Contacts of the helix formed by residues 410 - 416 (chain B) in PDB entry 6DWN
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 ASN 410 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B HIS* 3.4 12.0 + - - +
63B LEU* 3.9 14.6 + - - +
64B SER* 3.3 28.9 + - - +
85B VAL* 4.6 4.7 - - + +
86B LEU 3.0 17.3 + - - +
87B SER* 4.6 4.6 + - - +
92B ILE* 4.2 5.2 - - - +
383B PRO 3.8 1.9 - - - +
384B PHE* 3.8 20.6 - - + -
408B PHE 4.1 0.4 - - - -
409B VAL* 1.3 69.9 - - - +
411B GLN* 1.3 63.0 + - - +
412B TRP* 3.2 13.3 + - - +
413B GLN* 2.9 42.3 + - + +
414B ILE* 3.6 9.2 + - - +
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Residues in contact with GLN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B SER* 5.9 0.4 - - - -
382B VAL* 3.0 24.8 + - - +
383B PRO* 2.8 10.6 + - + +
385B THR* 3.4 38.7 - - + +
409B VAL* 3.2 4.9 + - + +
410B ASN* 1.3 70.4 - - - +
412B TRP* 1.3 68.2 + - - +
414B ILE* 3.0 22.2 + - + +
415B ASN* 3.1 17.9 + - - +
448B ILE* 3.3 26.5 - - + +
449B ILE* 3.0 36.0 + - - -
451B GLY 3.4 4.6 + - - -
601B HEM 3.5 18.4 - - - +
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Residues in contact with TRP 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B HIS* 3.5 27.1 + + + -
61B LEU* 3.4 28.7 - - + -
64B SER* 3.3 28.9 - - - -
378B HIS 4.7 1.2 + - - -
379B SER 4.1 8.8 + - - -
380B SER* 3.6 28.2 - - - -
383B PRO* 3.0 21.1 + - + +
410B ASN* 3.2 8.9 + - - +
411B GLN* 1.3 76.6 - - - +
413B GLN* 1.3 63.5 + - - +
415B ASN 3.4 0.2 + - - -
416B HIS* 3.2 61.8 + + + -
492B PRO* 6.0 2.2 - - - +
498B MET* 4.2 7.4 - - + +
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Residues in contact with GLN 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B SER* 3.8 17.5 - - - +
67B SER* 3.8 23.1 + - - +
68B GLN* 6.2 1.2 - - - +
72B ASP* 4.8 3.2 + - - -
87B SER* 3.8 8.4 - - - +
88B GLY* 3.0 30.5 + - - +
410B ASN* 2.9 33.7 + - + +
411B GLN 3.1 0.4 - - - -
412B TRP* 1.3 80.5 - - - +
414B ILE* 1.3 70.1 + - - +
416B HIS 3.3 2.6 + - - -
417B ASP* 3.0 46.4 + - - +
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Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY 3.9 17.9 - - - +
89B LEU* 4.0 21.5 - - + -
92B ILE* 3.4 33.9 - - + -
409B VAL* 5.7 0.2 - - + -
410B ASN 3.6 5.4 + - - +
411B GLN* 3.0 9.7 + - + +
413B GLN* 1.3 91.6 + - - +
415B ASN* 1.3 60.1 + - - +
416B HIS 2.9 4.0 + - - -
417B ASP* 3.1 14.1 + - - +
420B LEU* 4.0 7.4 - - + +
421B TRP* 2.9 17.5 + - - -
446B LYS 3.6 21.8 - - - +
448B ILE* 3.9 31.9 - - + -
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Residues in contact with ASN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B PHE 4.2 6.7 + - - -
377B ARG* 2.8 47.2 + - + +
380B SER* 2.9 34.6 + - - +
411B GLN* 3.1 11.0 + - - +
414B ILE* 1.3 75.3 - - - +
416B HIS* 1.3 59.9 + - + +
421B TRP* 3.3 14.2 + - - +
446B LYS 3.8 2.4 - - - +
447B VAL* 3.7 7.5 - - - +
448B ILE* 2.8 45.7 + - - +
449B ILE* 4.8 2.4 - - - +
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Residues in contact with HIS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B ARG* 3.3 12.1 + - - -
378B HIS* 3.0 37.5 + + - -
380B SER* 3.6 7.4 + - - -
412B TRP* 3.2 74.9 + + + +
413B GLN 3.5 3.6 - - - +
414B ILE 3.0 0.8 - - - -
415B ASN* 1.3 82.5 + - - +
417B ASP* 1.3 60.5 + - - +
418B GLN* 3.3 3.8 + - - +
424B PRO* 3.7 39.1 + - + +
425B SER* 5.2 2.1 - - - -
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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