Contacts of the helix formed by residues 53 - 63 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C VAL* 3.7 8.1 - - - -
31C ASP 2.7 11.7 + - - +
32C ASN* 3.7 22.3 - - + +
51C MET 3.8 0.4 + - - -
52C ASP* 1.3 76.9 - - - +
54C GLU* 1.3 64.5 + - + +
57C LEU* 3.0 17.7 + - - +
88C TYR* 3.0 15.4 + - - -
92C ASN* 2.8 26.1 + - - +
96C TYR* 2.7 27.2 + - + +
400C NAP 2.7 73.3 + - + +
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Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LYS* 5.6 3.8 - - - +
52C ASP* 2.9 15.6 + - - +
53C LYS* 1.3 82.8 - - + +
55C ASP* 1.3 65.2 + - - +
57C LEU* 3.4 19.0 + - - +
58C ILE* 3.1 41.6 + - + +
96C TYR* 5.6 1.0 - - - -
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Residues in contact with ASP 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LYS* 5.7 0.2 + - - -
91B ASP* 4.2 14.4 - - - +
95B GLN* 5.7 3.2 - - - +
51C MET* 4.0 15.0 - - + +
52C ASP* 3.1 27.5 + - - +
54C GLU* 1.3 76.4 - - - +
56C PHE* 1.3 67.9 + - - +
58C ILE* 3.2 14.1 + - - +
59C GLN* 3.0 33.2 + - - +
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Residues in contact with PHE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ILE* 4.1 28.9 - - + -
5C THR* 4.2 11.7 - - + -
28C LEU* 4.4 2.5 - - + -
30C VAL* 3.6 34.5 - - + -
51C MET* 4.0 16.5 - - + +
52C ASP 3.0 16.0 + - - +
53C LYS 3.6 3.8 - - - +
55C ASP* 1.3 78.7 - - - +
57C LEU* 1.3 57.3 + - - +
59C GLN* 3.1 4.6 + - - +
60C ILE* 2.8 47.6 + - + +
66C PHE* 3.6 31.6 - + - -
72C ILE* 4.7 5.2 - - + -
96C TYR* 3.5 16.8 - + - -
100C LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LYS 3.0 17.4 + - - +
54C GLU* 3.7 21.1 - - - +
56C PHE* 1.3 76.6 - - - +
58C ILE* 1.3 63.5 + - + +
60C ILE* 3.2 9.0 + - + +
61C MET* 2.9 47.4 + - + +
91C ASP 6.2 0.2 - - - +
96C TYR* 3.6 41.2 + - + +
99C GLU* 4.0 31.9 - - + -
100C LEU* 5.2 0.9 - - + -
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Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLU* 3.1 38.8 + - + +
55C ASP* 3.2 16.1 + - - +
57C LEU* 1.3 79.1 - - + +
59C GLN* 1.3 63.8 + - + +
61C MET* 3.3 13.5 + - + +
62C ALA* 3.0 29.2 + - + +
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Residues in contact with GLN 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C MET* 4.1 21.9 - - - +
55C ASP* 3.0 20.0 + - - +
56C PHE* 3.6 7.2 - - - +
58C ILE* 1.3 78.2 - - + +
60C ILE* 1.3 66.3 - - - +
62C ALA* 3.2 2.6 + - - -
63C GLY 3.0 4.9 + - - -
64C GLU* 3.0 53.1 + - + +
66C PHE* 3.4 28.7 - - + -
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C PHE* 2.8 44.9 + - + +
57C LEU* 3.4 10.5 - - + +
59C GLN* 1.3 75.0 - - - +
61C MET* 1.3 66.5 + - + +
63C GLY* 3.0 19.6 + - - -
66C PHE* 3.7 20.4 - - + -
72C ILE* 5.4 0.9 - - + -
99C GLU* 3.9 17.5 - - + +
100C LEU* 3.9 14.6 - - + -
103C TYR* 3.5 55.3 - - + +
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Residues in contact with MET 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LEU* 2.9 47.2 + - + +
58C ILE* 3.8 11.0 - - + +
60C ILE* 1.3 77.6 - - - +
62C ALA* 1.3 58.7 + - - +
63C GLY 3.2 1.0 + - - -
99C GLU* 3.4 45.5 - - + +
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ILE* 3.0 19.2 + - + +
59C GLN* 3.7 6.1 - - - +
60C ILE 3.2 0.4 - - - -
61C MET* 1.3 76.7 - - - +
63C GLY* 1.3 61.6 + - - +
64C GLU* 4.0 18.5 - - - +
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Residues in contact with GLY 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ILE 3.0 16.4 + - - -
61C MET 3.2 1.4 + - - -
62C ALA* 1.3 81.3 - - - +
64C GLU* 1.3 65.0 - - - +
65C GLU* 3.6 6.9 + - - +
103C TYR* 4.3 0.4 - - - -
107C ARG* 3.5 26.0 + - - -
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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