Contacts of the helix formed by residues 56 - 64 (chain G) in PDB entry 3PUY
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 TRP 56 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39G LEU* 3.7 29.4 - - + -
54G ILE* 4.3 21.5 + - + +
55G SER* 1.3 79.4 + - - +
57G ASP* 1.3 66.4 + - - +
58G HIS 3.3 2.9 - - - -
59G TRP* 3.2 18.2 + + + +
60G LYS* 3.0 42.3 + - + +
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Residues in contact with ASP 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G SER* 3.2 17.0 + - - +
56G TRP* 1.3 79.7 + - - +
58G HIS* 1.3 65.8 + - + +
60G LYS* 3.8 6.8 - - - +
61G LEU* 3.1 34.2 + - + +
67G VAL* 3.5 38.8 - - + +
68G GLU 5.0 2.1 - - - +
69G GLN* 5.5 3.1 - - - +
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Residues in contact with HIS 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G SER 3.7 20.0 - - - +
39G LEU 5.2 0.2 - - - -
40G ARG 3.3 18.7 + - - -
42G GLY* 2.8 29.5 + - - -
43G ASN* 3.2 29.8 - - - -
55G SER* 4.9 9.6 - - - +
56G TRP 3.3 0.8 - - - -
57G ASP* 1.3 79.4 - - + +
59G TRP* 1.3 63.2 + - - +
61G LEU* 3.5 4.0 + - - +
62G ALA* 3.2 21.8 + - - +
261G GLY* 3.6 22.3 - - - +
262G ASP* 3.3 34.1 + - - +
265G ALA* 4.4 5.3 - - + +
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Residues in contact with TRP 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G VAL* 5.8 3.4 - - + +
38G SER* 3.4 41.7 + - - -
39G LEU* 3.8 21.8 - - + +
55G SER 5.6 0.7 - - - -
56G TRP* 3.2 18.6 + + + +
58G HIS* 1.3 76.9 - - - +
60G LYS* 1.3 61.1 + - + +
62G ALA* 3.9 6.9 - - + +
63G LEU* 3.2 51.4 + - + +
265G ALA* 3.4 29.8 - - + -
268G VAL* 3.7 33.4 - - + -
269G MET* 3.6 27.4 - - + -
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Residues in contact with LYS 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G TRP* 3.0 37.3 + - + +
57G ASP* 3.8 8.5 - - - +
58G HIS 3.3 0.6 - - - -
59G TRP* 1.3 78.3 - - + +
61G LEU* 1.3 58.7 + - - +
63G LEU* 3.2 2.1 + - - -
64G GLY 2.9 9.4 + - - -
65G PHE* 2.8 58.2 + - + +
66G SER 5.0 4.3 + - - +
67G VAL* 4.1 17.0 - - + -
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Residues in contact with LEU 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ASP* 3.1 24.5 + - + +
58G HIS* 4.0 4.7 - - - +
59G TRP 3.4 0.2 - - - -
60G LYS* 1.3 74.9 - - - +
62G ALA* 1.3 64.1 + - - +
64G GLY* 3.7 5.2 + - - -
65G PHE 3.7 17.7 - - - +
67G VAL* 3.8 18.6 - - + -
75G THR* 4.0 22.9 - - + +
76G PRO 4.3 2.2 - - - +
77G PRO* 3.9 28.6 - - + +
78G PRO* 4.5 19.3 - - + +
79G PHE 4.2 8.1 - - - +
81G VAL* 4.3 3.5 - - - +
262G ASP* 4.2 20.4 - - - +
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G HIS 3.2 17.0 + - - +
59G TRP* 3.9 13.7 - - + +
61G LEU* 1.3 76.2 - - - +
63G LEU* 1.3 61.6 + - - +
64G GLY* 3.5 0.9 + - - -
81G VAL* 3.5 34.0 + - + +
82G LEU* 3.7 14.6 + - - +
252G TYR* 5.9 0.2 - - - +
262G ASP* 5.5 1.3 + - - +
265G ALA* 4.7 8.7 - - + -
266G ALA 5.6 0.4 - - - +
269G MET* 4.1 23.0 - - - +
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Residues in contact with LEU 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G TRP* 3.2 41.2 + - + +
60G LYS 3.2 1.5 + - - +
62G ALA* 1.3 80.0 - - - +
64G GLY* 1.3 57.5 + - - +
65G PHE* 3.5 33.1 + - + -
82G LEU* 3.6 37.8 - - + +
269G MET* 5.5 4.7 - - + -
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Residues in contact with GLY 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G LYS 2.9 2.2 + - - -
61G LEU 3.7 6.6 + - - -
62G ALA 3.3 4.8 + - - -
63G LEU* 1.3 78.4 - - - +
65G PHE* 1.3 66.5 - - - +
66G SER* 3.7 1.0 + - - -
77G PRO* 3.2 27.6 - - - +
82G LEU* 5.5 0.4 - - - -
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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