Contacts of the helix formed by residues 76 - 82 (chain A) in PDB entry 3DAN
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 SER 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A VAL* 3.9 15.1 - - - +
71A LEU* 3.7 23.2 - - - +
73A ASP* 2.7 31.3 + - - -
75A LYS* 1.3 77.6 - - - +
77A PHE* 1.3 66.0 + - - +
78A PRO* 3.3 1.3 - - - -
79A ILE* 3.2 26.7 + - - +
357A ILE* 4.8 9.3 - - - +
358A GLU 3.5 17.5 - - - +
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Residues in contact with PHE 77 (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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71A LEU* 4.1 15.0 - - + -
73A ASP 3.2 15.2 + - - +
76A SER* 1.3 81.2 + - - +
78A PRO* 1.3 63.6 - - + +
79A ILE 2.9 7.1 + - - -
80A LEU* 2.9 31.0 + - + +
81A PHE* 3.7 27.1 - + - -
347A GLN* 3.4 26.7 - - + -
374A GLY* 3.5 36.3 - - - -
375A TYR 4.4 0.2 - - - -
376A GLN* 3.7 22.0 - - + -
379A ALA* 3.6 11.9 - - + -
409A TRP* 3.5 29.4 - + + -
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Residues in contact with PRO 78 (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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74A ALA 3.3 23.3 - - - +
75A LYS 3.7 7.4 - - - +
76A SER 3.3 5.4 - - - +
77A PHE* 1.3 89.3 - - + +
79A ILE* 1.3 63.9 + - - +
80A LEU 2.9 0.7 - - - -
81A PHE* 2.9 38.0 + - + +
82A ASP* 3.6 4.5 + - - +
407A TYR* 6.4 0.2 - - + -
409A TRP* 3.8 19.7 - - + -
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Residues in contact with ILE 79 (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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71A LEU* 3.5 23.3 - - + -
76A SER 3.2 19.5 + - - +
77A PHE 2.9 0.8 + - - -
78A PRO* 1.3 77.0 - - - +
80A LEU* 1.3 66.6 + - + +
82A ASP* 3.1 21.9 + - + +
85A LYS* 3.4 40.2 - - + +
86A VAL* 3.6 15.1 - - + +
355A PHE* 3.8 30.1 - - + -
356A THR 5.7 0.4 - - - +
357A ILE* 4.3 13.0 - - + -
372A LEU* 4.0 12.1 - - + -
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Residues in contact with LEU 80 (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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71A LEU* 4.4 4.9 - - + -
77A PHE* 2.9 34.5 + - + +
78A PRO 2.9 0.4 - - - -
79A ILE* 1.3 83.2 - - + +
81A PHE* 1.3 66.0 + - + +
83A VAL* 5.8 0.3 - - - +
86A VAL* 3.9 13.7 - - + +
88A LYS* 4.3 15.0 + - - +
347A GLN* 3.9 14.1 - - + +
348A TYR 3.9 6.7 - - - +
349A GLY* 3.7 28.5 - - - +
372A LEU* 3.9 25.1 - - + +
373A PHE 4.3 0.9 - - - -
374A GLY* 3.6 32.5 - - - +
412A ASN* 4.3 6.7 + - - +
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Residues in contact with PHE 81 (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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77A PHE* 3.7 23.3 - + - -
78A PRO* 2.9 29.9 + - + +
80A LEU* 1.3 80.0 - - + +
82A ASP* 1.3 59.3 + - - +
83A VAL* 3.1 19.5 + - - +
347A GLN* 5.6 0.4 - - + -
409A TRP* 3.5 50.9 - + + -
412A ASN* 3.4 37.5 - - - +
413A GLY* 3.4 20.9 - - - -
414A PRO* 4.1 16.8 - - + -
423A ASN* 5.3 5.5 - - - +
424A LYS 5.8 0.2 + - - -
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Residues in contact with ASP 82 (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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78A PRO 3.6 3.5 + - - +
79A ILE* 3.1 23.3 + - + +
81A PHE* 1.3 75.1 - - - +
83A VAL* 1.3 58.8 + - - +
84A SER* 2.6 30.7 + - - -
85A LYS* 3.0 29.1 + - + +
86A VAL* 2.9 28.6 + - - +
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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