Contacts of the helix formed by residues 53 - 63 (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 LYS 53 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D VAL* 3.7 7.6 - - - -
31D ASP 2.7 14.2 + - - +
32D ASN* 3.7 24.5 - - + +
51D MET 3.8 0.4 + - - -
52D ASP* 1.3 76.1 - - - +
54D GLU* 1.3 64.4 + - + +
56D PHE 3.5 0.3 + - - -
57D LEU* 3.0 18.0 + - - +
88D TYR* 3.0 15.8 + - - -
92D ASN* 2.8 25.5 + - - +
96D TYR* 2.7 34.1 + - + +
400D NAP 2.7 60.2 + - + +
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Residues in contact with GLU 54 (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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87C LYS* 5.4 5.8 - - - +
52D ASP* 2.9 15.8 + - - +
53D LYS* 1.3 82.9 - - + +
55D ASP* 1.3 63.9 + - - +
57D LEU* 3.4 19.6 + - - +
58D ILE* 3.1 42.0 + - + +
96D TYR* 5.4 1.7 - - - -
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Residues in contact with ASP 55 (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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87C LYS* 5.7 0.2 + - - -
91C ASP* 4.1 14.9 - - - +
95C GLN* 5.7 3.3 - - - +
51D MET* 4.0 15.4 - - + +
52D ASP* 3.1 26.7 + - - +
54D GLU* 1.3 76.4 - - - +
56D PHE* 1.3 66.7 - - - +
58D ILE* 3.2 13.8 + - - +
59D GLN* 3.0 33.4 + - - +
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Residues in contact with PHE 56 (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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3D ILE* 4.1 27.8 - - + -
5D THR* 4.2 11.9 - - + -
28D LEU* 4.4 2.5 - - + -
30D VAL* 3.6 34.3 - - + -
51D MET* 4.0 15.9 - - + +
52D ASP 3.0 16.4 + - - +
53D LYS 3.6 4.0 - - - +
55D ASP* 1.3 78.4 - - - +
57D LEU* 1.3 57.0 + - - +
59D GLN* 3.1 4.4 + - - +
60D ILE* 2.8 48.1 + - + +
66D PHE* 3.6 31.0 - + - -
72D ILE* 4.6 5.6 - - + -
96D TYR* 3.5 17.0 - + - -
100D LEU* 3.7 25.6 - - + -
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Residues in contact with LEU 57 (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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53D LYS 3.0 18.3 + - - +
54D GLU* 3.7 19.3 - - - +
55D ASP 3.2 0.2 - - - -
56D PHE* 1.3 75.9 - - - +
58D ILE* 1.3 63.4 + - - +
60D ILE* 3.2 9.4 + - + +
61D MET* 2.9 47.9 + - + +
96D TYR* 3.6 42.3 + - + -
99D GLU* 4.0 32.1 - - + -
100D LEU* 5.2 1.3 - - + -
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Residues in contact with ILE 58 (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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54D GLU* 3.1 38.0 + - + +
55D ASP* 3.2 15.9 + - - +
57D LEU* 1.3 79.0 - - + +
59D GLN* 1.3 62.3 + - + +
61D MET* 3.3 13.6 + - + +
62D ALA* 3.0 29.5 + - + +
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Residues in contact with GLN 59 (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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51D MET* 4.1 21.5 - - - +
55D ASP* 3.0 21.2 + - - +
56D PHE 3.6 6.5 - - - +
58D ILE* 1.3 79.2 - - + +
60D ILE* 1.3 63.7 + - - +
62D ALA* 3.2 2.6 + - - -
63D GLY 3.0 4.3 + - - -
64D GLU* 3.0 54.6 + - + +
66D PHE* 3.4 28.9 - - + -
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Residues in contact with ILE 60 (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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56D PHE* 2.8 44.2 + - + +
57D LEU* 3.4 11.0 - - + +
59D GLN* 1.3 75.8 - - - +
61D MET* 1.3 65.0 + - + +
63D GLY* 3.0 19.4 + - - -
66D PHE* 3.7 19.7 - - + -
72D ILE* 5.4 1.1 - - + -
99D GLU* 3.9 16.8 - - + +
100D LEU* 3.9 15.7 - - + -
103D TYR* 3.5 54.6 - - + -
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Residues in contact with MET 61 (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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57D LEU* 2.9 43.8 + - + +
58D ILE* 3.8 12.1 - - + +
60D ILE* 1.3 76.9 - - + +
62D ALA* 1.3 59.6 + - - +
63D GLY 3.2 0.8 + - - -
99D GLU* 3.4 45.1 - - + +
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Residues in contact with ALA 62 (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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58D ILE* 3.0 20.4 + - + +
59D GLN* 3.7 6.5 - - - +
60D ILE 3.2 0.2 - - - -
61D MET* 1.3 76.7 - - - +
63D GLY* 1.3 61.7 + - - +
64D GLU* 3.4 18.6 - - - +
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Residues in contact with GLY 63 (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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60D ILE 3.0 15.5 + - - -
61D MET 3.2 1.2 - - - -
62D ALA* 1.3 80.4 - - - +
64D GLU* 1.3 66.0 + - - +
65D GLU* 3.6 6.8 + - - +
103D TYR* 4.3 0.9 - - - -
107D ARG* 3.5 25.5 + - - -
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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