Contacts of the helix formed by residues 376 - 380 (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 GLN 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A PHE* 3.7 18.1 - - + -
338A LEU 4.8 1.0 + - - -
342A PRO* 3.5 23.8 - - + +
344A VAL 3.9 2.9 - - - +
345A PRO 2.9 21.3 + - - +
347A GLN* 2.8 30.4 + - - +
374A GLY 3.5 2.4 + - - -
375A TYR* 1.3 71.9 - - - +
377A PRO* 1.3 65.8 - - + +
379A ALA* 3.0 2.7 + - - -
380A THR* 2.9 40.3 + - + +
409A TRP* 2.9 47.2 - - + +
410A TRP* 3.0 14.5 - - - +
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Residues in contact with PRO 377 (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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37A ASP* 5.4 0.9 - - - +
340A ILE 5.6 0.4 - - - +
342A PRO* 4.1 19.1 - - + +
345A PRO* 3.6 33.9 - - + -
375A TYR* 3.3 28.9 - - + +
376A GLN* 1.3 94.4 - - + +
378A PHE* 1.3 61.8 + - + +
380A THR* 3.7 6.5 + - - +
381A LYS* 3.2 42.1 + - - +
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Residues in contact with PHE 378 (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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37A ASP* 3.4 36.6 - - + -
40A PHE* 3.9 8.7 - - + -
41A ARG* 3.9 31.2 - - + -
44A MET* 4.1 11.9 - - + -
72A LEU* 3.4 37.4 - - + +
375A TYR* 3.2 35.2 + + + +
376A GLN 3.1 0.6 - - - -
377A PRO* 1.3 79.2 - - + +
379A ALA* 1.3 65.3 + - - +
381A LYS* 3.2 18.4 + - + +
382A ASP* 3.5 9.7 + - - -
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Residues in contact with ALA 379 (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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72A LEU 3.3 14.0 + - - +
73A ASP 4.1 10.1 - - - +
74A ALA* 3.8 9.2 - - - +
77A PHE* 3.6 32.8 - - + -
375A TYR 3.5 3.0 + - - +
376A GLN 3.0 7.0 + - - +
378A PHE* 1.3 80.2 - - - +
380A THR* 1.3 57.8 + - - +
381A LYS 3.1 3.7 + - - -
382A ASP* 3.4 17.9 + - - +
385A VAL* 5.6 0.2 - - - +
386A PHE* 5.3 1.2 - - - -
409A TRP* 3.9 17.1 - - + -
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Residues in contact with THR 380 (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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339A ARG* 2.9 54.0 + - + +
342A PRO* 3.7 6.1 - - - +
376A GLN* 2.9 42.9 + - + +
377A PRO* 3.7 6.1 + - - +
379A ALA* 1.3 74.8 - - - +
381A LYS* 1.3 57.4 + - - +
382A ASP 3.5 1.3 - - - -
386A PHE* 3.3 18.1 - - - -
407A TYR 3.7 20.0 - - - +
408A VAL* 5.0 0.2 - - - -
409A TRP* 4.2 12.8 - - + +
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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