Contacts of the helix formed by residues 60 - 73 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D GLU 5.1 0.4 + - - -
58D LEU 3.3 0.2 - - - -
59D LEU* 1.3 81.6 - - + +
61D THR* 1.3 58.7 + - - +
62D PRO* 3.5 2.2 - - - -
63D GLU* 3.3 40.1 + - - +
64D ARG* 3.0 60.7 + - - +
67D LYS* 5.4 1.0 - - - +
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D ALA* 6.2 0.4 - - + -
46D LEU* 4.4 14.4 - - + -
57D GLY 3.5 2.4 + - - -
58D LEU* 3.1 39.7 + - + +
60D LYS* 1.3 74.9 - - - +
62D PRO* 1.3 66.4 - - + +
64D ARG* 3.0 26.6 + - + +
65D VAL* 2.8 51.4 + - + +
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Residues in contact with PRO 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLN* 3.5 38.6 - - + +
42D ALA* 3.9 13.4 - - + +
43D ALA* 3.9 27.4 - - + +
46D LEU* 4.2 9.0 - - + -
53D PRO* 5.8 2.7 - - + -
58D LEU 3.4 13.2 - - - +
59D LEU 3.9 7.4 - - - +
60D LYS 3.7 2.9 - - - -
61D THR* 1.3 91.7 - - + +
63D GLU* 1.3 56.2 + - - +
65D VAL* 3.5 1.6 + - - +
66D ALA* 3.1 23.9 + - - +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLN* 3.8 29.8 + - - +
60D LYS* 3.3 43.0 + - - +
61D THR 3.1 0.4 - - - -
62D PRO* 1.3 76.8 - - - +
64D ARG* 1.3 66.0 + - - +
66D ALA* 3.4 2.8 + - - +
67D LYS* 3.1 51.8 + - + +
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Residues in contact with ARG 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D GLU 5.6 0.4 + - - -
57D GLY 3.4 16.2 + - - -
60D LYS* 3.0 49.8 + - + +
61D THR* 3.1 36.2 + - + +
63D GLU* 1.3 76.2 - - - +
65D VAL* 1.3 58.8 + - + +
67D LYS* 3.4 17.3 + - - +
68D ALA* 3.1 28.6 + - - +
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA* 4.3 18.2 - - + -
61D THR* 2.8 42.8 + - + +
62D PRO* 3.8 4.3 - - + +
64D ARG* 1.3 71.9 - - + +
66D ALA* 1.3 64.7 + - - +
68D ALA* 3.3 5.0 + - - +
69D TRP* 3.0 43.7 + - + +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 3.6 16.2 - - + +
38D LEU* 3.6 37.3 - - + +
39D GLN* 3.6 20.0 - - + +
62D PRO 3.1 18.3 + - - +
63D GLU 3.7 2.9 - - - +
64D ARG 3.4 0.2 - - - -
65D VAL* 1.3 78.8 - - - +
67D LYS* 1.3 62.9 + - + +
69D TRP* 3.4 0.6 + - - -
70D ALA* 3.1 22.3 + - - +
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 4.3 17.7 - - + -
39D GLN* 5.7 1.6 - - - +
60D LYS* 5.4 1.2 - - - +
63D GLU* 3.1 53.9 + - + +
64D ARG* 3.4 17.7 - - - +
66D ALA* 1.3 76.9 - - + +
68D ALA* 1.3 63.6 + - - +
70D ALA* 3.2 9.7 + - - +
71D PHE* 3.1 22.0 + - - +
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Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ARG 3.1 19.3 + - - +
65D VAL* 3.5 8.7 - - - +
67D LYS* 1.3 76.5 - - - +
69D TRP* 1.3 62.5 + - + +
71D PHE* 3.1 9.1 + - - +
72D LEU* 2.8 40.5 + - + +
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Residues in contact with TRP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU* 4.6 14.8 - - + -
65D VAL* 3.0 41.8 + - + +
66D ALA* 4.1 3.1 - - - +
68D ALA* 1.3 77.0 - - + +
70D ALA* 1.3 57.3 + - - +
72D LEU* 3.7 12.2 - - + +
73D THR* 2.7 54.9 + - + +
107D MET* 3.6 37.6 - - + +
112D LEU* 3.9 38.8 - - + -
146D LEU* 4.0 22.2 - - + -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLU* 5.1 4.9 - - - +
33D VAL* 3.6 29.6 - - + -
35D LEU* 3.9 9.6 - - + -
38D LEU* 4.9 0.6 - - - +
66D ALA 3.1 14.5 + - - +
67D LYS* 3.4 11.0 - - - +
68D ALA 3.2 0.2 - - - -
69D TRP* 1.3 76.5 - - - +
71D PHE* 1.3 61.9 + - - +
73D THR* 4.0 3.6 - - - -
74D ARG* 3.2 9.2 + - - +
77D ARG* 2.9 23.3 + - - +
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Residues in contact with PHE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LYS 3.1 11.1 + - - +
68D ALA* 3.4 9.6 - - - +
70D ALA* 1.3 78.3 - - - +
72D LEU* 1.3 74.5 + - + +
74D ARG* 3.1 55.5 - - - +
144D ARG* 3.5 45.0 - - - -
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ALA* 2.8 34.3 + - + +
69D TRP* 3.4 19.9 + - + +
71D PHE* 1.3 87.9 - - + +
73D THR* 1.3 61.9 + - + +
74D ARG 3.5 0.4 - - - -
105D TYR* 6.2 4.3 - - + +
107D MET* 3.6 38.6 - - + +
144D ARG* 3.0 32.2 - - + +
145D ARG* 3.4 4.3 + - - +
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D VAL* 4.6 2.6 - - - +
69D TRP* 2.7 43.4 + - + +
70D ALA* 4.0 1.4 - - - -
72D LEU* 1.3 80.5 - - - +
74D ARG* 1.3 62.3 + - - +
75D GLY 3.0 7.3 + - - -
76D TYR* 3.2 32.9 + - + -
77D ARG* 3.1 32.4 + - - -
144D ARG 3.3 6.1 - - - -
145D ARG* 5.1 1.1 - - - -
146D LEU* 5.0 9.2 - - + -
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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