Contacts of the helix formed by residues 64 - 75 (chain Z) in PDB entry 2W4T
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 PRO 64 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15Z PHE* 3.9 6.7 - - - -
26Z GLY 4.0 14.1 - - - +
27Z ALA* 5.2 1.8 - - + -
62Z SER 4.2 2.0 - - - +
63Z LEU* 1.3 111.0 - - + +
65Z PHE* 1.3 61.9 + - - +
66Z GLU* 3.2 15.0 - - + +
67Z GLU* 4.2 13.5 - - + -
68Z PHE* 3.4 19.6 + - - +
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Residues in contact with PHE 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z ILE* 4.0 19.7 - - + -
11Z LEU* 3.9 11.0 - - + -
12Z LYS* 3.7 31.6 - - + -
15Z PHE* 4.0 35.0 - + + -
26Z GLY 4.9 1.2 + - - -
64Z PRO* 1.3 73.9 - - - +
66Z GLU* 1.3 74.9 + - + +
67Z GLU 3.4 0.4 - - - -
68Z PHE* 3.7 13.5 - + - -
69Z LEU* 3.3 50.6 + - + +
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Residues in contact with GLU 66 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Z PRO* 3.2 10.3 - - + -
65Z PHE* 1.3 93.2 - - + +
67Z GLU* 1.3 69.1 + - + +
69Z LEU* 4.0 8.1 + - - +
70Z PRO* 3.6 14.6 - - - +
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Residues in contact with GLU 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Z LEU* 3.8 38.3 - - + +
64Z PRO* 4.0 14.5 + - + -
65Z PHE 3.4 0.2 - - - -
66Z GLU* 1.3 82.5 - - + +
68Z PHE* 1.3 63.2 + - - +
70Z PRO* 3.2 18.4 - - - +
71Z ALA* 3.9 8.0 + - - +
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Residues in contact with PHE 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Z LEU* 3.1 51.4 - - + -
14Z VAL* 5.4 2.5 - - + -
15Z PHE* 4.6 17.0 - + + -
28Z VAL* 5.2 0.9 - - + -
33Z LEU* 3.0 38.6 - - + -
36Z VAL* 3.4 27.8 - - + -
37Z CYS* 5.0 1.8 - - + -
63Z LEU* 5.1 3.3 - - + +
64Z PRO 3.4 19.2 + - - +
65Z PHE* 3.5 24.9 - + + +
66Z GLU 3.3 0.2 - - - -
67Z GLU* 1.3 78.9 - - - +
69Z LEU* 1.3 66.2 + - - +
71Z ALA* 3.0 18.7 + - + +
72Z TYR* 3.3 15.2 + + + -
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Residues in contact with LEU 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z ILE* 4.9 17.0 - - + -
11Z LEU* 3.8 22.4 - - + -
65Z PHE* 3.3 34.8 + - + +
66Z GLU* 4.1 10.1 - - - +
68Z PHE* 1.3 78.0 - - - +
70Z PRO* 1.3 69.9 - - + +
72Z TYR* 3.4 4.9 + - - +
73Z GLU* 2.8 36.9 + - + +
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Residues in contact with PRO 70 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Z VAL* 5.3 0.7 - - - +
66Z GLU 3.6 10.3 - - - +
67Z GLU* 3.2 21.8 - - - +
69Z LEU* 1.3 98.2 - - + +
71Z ALA* 1.3 55.3 + - - +
72Z TYR 3.1 1.8 - - - -
73Z GLU* 3.4 13.3 - - + +
74Z GLY* 2.7 30.0 + - - -
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Residues in contact with ALA 71 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Z LEU* 4.2 28.9 - - + -
52Z VAL* 4.1 31.0 - - + +
63Z LEU* 6.3 0.2 - - + -
67Z GLU 3.9 5.7 + - - +
68Z PHE* 3.0 15.3 + - + +
70Z PRO* 1.3 79.7 - - - +
72Z TYR* 1.3 59.2 + - - +
74Z GLY* 3.4 0.9 + - - -
75Z LEU* 2.9 30.0 + - - +
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Residues in contact with TYR 72 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Z GLU* 4.9 13.4 + - + -
11Z LEU* 3.5 41.7 - - + -
37Z CYS* 4.3 17.9 - - + -
40Z LEU* 3.8 36.4 + - + +
42Z ILE* 4.0 23.9 - - + +
68Z PHE* 3.3 11.4 + + + +
69Z LEU 3.6 3.4 - - - +
70Z PRO 3.1 0.4 - - - -
71Z ALA* 1.3 78.3 - - - +
73Z GLU* 1.3 76.8 + - - +
74Z GLY 3.1 0.9 - - - -
75Z LEU* 4.0 6.3 - - + +
76Z MET* 3.4 38.3 + - + +
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Residues in contact with GLU 73 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69Z LEU* 2.8 32.0 + - + +
70Z PRO* 3.2 12.1 + - + +
72Z TYR* 1.3 93.6 - - - +
74Z GLY* 1.3 64.3 + - - +
76Z MET* 3.4 14.8 - - - +
77Z ASP* 3.1 18.8 - - - +
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Residues in contact with GLY 74 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Z VAL* 4.6 11.0 - - - -
70Z PRO 2.7 16.6 + - - -
71Z ALA 3.6 1.8 - - - -
73Z GLU* 1.3 73.5 - - - +
75Z LEU* 1.3 52.2 + - - +
76Z MET 2.6 17.4 + - - -
77Z ASP* 3.0 18.7 + - - +
78Z CYS* 3.9 5.8 + - - +
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Residues in contact with LEU 75 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Z CYS* 2.7 23.3 - - + -
42Z ILE* 2.5 40.2 - - + -
43Z ASN 5.6 0.2 - - - -
44Z PRO* 2.3 46.2 - - + -
48Z ASP* 3.9 10.8 - - - +
49Z VAL* 5.4 1.6 - - + -
52Z VAL* 4.4 6.4 - - + +
71Z ALA 2.9 19.5 + - - +
72Z TYR* 3.9 8.5 + - + +
73Z GLU 3.7 0.2 - - - -
74Z GLY* 1.3 66.5 - - - +
76Z MET* 1.3 54.5 + - - +
78Z CYS* 3.1 22.6 - - - -
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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