Contacts of the helix formed by residues 60 - 71 (chain J) in PDB entry 5XTE
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 SER 60 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58J ASP* 4.2 4.2 - - - +
59J ALA* 1.3 80.0 - - - +
61J THR* 1.3 82.6 + - - +
62J ALA 3.3 2.7 + - - -
63J PHE* 4.3 6.9 + - - +
64J SER* 4.2 11.1 + - - -
135J TRP* 5.8 0.2 - - - -
258J LEU* 5.5 5.4 - - - +
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Residues in contact with THR 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J SER* 2.8 30.6 + - - -
58J ASP* 3.2 25.1 + - + +
60J SER* 1.3 91.2 + - - +
62J ALA* 1.3 58.2 + - - +
63J PHE 3.5 0.4 - - - -
64J SER* 3.6 8.2 + - - -
65J SER* 2.9 24.1 + - - -
58V ASP* 3.9 14.5 + - - +
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Residues in contact with ALA 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J TYR* 3.6 23.8 - - + +
56J SER 3.3 15.7 - - - +
58J ASP 3.1 20.2 + - - +
60J SER 3.3 0.8 - - - -
61J THR* 1.3 77.6 + - - +
63J PHE* 1.3 59.2 + - - +
65J SER* 2.2 24.1 + - - -
66J ILE* 2.9 18.6 + - - +
133J LEU 4.2 5.2 - - - +
135J TRP* 4.4 9.0 - - + -
175J LEU* 3.8 6.5 - - + -
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Residues in contact with PHE 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H PHE* 3.6 33.9 - + - -
199H TYR* 4.5 20.0 - + + -
60J SER 4.3 4.5 + - - +
61J THR 3.5 0.2 - - - -
62J ALA* 1.3 77.6 - - - +
64J SER* 1.3 59.2 + - - +
66J ILE* 3.0 21.0 + - + +
67J ALA* 3.0 24.4 + - + +
134J PRO 4.3 14.8 + - - +
135J TRP* 4.7 16.0 - - + +
136J GLY* 5.1 2.5 - - - -
255J ASN 5.1 1.3 - - - -
256J TYR* 3.0 39.5 - + + -
257J THR 4.9 0.2 - - - -
258J LEU* 4.0 38.4 - - + -
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Residues in contact with SER 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H PHE* 3.8 27.5 - - - -
60J SER 4.2 8.6 + - - -
61J THR* 3.6 12.4 + - - -
62J ALA 3.3 0.4 - - - -
63J PHE* 1.3 80.3 - - - +
65J SER* 1.3 58.4 + - - +
67J ALA* 3.3 4.0 + - - +
68J HIS* 2.9 26.0 + - - +
258J LEU* 5.9 1.4 - - - +
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Residues in contact with SER 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J HIS 3.8 11.2 - - - -
55J TYR* 3.6 7.3 - - - -
56J SER* 3.5 28.0 + - - -
61J THR 2.9 15.0 + - - -
62J ALA* 2.2 33.3 + - - -
64J SER* 1.3 75.5 - - - +
66J ILE* 1.3 57.8 + - - +
68J HIS* 3.2 11.8 - - - +
69J ILE* 2.9 32.9 + - - +
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Residues in contact with ILE 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J TYR* 4.4 10.5 - - + -
62J ALA 2.9 19.0 + - - +
63J PHE* 3.0 17.0 + - + +
65J SER* 1.3 75.6 - - - +
67J ALA* 1.3 60.6 + - - +
69J ILE* 3.0 10.2 + - + +
70J THR* 2.9 31.4 + - + +
80J ARG* 3.4 35.0 - - - +
133J LEU 4.6 1.6 - - - +
134J PRO* 3.3 47.8 - - + +
401J HEM 4.6 9.4 - - - +
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Residues in contact with ALA 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H PHE* 3.4 40.2 - - + -
199H TYR* 3.6 19.1 - - + +
63J PHE* 3.0 11.0 + - + +
64J SER 3.6 5.2 - - - +
66J ILE* 1.3 75.6 - - - +
68J HIS* 1.3 57.1 + - - +
70J THR* 2.9 21.6 + - - -
71J ARG* 2.9 23.6 + - - +
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Residues in contact with HIS 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C SER* 3.9 14.7 + - - -
145C ASP* 3.6 27.8 + - - -
146C VAL* 5.7 1.1 - - + -
54J HIS* 4.0 24.9 + - + -
64J SER 2.9 13.9 + - - +
65J SER* 3.2 13.9 - - - +
67J ALA* 1.3 78.6 - - - +
69J ILE* 1.3 55.4 + - - +
72J ASP* 3.2 31.7 + - + +
73J VAL* 2.9 49.6 + - + +
173V PRO* 6.4 0.2 - - - +
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Residues in contact with ILE 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J LEU* 3.7 36.8 - - + +
54J HIS* 3.6 30.5 - - + -
55J TYR* 4.1 18.6 - - + +
65J SER 2.9 20.5 + - - +
66J ILE* 3.0 15.9 + - + +
68J HIS* 1.3 76.9 - - - +
70J THR* 1.3 66.3 + - + +
71J ARG 3.3 0.7 + - - -
73J VAL* 3.6 16.3 - - + +
76J GLY* 3.3 36.8 - - - +
80J ARG* 4.6 7.6 - - + -
401J HEM 5.1 7.4 - - + +
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Residues in contact with THR 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H TYR* 3.3 15.9 + - + +
202H ARG* 6.3 0.4 - - - +
280H PRO* 4.9 1.6 - - - +
281H GLU* 4.6 8.0 - - - +
66J ILE* 2.9 21.2 + - + +
67J ALA* 2.9 22.2 + - - -
69J ILE* 1.3 76.5 - - - +
71J ARG* 1.3 63.4 + - - +
73J VAL 5.0 0.4 - - - +
77J TRP* 3.8 38.4 - - + +
80J ARG* 3.8 30.3 - - - +
81J TYR* 5.2 7.2 - - + +
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Residues in contact with ARG 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ALA* 4.8 2.1 - - - +
129H PHE* 3.1 46.8 + - - +
130H VAL* 3.4 14.0 - - - +
134H HIS* 4.5 15.7 - - + +
198H SER* 3.4 17.2 + - - -
199H TYR* 3.7 23.4 + - - -
277H ALA 2.3 32.6 + - - -
278H SER* 3.9 3.6 - - - +
280H PRO* 4.0 25.7 - - + +
67J ALA 2.9 15.8 + - - +
70J THR* 1.3 87.9 - - - +
72J ASP* 1.3 75.1 + - - +
73J VAL 3.2 10.5 - - - +
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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