Contacts of the helix formed by residues 66 - 74 (chain N) in PDB entry 3J0S
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 66 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64N VAL* 3.4 8.8 - - + +
65N ASP* 1.3 108.2 + - - +
67N PRO* 1.4 66.0 - - - +
68N TYR 3.1 7.2 + - - +
69N ALA* 3.3 27.1 - - + +
70N THR* 3.5 8.5 + - - -
146N ARG* 5.0 12.6 + - - +
162N GLU* 5.1 12.4 - - - +
164N LYS* 4.4 20.1 + - - -
165N PRO* 5.9 1.2 - - - +
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Residues in contact with PRO 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N LYS* 3.3 36.1 - - + +
55N ILE* 3.8 21.4 - - + +
56N LEU 4.8 4.0 - - - +
59N ASP* 5.2 3.1 - - + -
60N VAL* 3.2 36.8 - - + +
64N VAL* 4.2 6.0 - - + +
65N ASP 3.6 2.5 - - - +
66N ASP* 1.4 86.5 - - - +
68N TYR* 1.3 57.4 + - - +
69N ALA 3.0 6.6 + - - -
70N THR* 3.2 16.9 + - - +
71N PHE* 3.3 14.9 + - - +
85N TYR* 4.4 2.7 - - + -
162N GLU* 5.2 6.3 - - - +
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Residues in contact with TYR 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N ASP* 3.1 3.7 - - - +
67N PRO* 1.3 75.8 - - - +
69N ALA* 1.3 63.4 - - - +
71N PHE* 4.7 17.5 - + - -
72N VAL* 4.8 2.6 - - + +
85N TYR* 3.2 37.2 + + - +
102N ILE* 5.8 4.3 - - + -
135N LEU* 4.9 7.9 - - + +
142N GLU 4.4 1.6 + - - -
143N VAL* 2.8 33.0 + - + +
144N LYS* 4.0 9.2 - - - +
145N ASP 3.6 21.0 + - - -
146N ARG* 3.6 31.8 + - - +
148N THR* 5.0 2.1 - - - +
149N LEU* 3.7 35.9 + - + +
161N LEU* 5.1 4.5 - - + -
162N GLU* 5.3 9.8 - - + +
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Residues in contact with ALA 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N ASP* 3.3 21.1 - - + +
67N PRO 3.0 1.0 + - - -
68N TYR* 1.3 76.0 - - - +
70N THR* 1.3 63.6 + - - +
71N PHE 3.1 2.4 - - - +
72N VAL* 3.1 20.5 + - - +
73N LYS* 2.9 40.7 + - - +
146N ARG* 5.5 1.3 - - - +
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Residues in contact with THR 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N ILE* 4.7 8.5 - - + -
64N VAL* 3.6 29.1 - - + +
66N ASP 3.6 2.4 + - - -
67N PRO* 3.2 11.6 + - - +
69N ALA* 1.3 78.4 - - - +
71N PHE* 1.3 58.2 + - - +
73N LYS* 3.1 11.1 + - + +
74N MET* 2.9 48.4 + - + +
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Residues in contact with PHE 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N ALA* 4.4 13.0 - - + -
37N LEU* 4.1 11.4 - - + -
55N ILE* 3.4 28.7 - - + +
67N PRO 3.3 8.3 + - - +
68N TYR* 4.7 15.5 - + - -
69N ALA 4.5 2.7 - - - +
70N THR* 1.3 80.5 - - - +
72N VAL* 1.3 62.9 + - + +
74N MET* 3.5 6.7 + - + +
75N LEU* 3.1 55.5 + - + +
83N ALA* 3.7 21.3 - - + -
85N TYR* 4.6 10.5 - + + -
102N ILE* 3.5 41.1 - - + -
143N VAL* 4.0 18.8 - - + -
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Residues in contact with VAL 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N TYR* 4.8 4.9 - - + +
69N ALA* 3.1 24.7 + - - +
71N PHE* 1.3 80.6 - - + +
73N LYS* 1.3 70.3 + - + +
75N LEU* 3.5 9.9 + - - +
140N TYR* 3.2 37.2 - - + +
143N VAL* 3.6 29.8 - - + +
144N LYS* 3.7 44.6 - - + +
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Residues in contact with LYS 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69N ALA* 2.9 29.7 + - - +
70N THR* 3.3 12.3 - - + +
72N VAL* 1.3 84.7 - - + +
74N MET* 1.3 57.2 + - + +
75N LEU 3.3 3.1 + - - -
76N PRO* 4.4 9.4 - - - +
140N TYR* 4.6 7.7 + - + -
144N LYS* 4.7 14.6 - - - +
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Residues in contact with MET 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N LEU* 3.9 12.8 - - + -
52N GLY 5.2 0.7 - - - +
53N LYS* 3.4 53.0 - - + +
54N GLU 3.9 9.0 - - - +
55N ILE* 4.1 20.2 - - - -
70N THR* 2.9 36.7 + - + +
71N PHE* 3.7 10.3 - - + +
72N VAL 3.4 0.2 - - - -
73N LYS* 1.3 74.6 - - + +
75N LEU* 1.3 60.2 + - + +
76N PRO* 3.4 7.1 - - - +
81N ARG* 3.3 18.0 + - - -
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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
------------------------------------------------------------
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