Contacts of the helix formed by residues 116 - 121 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F SER* 1.3 86.3 + - - +
117F ALA* 1.3 54.1 + - - +
118F ALA* 2.9 14.6 + - - +
119F THR* 2.7 36.6 + - - +
140F PHE* 4.1 14.1 - - - -
144F LYS* 4.2 11.9 - - - +
166F ARG* 3.3 7.5 - - - +
167F TYR 3.8 7.2 - - - -
400F NAP 3.7 11.3 - - - -
402F BMA 2.6 27.3 + - - -
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Residues in contact with ALA 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F SER* 1.3 69.3 + - - +
118F ALA* 1.3 60.3 + - - +
119F THR 3.0 5.4 - - - -
120F TYR* 3.0 22.8 + - + -
166F ARG* 3.6 4.3 - - - +
167F TYR 3.0 19.4 + - - +
168F PHE* 3.6 45.3 - - + -
273F GLN* 2.9 21.4 + - - +
276F THR* 5.2 4.0 - - + +
402F BMA 5.9 0.2 - - - +
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Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F THR* 5.5 2.5 - - + -
116F SER* 2.9 16.7 + - - +
117F ALA* 1.3 78.1 - - - +
119F THR* 1.3 61.3 + - - +
121F GLY* 3.1 17.1 + - - -
136F PRO* 3.5 12.5 - - - +
137F LEU 4.4 1.7 + - - -
138F ASN* 5.0 7.2 - - - +
140F PHE* 4.1 18.4 - - + -
141F GLY* 4.4 7.2 - - - -
273F GLN* 3.7 17.8 + - - +
401F ADP 5.9 0.7 - - - +
402F BMA 3.7 11.0 + - - +
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Residues in contact with THR 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F SER* 4.2 0.2 - - - +
116F SER* 2.7 24.0 + - - +
117F ALA 4.2 0.2 - - - -
118F ALA* 1.3 79.0 - - - +
120F TYR* 1.3 58.6 + - - +
121F GLY 3.3 0.2 - - - -
134F GLU* 3.3 9.8 - - - -
135F LYS 2.8 24.8 + - - -
136F PRO* 3.4 13.3 - - - +
141F GLY* 3.9 5.1 - - - +
144F LYS* 3.9 10.8 - - + -
145F PHE* 3.5 38.8 - - - +
148F ASP* 4.2 9.0 - - - +
166F ARG* 3.2 28.3 + - - -
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Residues in contact with TYR 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ALA* 3.0 27.1 + - + +
119F THR* 1.3 79.1 - - - +
121F GLY* 1.3 67.3 + - - +
122F GLY 3.4 1.5 + - - -
123F ARG* 3.8 13.4 + - - -
127F PHE* 3.6 42.0 - + + -
128F ILE 3.2 42.0 - - - -
129F GLU 3.3 1.4 + - - -
133F TYR* 3.6 30.3 - - + +
134F GLU* 4.4 2.7 - - + -
135F LYS* 3.9 8.0 + - - +
166F ARG* 3.1 33.7 + - - -
168F PHE* 3.9 12.1 - + - -
234F ASN* 2.6 30.2 + - - -
273F GLN* 4.2 0.7 - - - +
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Residues in contact with GLY 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ALA 3.1 15.3 + - - -
119F THR 3.3 0.2 - - - -
120F TYR* 1.3 80.7 - - - +
122F GLY* 1.3 67.0 + - - +
135F LYS* 3.4 21.3 - - - +
136F PRO* 4.1 0.4 - - - -
137F LEU* 3.7 27.9 - - - +
273F 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