Contacts of the helix formed by residues 113 - 120 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102M TYR* 5.2 1.4 + - - -
2O LEU* 3.6 17.4 - - - +
3O SER 5.5 0.5 + - - -
6O MET* 3.8 15.0 - - + +
64O ARG* 4.4 7.0 + - - -
108O ALA* 2.9 18.7 + - - +
111O GLU* 3.1 8.8 - - + +
112O LYS* 1.3 72.4 - - - +
114O TYR* 1.3 57.1 + - - +
115O SER* 3.6 10.9 + - - -
116O THR* 2.7 38.0 + - - +
117O ARG* 3.1 27.4 + - - +
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Residues in contact with TYR 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M TYR* 3.6 55.6 - + + -
105M ALA* 4.3 7.2 - - + -
106M ALA* 3.4 20.3 - - - +
109M GLU* 3.2 36.3 + - - -
117M ARG* 3.7 20.5 + - - -
124M ILE* 3.4 14.3 - - + +
112O LYS* 3.0 52.6 + - + +
113O ASP* 1.3 70.7 + - - +
115O SER* 1.3 59.7 + - - +
117O ARG* 3.7 8.0 - - + +
118O ALA* 2.8 32.2 + - - +
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Residues in contact with SER 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M TYR* 2.6 29.0 + - - -
124M ILE* 3.7 11.8 + - - +
125M ASN* 4.9 1.2 - - - +
128M VAL* 3.7 17.7 - - - +
60O TYR* 3.1 16.5 + - - -
64O ARG* 3.4 25.0 + - - -
113O ASP* 3.3 4.2 + - - -
114O TYR* 1.3 78.3 - - - +
116O THR* 1.3 57.4 + - - +
118O ALA* 3.5 3.1 + - - +
119O PHE* 3.0 24.6 + - - +
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Residues in contact with THR 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2O LEU* 3.5 9.4 - - - +
6O MET* 3.8 22.2 - - - -
10O LEU* 4.1 18.8 - - + -
60O TYR* 2.7 23.8 + - + -
108O ALA* 4.3 3.4 - - + -
113O ASP* 2.7 32.6 + - - -
114O TYR 3.4 0.2 - - - -
115O SER* 1.3 74.6 - - - +
117O ARG* 1.3 60.3 + - - +
119O PHE* 3.2 2.0 + - + +
120O LEU* 2.9 45.7 + - + +
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Residues in contact with ARG 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M ARG* 5.1 10.1 - - - +
121M GLU* 4.7 1.5 + - - +
105O ALA* 3.6 31.2 - - - +
108O ALA* 3.9 9.1 - - + +
109O GLU* 3.0 29.3 + - + +
113O ASP 3.1 18.5 + - - +
114O TYR* 3.8 10.1 - - + +
116O THR* 1.3 78.3 - - - +
118O ALA* 1.3 59.4 + - - +
120O LEU* 3.7 3.2 + - - +
121O GLU* 2.9 36.3 + - - +
124O ILE* 3.6 19.5 - - - +
114P TYR* 3.6 23.2 + - - +
117P ARG* 5.1 12.1 - - - +
118P ALA* 5.7 0.6 - - - +
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Residues in contact with ALA 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M ARG* 5.8 0.2 - - - +
121M GLU* 3.6 30.8 + - - +
124M ILE* 3.8 16.8 - - + -
125M ASN* 3.4 28.1 + - - +
114O TYR 2.8 18.8 + - - +
115O SER 3.8 2.0 - - - +
117O ARG* 1.3 75.0 - - - +
119O PHE* 1.3 63.8 + - - +
121O GLU* 3.4 15.2 - - - +
122O TRP* 4.5 1.4 + - - +
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Residues in contact with PHE 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M ASN* 4.1 5.1 + - - +
10O LEU* 4.2 2.0 - - + -
56O ARG* 3.7 16.8 - - + -
57O PHE* 3.6 35.2 - + - -
60O TYR* 3.5 59.2 - + + -
115O SER 3.0 17.8 + - - +
116O THR* 3.2 9.8 + - + +
118O ALA* 1.3 73.1 - - - +
120O LEU* 1.3 68.6 + - + +
121O GLU 3.1 6.1 + - - -
122O TRP* 3.4 19.0 + - + +
123O PHE* 3.5 29.9 - + - -
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Residues in contact with LEU 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O LEU* 5.1 0.2 - - + -
57O PHE* 4.2 22.2 - - + -
101O ILE* 4.3 16.5 - - + +
104O LEU* 3.5 59.0 - - + +
105O ALA* 3.7 9.0 - - + +
108O ALA* 4.5 1.6 - - + -
116O THR* 2.9 36.5 + - + +
117O ARG* 4.1 8.7 - - - +
118O ALA 3.4 0.2 - - - -
119O PHE* 1.3 80.3 - - + +
121O GLU* 1.3 63.1 + - - +
122O TRP 3.3 0.9 - - - -
123O PHE* 3.2 17.3 + - + +
124O ILE* 3.2 22.3 + - + +
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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