Contacts of the helix formed by residues 53 - 63 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I VAL* 3.7 7.9 - - - -
31I ASP 2.7 12.2 + - - +
32I ASN* 3.7 21.7 - - + +
51I MET 3.8 0.2 + - - -
52I ASP* 1.3 76.7 - - - +
54I GLU* 1.3 63.6 + - + +
56I PHE 3.5 0.3 + - - -
57I LEU* 3.0 18.0 + - - +
88I TYR* 3.0 15.0 + - - -
92I ASN* 2.7 25.9 + - - +
96I TYR* 2.7 26.5 + - + +
400I NAP 2.8 74.1 + - + +
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Residues in contact with GLU 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H LYS* 5.3 6.1 - - - +
52I ASP* 2.9 15.6 + - - +
53I LYS* 1.3 83.4 - - + +
55I ASP* 1.3 64.9 + - - +
57I LEU* 3.4 18.6 + - - +
58I ILE* 3.1 41.5 + - + +
96I TYR* 5.4 1.7 - - - -
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Residues in contact with ASP 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H LYS* 5.6 0.3 + - - -
91H ASP* 4.1 15.6 - - - +
95H GLN* 5.6 4.1 - - - +
51I MET* 4.0 15.6 - - + +
52I ASP* 3.1 26.6 + - - +
54I GLU* 1.3 75.8 - - - +
56I PHE* 1.3 66.5 + - - +
58I ILE* 3.2 14.2 + - - +
59I GLN* 3.0 33.5 + - - +
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Residues in contact with PHE 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I ILE* 4.1 28.7 - - + -
5I THR* 4.2 11.9 - - + -
28I LEU* 4.4 2.7 - - + -
30I VAL* 3.6 34.5 - - + -
51I MET* 4.0 16.1 - - + +
52I ASP 3.0 15.8 + - - +
53I LYS 3.6 4.3 - - - +
55I ASP* 1.3 78.2 - - - +
57I LEU* 1.3 55.7 + - - +
59I GLN* 3.1 4.6 + - - +
60I ILE* 2.8 47.9 + - + +
66I PHE* 3.6 31.9 - + - -
72I ILE* 4.6 5.4 - - + -
96I TYR* 3.5 16.8 - + - -
100I LEU* 3.7 25.6 - - + -
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Residues in contact with LEU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53I LYS 3.0 18.3 + - - +
54I GLU* 3.7 20.2 - - - +
55I ASP 3.2 0.2 - - - -
56I PHE* 1.3 75.9 - - - +
58I ILE* 1.3 62.1 + - - +
60I ILE* 3.2 9.2 + - + +
61I MET* 2.9 48.7 + - + +
96I TYR* 3.6 42.3 + - + -
99I GLU* 4.0 31.9 - - + -
100I LEU* 5.2 1.3 - - + -
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Residues in contact with ILE 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I GLU* 3.1 38.2 + - + +
55I ASP* 3.2 15.9 + - - +
57I LEU* 1.3 79.2 - - + +
59I GLN* 1.3 62.6 + - + +
61I MET* 3.3 13.9 + - + +
62I ALA* 3.0 29.7 + - + +
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Residues in contact with GLN 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I MET* 4.1 21.4 - - - +
55I ASP* 3.0 21.2 + - - +
56I PHE 3.6 7.0 - - - +
58I ILE* 1.3 79.4 - - + +
60I ILE* 1.3 64.0 + - - +
62I ALA* 3.2 2.6 + - - -
63I GLY 3.0 4.3 + - - -
64I GLU* 3.0 54.2 + - + +
66I PHE* 3.4 28.7 - - + -
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Residues in contact with ILE 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I PHE* 2.8 45.0 + - + +
57I LEU* 3.4 10.8 - - + +
59I GLN* 1.3 74.4 - - - +
61I MET* 1.3 66.3 + - + +
63I GLY* 3.0 19.8 + - - -
66I PHE* 3.7 19.7 - - + -
72I ILE* 5.4 1.1 - - + -
99I GLU* 3.9 17.3 - - + +
100I LEU* 3.9 15.9 - - + -
103I TYR* 3.5 54.6 - - + -
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Residues in contact with MET 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I LEU* 2.9 45.0 + - + +
58I ILE* 3.8 12.1 - - + +
60I ILE* 1.3 76.7 - - + +
62I ALA* 1.3 60.1 + - - +
63I GLY 3.2 0.9 - - - -
99I GLU* 3.4 45.1 - - + +
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Residues in contact with ALA 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I ILE* 3.0 21.1 + - + +
59I GLN* 3.7 5.8 - - - +
60I ILE 3.2 0.2 - - - -
61I MET* 1.3 76.4 - - - +
63I GLY* 1.3 61.4 + - - +
64I GLU* 3.4 18.8 - - - +
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Residues in contact with GLY 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I ILE 3.0 15.8 + - - -
61I MET 3.2 1.4 - - - -
62I ALA* 1.3 80.8 - - - +
64I GLU* 1.3 65.8 + - - +
65I GLU* 3.6 6.9 + - - +
103I TYR* 4.3 0.4 - - - -
107I ARG* 3.5 25.7 + - - -
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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