Contacts of the helix formed by residues 71 - 79 (chain D) in PDB entry 3NA0
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 THR 71 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B GLN* 3.9 22.7 - - - +
50D LEU* 4.5 7.1 - - + +
72D ASP* 1.3 64.3 + - - +
73D GLU* 3.3 15.5 + - - +
74D GLU* 3.3 34.8 + - - +
75D ASN* 3.2 28.4 + - - +
93D GLN* 5.5 2.7 + - - +
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Residues in contact with ASP 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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371B LEU 3.6 4.6 - - - +
372B GLN* 3.2 26.1 + - - +
374B VAL 6.3 0.2 - - - -
375B PRO* 4.8 16.3 - - - +
378B LYS* 3.0 43.6 + - + +
71D THR* 1.3 73.9 - - - +
73D GLU* 1.3 63.7 + - - +
75D ASN* 3.3 21.2 + - - +
76D ASP* 3.1 25.9 - - - +
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Residues in contact with GLU 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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372B GLN* 4.2 5.9 - - - +
378B LYS* 3.2 31.5 + - - +
466B ARG* 3.9 36.5 + - - +
469B GLU* 4.4 9.2 - - - +
470B LEU* 5.9 5.8 - - - +
50D LEU* 4.1 19.7 - - + -
71D THR* 3.2 10.2 - - - +
72D ASP* 1.3 82.5 + - - +
74D GLU* 1.3 62.9 + - - +
75D ASN 3.2 0.4 - - - -
76D ASP* 3.5 12.7 + - - +
77D MET* 3.4 26.2 + - - +
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Residues in contact with GLU 74 (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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50D LEU* 4.4 9.0 - - + +
71D THR* 3.3 29.7 + - - +
73D GLU* 1.3 78.0 - - - +
75D ASN* 1.3 59.3 + - - +
77D MET* 3.4 7.6 + - - +
78D LEU* 3.0 35.4 + - + +
90D LEU* 2.8 46.0 + - + +
93D GLN* 3.2 31.5 - - - +
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Residues in contact with ASN 75 (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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71D THR 3.2 19.0 + - - +
72D ASP* 3.3 23.2 + - - +
73D GLU 3.2 0.2 - - - -
74D GLU* 1.3 79.4 - - - +
76D ASP* 1.3 60.8 + - - +
78D LEU* 3.2 15.8 + - - +
79D ASP* 3.2 34.5 + - - +
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Residues in contact with ASP 76 (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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382B LYS* 2.6 39.8 + - - -
452B ASN* 3.9 19.3 + - - +
465B ARG* 4.3 10.0 - - - +
466B ARG* 5.4 1.9 + - - +
469B GLU* 4.5 12.6 - - - +
72D ASP* 3.1 19.3 - - - +
73D GLU* 3.5 12.2 + - - +
74D GLU 3.3 0.6 - - - -
75D ASN* 1.3 77.3 - - - +
77D MET* 1.3 67.2 + - + +
78D LEU 3.1 1.9 + - - -
79D ASP* 3.6 15.3 + - - +
80D LEU* 3.9 19.8 - - - +
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Residues in contact with MET 77 (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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457B TRP* 6.2 1.6 - - + -
458B GLY 5.6 3.8 - - - +
461B GLN* 3.7 17.0 - - - +
465B ARG* 3.4 29.4 - - - +
466B ARG* 5.2 5.8 - - - +
50D LEU* 4.7 11.9 - - + +
51D ALA* 4.3 3.6 - - - -
52D CYS* 3.7 35.0 - - - +
53D SER* 3.3 25.5 + - - -
73D GLU 3.4 14.0 + - - +
74D GLU* 3.6 9.6 - - - +
75D ASN 3.4 0.2 - - - -
76D ASP* 1.3 80.2 - - + +
78D LEU* 1.3 60.7 + - - +
80D LEU* 3.7 17.9 + - + +
90D LEU* 3.7 23.1 - - + -
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Residues in contact with LEU 78 (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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53D SER* 5.5 0.2 - - - -
74D GLU* 3.0 20.9 + - + +
75D ASN* 3.4 16.8 - - - +
76D ASP 3.1 0.4 - - - -
77D MET* 1.3 75.3 - - - +
79D ASP* 1.3 58.7 + - - +
80D LEU 3.0 9.9 + - - -
81D ALA* 3.4 21.3 + - + +
90D LEU* 3.8 43.3 - - + +
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Residues in contact with ASP 79 (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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382B LYS* 5.3 3.8 + - - -
440B TRP* 5.7 1.2 - - - +
445B LYS* 3.8 23.2 - - - +
448B THR* 3.8 28.5 + - - +
449B TYR* 4.0 22.7 - - - -
450B PHE 4.0 2.6 + - - -
452B ASN* 6.3 3.1 - - + -
75D ASN* 3.2 18.9 + - - +
76D ASP* 3.6 11.6 + - - +
77D MET 3.5 0.4 - - - -
78D LEU* 1.3 75.7 - - - +
80D LEU* 1.3 67.0 + - + +
81D ALA 3.7 1.3 - - - -
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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