Contacts of the helix formed by residues 76 - 86 (chain B) in PDB entry 5PT3
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 ASP 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B PHE* 3.5 9.9 - - - +
56B ALA 3.5 1.2 - - - +
57B GLN 3.4 21.5 - - - +
58B PRO* 3.2 27.9 - - + +
74B PRO* 5.5 0.5 - - - +
75B MET* 1.3 80.0 - - - +
77B PHE* 1.3 63.8 + - - +
78B ALA* 2.9 18.9 + - - +
79B THR* 2.6 43.9 + - - -
80B MET* 3.1 23.2 + - - +
102B ILE* 3.6 12.1 - - - -
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 3.7 21.3 - - + +
46B LEU* 4.0 27.1 - - + -
47B GLN* 3.4 52.2 - - + +
50B ASP* 4.1 10.1 - - + -
55B PHE* 2.9 42.3 + - + +
56B ALA 4.2 0.2 - - - +
76B ASP* 1.3 70.0 - - - +
78B ALA* 1.3 59.1 + - - +
80B MET* 3.3 7.4 + - - +
81B ARG* 2.9 29.1 + - - +
99B PHE* 4.1 13.2 - + - -
102B ILE* 3.7 20.0 - - + -
123B LEU* 3.8 25.1 - - + -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 5.2 1.0 - - - +
56B ALA 3.0 19.7 + - - +
57B GLN* 3.6 25.1 - - - +
58B PRO* 4.9 1.3 - - + -
76B ASP* 2.9 7.8 + - - +
77B PHE* 1.3 73.8 - - - +
79B THR* 1.3 57.4 - - - +
81B ARG* 3.2 8.8 + - - +
82B LYS* 3.0 28.8 + - - +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PRO* 4.1 9.4 - - - +
74B PRO 5.7 0.7 - - - +
75B MET* 3.7 25.4 - - + -
76B ASP* 2.6 33.3 + - - -
78B ALA* 1.3 72.1 - - - +
80B MET* 1.3 64.8 + - - +
82B LYS* 3.4 12.4 + - + +
83B ARG* 3.1 22.7 + - + +
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Residues in contact with MET 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.3 10.1 - - + -
46B LEU* 5.6 0.2 - - + -
75B MET* 3.9 6.3 - - - -
76B ASP 3.1 15.6 + - - +
77B PHE* 3.6 17.3 - - - +
78B ALA 3.3 0.2 - - - -
79B THR* 1.3 76.8 - - - +
81B ARG* 1.3 56.6 + - - +
83B ARG* 3.2 0.7 + - - -
84B LEU* 2.8 30.3 + - - +
89B TYR* 3.4 26.5 - - + +
95B PHE* 3.6 54.5 - - + +
98B ASP* 3.9 9.6 - - + -
99B PHE* 3.9 17.9 - - + +
102B ILE* 3.7 25.8 - - - -
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 4.5 13.5 - - - +
43B LEU* 3.6 35.6 + - + +
44B ASP* 2.8 32.5 + - - +
47B GLN* 2.9 30.3 + - - +
77B PHE 2.9 14.9 + - - +
78B ALA* 3.2 8.6 + - - +
80B MET* 1.3 76.8 - - - +
82B LYS* 1.3 58.6 + - - +
84B LEU* 3.6 2.5 - - + +
85B GLU* 2.9 46.2 + - + +
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA 3.0 12.6 + - - +
79B THR* 3.6 15.5 - - + +
81B ARG* 1.3 78.7 - - - +
83B ARG* 1.3 62.3 + - - +
85B GLU* 3.5 3.3 + - - +
86B ALA* 3.0 30.4 + - + +
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B THR* 3.1 14.7 + - + +
80B MET* 3.7 7.0 - - - +
82B LYS* 1.3 76.0 - - - +
84B LEU* 1.3 61.3 + - - +
86B ALA* 3.4 8.3 + - - +
88B GLY* 2.8 53.0 + - - -
89B TYR* 3.5 25.3 - - + +
94B GLU* 3.1 40.8 + - - +
98B ASP* 3.2 28.4 + - - -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B THR* 4.1 26.4 - - + +
39B LEU* 3.6 39.3 - - + +
40B ARG* 3.6 33.9 - - + +
43B LEU* 4.1 17.9 - - + -
80B MET 2.8 20.1 + - - +
81B ARG* 3.6 5.2 - - + +
83B ARG* 1.3 72.6 - - - +
85B GLU* 1.3 70.2 + - - +
87B GLN* 3.1 21.3 + - - +
88B GLY 4.8 0.7 - - - +
89B TYR* 3.6 16.8 + - + +
95B PHE* 4.9 1.8 - - + -
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B THR* 5.1 1.0 - - - +
40B ARG* 2.8 51.5 + - - +
81B ARG* 2.9 37.4 + - + +
82B LYS* 3.9 3.8 - - - +
84B LEU* 1.3 81.5 - - + +
86B ALA* 1.3 56.8 - - - +
87B GLN* 3.2 8.6 + - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LYS* 3.0 22.9 + - + +
83B ARG* 3.8 5.6 - - - +
84B LEU 3.1 0.4 - - - -
85B GLU* 1.3 77.5 - - - +
87B GLN* 1.3 67.3 + - - +
88B GLY* 3.3 2.5 + - - +
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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