Contacts of the helix formed by residues 60 - 73 (chain A) in PDB entry 1WUR
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 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU 4.9 1.7 + - - +
58A LEU 3.3 0.2 - - - -
59A LEU* 1.3 84.2 - - + +
61A THR* 1.3 58.1 + - - +
62A PRO* 3.5 2.0 - - - -
63A GLU* 3.3 30.5 + - + +
64A ARG* 3.0 56.5 + - + +
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Residues in contact with THR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 6.1 0.7 - - + -
46A LEU* 4.3 14.6 - - + -
57A GLY 3.4 2.6 + - - -
58A LEU* 3.3 39.8 - - + +
60A LYS* 1.3 73.9 - - - +
62A PRO* 1.3 64.6 - - + +
64A ARG* 3.0 25.7 + - + +
65A VAL* 2.8 51.1 + - + +
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Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 3.4 34.7 - - + +
42A ALA* 3.9 12.9 - - + +
43A ALA* 3.9 27.1 - - + +
46A LEU* 4.2 9.4 - - + -
53A PRO* 6.0 2.0 - - + +
58A LEU 3.2 13.5 - - - +
59A LEU 3.7 9.0 - - - +
60A LYS 3.7 2.2 - - - -
61A THR* 1.3 91.1 - - + +
63A GLU* 1.3 56.4 + - - +
65A VAL* 3.5 1.4 + - - +
66A ALA* 3.0 30.1 + - - +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 3.8 29.3 + - - +
59A LEU 5.8 0.2 - - - +
60A LYS* 3.3 35.1 + - - +
61A THR 3.1 0.2 - - - -
62A PRO* 1.3 78.1 - - - +
64A ARG* 1.3 65.9 + - + +
66A ALA* 3.4 2.3 + - - +
67A LYS* 3.1 44.9 + - + +
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU 5.6 0.2 + - - -
57A GLY 3.1 18.2 + - - -
60A LYS* 3.0 39.4 + - + +
61A THR* 3.0 36.9 + - + +
63A GLU* 1.3 78.8 - - + +
65A VAL* 1.3 58.5 + - + +
67A LYS* 3.4 7.8 + - - +
68A ALA* 2.9 29.9 + - - +
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 4.3 18.4 - - + -
61A THR* 2.8 42.5 + - + +
62A PRO* 3.9 4.9 - - + +
64A ARG* 1.3 69.2 - - + +
66A ALA* 1.3 66.0 + - - +
68A ALA* 3.2 5.2 + - - +
69A TRP* 2.9 44.9 + - + +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.6 29.3 - - + +
38A LEU* 3.7 26.3 - - + +
39A GLN* 3.7 21.5 - - + +
62A PRO 3.0 20.2 + - - +
63A GLU 3.7 3.4 - - - +
65A VAL* 1.3 78.0 - - - +
67A LYS* 1.3 62.2 + - + +
69A TRP* 3.5 0.6 + - - -
70A ALA 3.2 16.8 + - - -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.3 27.4 - - + +
39A GLN* 6.1 1.3 - - - +
63A GLU* 3.1 33.9 + - + +
64A ARG* 3.9 5.4 - - - +
66A ALA* 1.3 74.1 - - + +
68A ALA* 1.3 66.0 + - - +
70A ALA* 3.3 4.6 + - - +
71A PHE* 3.2 22.0 + - - +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG 2.9 18.2 + - - +
65A VAL* 3.2 8.5 + - - +
67A LYS* 1.3 76.9 - - - +
69A TRP* 1.3 61.9 + - + +
71A PHE* 3.2 8.4 + - - +
72A LEU* 2.8 40.6 + - + +
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Residues in contact with TRP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.5 14.6 - - + -
65A VAL* 2.9 44.6 + - + +
66A ALA 4.1 2.9 - - - +
68A ALA* 1.3 79.0 - - + +
70A ALA* 1.3 57.9 + - - +
72A LEU* 4.2 11.2 - - + +
73A THR* 2.7 53.3 + - + +
107A MET* 3.7 36.5 - - + +
112A LEU* 4.0 38.1 - - + -
146A LEU* 4.0 23.1 - - + -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.4 18.6 - - + -
35A LEU* 3.9 18.2 - - + -
38A LEU* 4.8 0.6 - - - +
66A ALA 3.2 13.4 + - - +
67A LYS* 3.6 9.6 - - - +
68A ALA 3.3 0.2 - - - -
69A TRP* 1.3 76.0 - - - +
71A PHE* 1.3 62.5 + - - +
73A THR* 3.9 4.0 - - - -
74A ARG* 3.1 8.8 + - - +
77A ARG* 2.8 26.6 + - - +
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LYS 3.2 10.4 + - - +
68A ALA* 3.4 9.2 - - - +
70A ALA* 1.3 79.8 - - - +
72A LEU* 1.3 79.9 + - + +
73A THR 3.1 1.9 + - - -
74A ARG* 3.1 51.1 + - - +
144A ARG* 3.4 45.5 - - - -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA* 2.8 30.4 + - + +
69A TRP* 3.4 19.9 + - + +
71A PHE* 1.3 92.5 - - + +
73A THR* 1.3 62.6 + - + +
74A ARG 3.6 0.2 - - - -
105A TYR* 6.2 4.3 - - + -
107A MET* 3.7 38.9 - - + +
144A ARG* 3.0 32.6 - - + -
145A ARG 3.3 4.0 + - - +
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.5 3.5 - - - +
69A TRP* 2.7 44.1 + - + +
70A ALA* 3.5 6.1 + - - -
72A LEU* 1.3 80.6 - - - +
74A ARG* 1.3 64.0 + - - +
75A GLY 3.1 4.4 + - - -
76A TYR* 3.2 38.4 + - + -
77A ARG* 3.4 19.0 + - - -
144A ARG 3.3 6.1 - - - -
145A ARG* 5.0 1.3 - - - -
146A LEU* 4.9 9.6 - - + -
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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