Contacts of the helix formed by residues 53 - 63 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30P VAL* 3.7 8.5 - - - -
31P ASP 2.7 12.0 + - - +
32P ASN* 3.7 26.7 - - + +
51P MET 3.8 0.2 + - - -
52P ASP* 1.3 77.1 - - - +
54P GLU* 1.3 64.5 + - + +
56P PHE 3.5 0.2 + - - -
57P LEU* 3.0 18.4 + - - +
88P TYR* 3.0 15.0 + - - -
92P ASN* 2.8 25.3 + - - +
96P TYR* 2.7 26.9 + - + +
400P NAP 2.9 71.1 + - + +
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Residues in contact with GLU 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P ASP* 2.9 15.5 + - - +
53P LYS* 1.3 83.4 - - + +
55P ASP* 1.3 64.5 + - - +
57P LEU* 3.4 19.1 + - - +
58P ILE* 3.1 41.5 + - + +
96P TYR* 5.4 1.4 - - - -
87T LYS* 5.6 4.9 - - - +
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Residues in contact with ASP 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P MET* 4.0 15.4 - - + +
52P ASP* 3.1 26.5 + - - +
54P GLU* 1.3 75.8 - - - +
56P PHE* 1.3 68.2 + - - +
58P ILE* 3.2 14.4 + - - +
59P GLN* 3.0 33.5 + - - +
87T LYS* 5.8 0.3 + - - -
91T ASP* 4.1 15.1 - - - +
95T GLN* 5.6 4.0 - - - +
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Residues in contact with PHE 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P ILE* 4.1 29.4 - - + -
5P THR* 4.2 11.4 - - + -
28P LEU* 4.4 2.9 - - + -
30P VAL* 3.6 35.4 - - + -
51P MET* 4.0 15.7 - - + +
52P ASP 3.0 15.6 + - - +
53P LYS 3.6 4.5 - - - +
55P ASP* 1.3 78.9 - - - +
57P LEU* 1.3 57.5 + - - +
59P GLN* 3.1 4.6 + - - +
60P ILE* 2.8 47.8 + - + +
66P PHE* 3.6 31.0 - + - -
72P ILE* 4.7 5.6 - - + -
96P TYR* 3.5 17.0 - + - -
100P LEU* 3.7 26.0 - - + -
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Residues in contact with LEU 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P LYS 3.0 17.9 + - - +
54P GLU* 3.7 19.5 - - - +
56P PHE* 1.3 76.9 - - - +
58P ILE* 1.3 64.2 + - + +
60P ILE* 3.2 9.4 + - + +
61P MET* 2.9 47.8 + - + +
91P ASP 6.1 0.2 - - - +
96P TYR* 3.6 42.5 + - + +
99P GLU* 4.0 31.9 - - + -
100P LEU* 5.2 1.1 - - + -
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Residues in contact with ILE 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P GLU* 3.1 37.7 + - + +
55P ASP* 3.2 15.9 + - - +
57P LEU* 1.3 79.4 - - + +
59P GLN* 1.3 63.1 + - + +
61P MET* 3.3 13.6 + - + +
62P ALA* 3.0 29.4 + - + +
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Residues in contact with GLN 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P MET* 4.1 21.7 - - - +
55P ASP* 3.0 20.4 + - - +
56P PHE 3.6 7.2 - - - +
58P ILE* 1.3 79.5 - - + +
60P ILE* 1.3 66.1 + - - +
62P ALA* 3.2 2.7 + - - -
63P GLY 3.0 4.3 + - - -
64P GLU* 3.0 53.8 + - + +
66P PHE* 3.4 28.7 - - + -
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Residues in contact with ILE 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P PHE* 2.8 45.5 + - + +
57P LEU* 3.4 11.2 - - + +
59P GLN* 1.3 75.0 - - - +
61P MET* 1.3 66.3 + - + +
63P GLY* 3.0 19.1 + - - -
66P PHE* 3.7 20.4 - - + -
72P ILE* 5.4 0.9 - - + -
99P GLU* 3.9 20.6 - - + +
100P LEU* 3.9 11.7 - - + -
103P TYR* 3.5 55.2 - - + +
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Residues in contact with MET 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P LEU* 2.9 45.9 + - + +
58P ILE* 3.8 11.7 - - + +
60P ILE* 1.3 77.2 - - + +
62P ALA* 1.3 59.6 + - - +
63P GLY 3.2 1.3 + - - -
99P GLU* 3.4 46.2 - - + +
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Residues in contact with ALA 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58P ILE* 3.0 20.1 + - + +
59P GLN* 3.7 6.3 - - - +
60P ILE 3.2 0.4 - - - -
61P MET* 1.3 77.0 - - - +
63P GLY* 1.3 61.9 + - - +
64P GLU* 3.7 18.1 + - - +
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Residues in contact with GLY 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202O GLU* 5.2 1.6 - - - +
60P ILE 3.0 16.5 + - - -
61P MET 3.2 1.8 + - - -
62P ALA* 1.3 79.8 - - - +
64P GLU* 1.3 65.7 + - - +
65P GLU* 3.6 6.4 + - - +
103P TYR* 4.3 0.4 - - - -
107P ARG* 3.5 26.5 + - - -
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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