Contacts of the helix formed by residues 53 - 63 (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 LYS 53 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F VAL* 3.7 7.9 - - - -
31F ASP 2.7 10.9 + - - +
32F ASN* 3.7 24.5 - - + +
51F MET 3.8 0.4 + - - -
52F ASP* 1.3 77.1 - - - +
54F GLU* 1.3 63.5 + - + +
56F PHE 3.5 0.2 + - - -
57F LEU* 3.0 17.5 + - - +
88F TYR* 3.0 14.8 + - - -
92F ASN* 2.8 25.0 + - - +
96F TYR* 2.7 27.6 + - + +
400F NAP 2.5 73.2 + - + +
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Residues in contact with GLU 54 (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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52F ASP* 2.9 16.4 + - - +
53F LYS* 1.3 83.7 - - + +
55F ASP* 1.3 63.7 + - - +
57F LEU* 3.4 17.7 + - - +
58F ILE* 3.1 42.2 + - + +
96F TYR* 5.5 1.9 - - - -
87J LYS* 5.4 5.8 - - - +
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Residues in contact with ASP 55 (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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51F MET* 4.0 15.8 - - + +
52F ASP* 3.1 27.2 + - - +
54F GLU* 1.3 75.0 - - - +
56F PHE* 1.3 68.2 + - - +
58F ILE* 3.2 14.0 + - - +
59F GLN* 3.0 33.6 + - - +
87J LYS* 5.6 0.7 + - - -
91J ASP* 4.1 14.9 - - - +
95J GLN* 5.7 2.6 - - - +
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Residues in contact with PHE 56 (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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3F ILE* 4.1 29.2 - - + -
5F THR* 4.2 11.2 - - + -
28F LEU* 4.4 2.5 - - + -
30F VAL* 3.6 34.1 - - + -
51F MET* 4.0 16.1 - - + +
52F ASP 3.0 16.0 + - - +
53F LYS 3.6 4.7 - - - +
55F ASP* 1.3 77.2 - - - +
57F LEU* 1.3 56.9 + - - +
59F GLN* 3.1 4.8 + - - +
60F ILE* 2.8 47.4 + - + +
66F PHE* 3.6 31.4 - + - -
72F ILE* 4.7 4.9 - - + -
96F TYR* 3.5 17.0 - + - -
100F LEU* 3.7 25.6 - - + -
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Residues in contact with LEU 57 (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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53F LYS 3.0 17.4 + - - +
54F GLU* 3.7 20.4 - - - +
55F ASP 3.2 0.2 - - - -
56F PHE* 1.3 76.0 - - - +
58F ILE* 1.3 63.6 + - + +
60F ILE* 3.2 10.2 + - + +
61F MET* 2.9 48.2 + - + +
96F TYR* 3.6 41.7 + - + -
99F GLU* 4.0 32.3 - - + -
100F LEU* 5.2 1.3 - - + -
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Residues in contact with ILE 58 (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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54F GLU* 3.1 38.3 + - + +
55F ASP* 3.6 15.3 - - - +
57F LEU* 1.3 79.2 - - + +
59F GLN* 1.3 62.8 + - + +
61F MET* 3.3 14.6 + - + +
62F ALA* 3.0 28.9 + - + +
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Residues in contact with GLN 59 (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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51F MET* 4.1 21.1 - - - +
55F ASP* 3.0 21.8 + - - +
56F PHE 3.6 7.2 - - - +
58F ILE* 1.3 80.1 - - + +
60F ILE* 1.3 65.1 + - - +
62F ALA* 3.2 2.2 + - - -
63F GLY 3.0 4.3 + - - -
64F GLU* 3.0 54.8 + - + +
66F PHE* 3.4 28.6 - - + -
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Residues in contact with ILE 60 (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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56F PHE* 2.8 46.8 + - + +
57F LEU* 3.4 11.0 - - + +
59F GLN* 1.3 75.4 - - - +
61F MET* 1.3 63.2 + - + +
63F GLY* 3.0 19.6 + - - -
66F PHE* 3.7 20.6 - - + -
72F ILE* 5.4 0.9 - - + -
99F GLU* 3.9 17.5 - - + +
100F LEU* 3.9 15.7 - - + -
103F TYR* 3.5 54.7 - - + -
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Residues in contact with MET 61 (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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57F LEU* 2.9 45.7 + - + +
58F ILE* 3.8 11.2 - - + +
60F ILE* 1.3 77.7 - - - +
62F ALA* 1.3 58.9 + - - +
63F GLY 3.2 0.8 + - - -
99F GLU* 3.4 44.6 - - + +
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Residues in contact with ALA 62 (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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58F ILE* 3.0 20.7 + - + +
59F GLN* 3.7 6.3 - - - +
60F ILE 3.2 0.2 - - - -
61F MET* 1.3 76.5 - - - +
63F GLY* 1.3 61.7 + - - +
64F GLU* 4.0 18.1 - - - +
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Residues in contact with GLY 63 (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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60F ILE 3.0 15.7 + - - -
61F MET 3.2 1.2 + - - -
62F ALA* 1.3 80.6 - - - +
64F GLU* 1.3 66.0 + - - +
65F GLU* 3.6 6.9 + - - +
103F TYR* 4.3 0.7 - - - -
107F ARG* 3.5 25.9 + - - -
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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