Contacts of the helix formed by residues 116 - 121 (chain D) in PDB entry 2X86
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 116 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D SER* 1.3 85.7 + - - +
117D ALA* 1.3 54.0 + - - +
118D ALA* 2.9 24.9 + - - +
119D THR* 2.7 37.0 + - - +
140D PHE* 4.0 15.0 - - - -
144D LYS* 4.2 11.6 - - - +
166D ARG* 3.3 7.1 - - - +
167D TYR 3.8 7.0 - - - -
400D NAP 3.6 10.8 - - - -
402D BMA 3.3 16.1 - - - -
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D SER* 1.3 69.3 + - - +
118D ALA* 1.3 58.9 + - - +
119D THR 3.0 5.4 - - - -
120D TYR* 3.0 24.6 + - + +
166D ARG* 3.6 4.5 - - - +
167D TYR 3.0 18.8 + - - +
168D PHE* 3.6 45.5 - - + -
273D GLN* 2.9 21.4 + - - +
276D THR* 5.3 3.6 - - + -
402D BMA 5.6 1.1 - - - +
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D THR* 5.4 2.7 - - + -
116D SER* 2.9 16.5 + - - +
117D ALA* 1.3 77.7 - - - +
119D THR* 1.3 60.8 + - - +
120D TYR 3.1 0.2 - - - -
121D GLY* 3.1 17.0 + - - -
136D PRO* 3.5 12.3 - - - +
137D LEU 4.3 1.6 + - - -
138D ASN* 5.0 7.6 - - - +
140D PHE* 4.1 22.0 - - + -
141D GLY* 4.4 7.0 - - - -
273D GLN* 3.7 17.8 + - - +
401D ADP 5.8 0.7 - - - +
402D BMA 4.4 8.3 + - - +
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Residues in contact with THR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D SER* 4.2 0.4 - - - +
116D SER 2.7 22.7 + - - +
117D ALA 4.2 0.5 - - - -
118D ALA* 1.3 79.6 - - - +
120D TYR* 1.3 58.1 + - - +
121D GLY 3.3 0.2 - - - -
134D GLU* 3.3 9.9 - - - -
135D LYS 2.8 24.9 + - - -
136D PRO* 3.4 13.6 - - - +
141D GLY 3.9 4.9 - - - +
144D LYS* 3.9 11.2 - - + -
145D PHE* 3.5 38.1 - - - +
148D ASP* 4.2 9.2 - - - +
166D ARG* 3.2 27.8 + - - -
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Residues in contact with TYR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ALA* 3.0 28.4 + - + +
119D THR* 1.3 78.6 + - - +
121D GLY* 1.3 67.0 - - - +
122D GLY 3.4 1.1 + - - -
123D ARG* 3.8 13.8 + - - -
127D PHE* 3.4 40.3 + + + -
128D ILE 3.2 42.2 - - - -
129D GLU* 3.3 1.0 + - - -
133D TYR* 3.5 30.4 - - + +
134D GLU* 4.4 2.0 - - + -
135D LYS* 3.9 8.4 + - - +
166D ARG* 3.1 35.3 + - - -
168D PHE* 3.9 12.1 - + - -
234D ASN* 2.6 30.2 + - - -
273D GLN* 4.2 0.4 - - - +
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Residues in contact with GLY 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ALA 3.1 15.1 + - - -
120D TYR* 1.3 81.6 - - - +
122D GLY* 1.3 66.0 + - - +
135D LYS* 3.4 21.8 - - - +
136D PRO* 4.1 0.7 - - - -
137D LEU* 3.7 28.2 - - - +
273D GLN* 3.3 8.5 - - - +
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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