Contacts of the helix formed by residues 72 - 79 (chain D) in PDB entry 3N9Z
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 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332B LEU 3.6 6.4 - - - +
333B GLN* 4.0 32.6 + - - +
336B PRO* 5.1 14.8 - - - +
339B LYS* 2.7 46.9 + - + +
73D GLU* 1.3 68.9 + - - +
74D GLU* 3.4 5.5 - - - +
75D ASN* 3.4 24.2 + - - +
76D ASP* 3.0 34.4 + - - +
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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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333B GLN* 4.0 14.4 + - - +
339B LYS* 3.2 28.7 + - - +
427B ARG* 4.0 36.1 + - - +
430B GLU* 4.5 6.4 - - - +
431B LEU* 5.9 4.4 - - - +
50D LEU* 4.0 19.5 - - + -
72D ASP* 1.3 75.5 + - - +
74D GLU* 1.3 65.3 + - - +
76D ASP* 3.3 12.5 + - - +
77D MET* 3.2 26.0 + - - +
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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* 4.3 22.2 - - + +
72D ASP 4.4 3.5 - - - +
73D GLU* 1.3 79.7 - - - +
75D ASN* 1.3 59.2 + - - +
77D MET* 3.5 3.3 + - - +
78D LEU* 3.1 32.8 + - + +
89D ARG* 3.0 44.0 + - - +
90D LEU* 3.6 41.6 + - + +
92D CYS* 6.1 1.8 - - - -
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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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72D ASP* 3.4 27.2 + - - +
73D GLU 3.2 0.6 - - - -
74D GLU* 1.3 77.4 - - - +
76D ASP* 1.3 64.6 + - - +
78D LEU* 3.5 19.0 + - - +
79D ASP* 3.0 33.3 + - - +
89D ARG* 6.1 0.2 - - - -
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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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343B LYS* 2.7 40.4 + - - +
413B ASN* 4.1 16.9 + - - +
426B ARG* 4.6 8.6 + - - +
427B ARG* 5.4 3.0 + - - +
430B GLU* 4.8 9.5 - - - +
72D ASP* 3.0 21.4 - - - +
73D GLU* 3.3 10.6 + - - +
75D ASN* 1.3 76.7 - - - +
77D MET* 1.3 67.3 + - + +
78D LEU 3.1 2.3 + - - -
79D ASP* 3.5 13.6 + - - +
80D LEU* 3.4 19.9 - - - +
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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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418B TRP* 6.0 0.2 - - - -
419B GLY 5.5 4.0 - - - +
422B GLN* 3.7 22.2 - - - +
426B ARG* 3.6 31.2 - - - +
427B ARG* 5.1 7.2 - - - +
50D LEU* 4.3 18.6 - - + +
51D ALA 4.3 1.6 - - - -
52D CYS* 3.3 29.8 - - - +
53D SER* 3.5 21.0 - - - -
73D GLU 3.2 12.8 + - - +
74D GLU 3.7 9.0 - - - +
76D ASP* 1.3 78.2 - - + +
78D LEU* 1.3 60.4 + - - +
80D LEU* 3.9 27.8 + - + +
90D LEU* 3.8 18.4 - - + -
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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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56D HIS* 4.2 15.0 - - + +
74D GLU* 3.1 17.8 + - + +
75D ASN* 3.6 22.9 - - - +
76D ASP 3.1 0.4 - - - -
77D MET* 1.3 75.3 - - - +
79D ASP* 1.3 57.7 + - - +
80D LEU 2.9 18.0 + - - +
89D ARG* 4.1 29.4 - - - +
90D LEU* 3.8 38.8 - - + +
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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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343B LYS* 5.6 2.1 + - - -
406B LYS* 4.2 27.6 + - - +
409B THR* 4.4 21.9 + - - +
410B TYR* 4.2 13.6 - - - -
411B PHE 4.0 16.1 + - - -
75D ASN* 3.0 21.9 + - - +
76D ASP* 3.5 10.1 + - - +
77D MET 3.5 1.0 - - - -
78D LEU* 1.3 74.9 - - - +
80D LEU* 1.3 62.7 + - + +
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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