +
10Q LEU* 4.2 5.2 - - + -
56Q ARG* 3.7 16.2 - - + -
57Q PHE* 3.6 35.2 - + - -
60Q TYR* 3.5 59.2 - + + -
115Q SER 3.0 18.2 + - - +
116Q THR 3.3 7.8 + - - +
118Q ALA* 1.3 76.7 - - - +
120Q LEU* 1.3 69.2 + - + +
121Q GLU 3.1 2.4 + - - -
122Q TRP* 3.5 19.6 + - + +
123Q PHE* 3.5 30.5 - + - -
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Residues in contact with LEU 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q LEU* 5.2 0.2 - - + -
57Q PHE* 4.2 16.4 - - + -
101Q ILE* 4.2 21.3 - - + +
104Q LEU* 3.7 58.6 - - + +
105Q ALA* 3.8 8.7 - - + +
108Q ALA* 4.6 0.4 - - + -
116Q THR* 3.0 35.4 + - + +
117Q ARG* 4.0 11.4 - - - +
118Q ALA 3.4 0.4 - - - -
119Q PHE* 1.3 80.1 - - + +
121Q GLU* 1.3 59.5 + - - +
122Q TRP 3.2 1.8 - - - -
123Q PHE* 3.1 9.4 + - + +
124Q ILE* 3.1 35.7 + - + +
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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