Contacts of the helix formed by residues 406 - 418 (chain B) in PDB entry 2DB3
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 406 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402B ASP 3.3 14.2 + - - +
403B ARG* 3.4 26.9 + - - +
405B LEU* 1.3 78.4 - - - +
407B MET* 1.3 86.9 + - - +
408B GLY 2.9 5.5 + - - +
409B PHE 3.0 4.0 + - - -
410B SER* 2.9 19.9 + - - -
439B ILE* 4.0 17.9 - - + +
442B MET* 5.0 6.1 - - - +
569B LYS* 4.5 15.2 + - - +
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Residues in contact with MET 407 (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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406B ASP* 1.3 84.6 + - - +
408B GLY* 1.3 65.1 + - - +
410B SER* 3.3 17.3 + - - -
411B GLU* 4.8 2.6 + - - +
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Residues in contact with GLY 408 (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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403B ARG* 6.4 2.9 - - - -
406B ASP* 2.9 8.3 + - - +
407B MET* 1.3 77.8 - - - +
409B PHE* 1.3 64.6 + - - -
411B GLU* 5.4 1.0 + - - +
412B ASP* 6.1 0.7 - - - -
4F U 5.4 8.7 + - - +
5F U 5.5 2.3 - - - +
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Residues in contact with PHE 409 (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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326B PRO* 3.6 37.9 - - + -
376B PRO* 3.7 25.4 - - + -
403B ARG* 3.5 28.4 + - + +
404B MET* 3.5 29.8 - - + +
406B ASP 3.0 3.2 + - - -
408B GLY* 1.3 80.8 - - - +
410B SER* 1.3 65.8 + - - +
411B GLU 3.3 2.7 - - - -
412B ASP* 3.0 21.1 + - + +
413B MET* 3.0 12.4 + - + +
4F U 3.7 17.5 - - - -
5F U 3.4 45.3 - - - -
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Residues in contact with SER 410 (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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404B MET 3.9 7.8 + - - -
405B LEU* 3.7 15.9 - - - +
406B ASP 2.9 13.0 + - - -
407B MET* 3.3 19.8 + - - -
409B PHE* 1.3 73.8 - - - +
411B GLU* 1.3 63.3 + - - +
413B MET* 3.3 3.5 + - - +
414B ARG* 2.9 35.8 + - - +
442B MET* 6.1 2.0 - - - -
446B PHE* 5.5 0.9 - - - -
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Residues in contact with GLU 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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407B MET 4.8 2.5 + - - +
408B GLY 6.0 0.7 - - - +
409B PHE 3.3 1.2 - - - -
410B SER* 1.3 82.0 + - - +
412B ASP* 1.3 67.9 + - - +
414B ARG* 3.5 7.5 + - - +
415B ARG* 3.1 36.1 + - + +
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Residues in contact with ASP 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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376B PRO* 4.1 20.3 - - + +
377B GLY* 4.6 8.0 + - - -
380B LEU* 3.4 25.5 - - + +
409B PHE* 3.0 13.5 + - + +
411B GLU* 1.3 85.3 - - - +
413B MET* 1.3 67.3 + - - +
415B ARG* 3.3 14.0 + - - +
416B ILE* 3.1 28.5 + - - +
5F U 4.7 5.0 + - - +
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Residues in contact with MET 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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324B VAL* 4.0 15.5 - - + -
376B PRO* 3.7 20.0 - - + -
398B LEU* 3.9 37.2 - - + -
404B MET* 3.6 46.0 - - + +
405B LEU* 4.4 8.7 - - + -
409B PHE* 3.0 17.6 + - + +
410B SER* 3.7 5.4 - - - +
412B ASP* 1.3 77.5 - - - +
414B ARG* 1.3 59.0 + - - +
416B ILE* 3.2 10.5 + - + +
417B MET* 2.8 44.0 + - + +
446B PHE* 4.9 2.7 - - + -
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Residues in contact with ARG 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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410B SER* 2.9 26.8 + - - +
411B GLU* 3.7 7.7 - - - +
413B MET* 1.3 77.4 - - - +
415B ARG* 1.3 57.3 + - + +
418B THR* 2.8 51.5 + - + +
445B GLU* 3.7 31.4 + - - +
446B PHE* 4.0 33.7 - - + -
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Residues in contact with ARG 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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380B LEU* 3.5 36.4 - - + +
383B VAL* 5.6 1.0 - - - +
384B ASP* 2.6 43.2 + - - -
411B GLU* 3.1 28.7 + - + +
412B ASP* 3.3 21.0 + - - +
414B ARG* 1.3 76.5 - - - +
416B ILE* 1.3 59.3 + - - +
418B THR* 5.1 2.5 - - - -
419B HIS* 3.3 32.3 + - - +
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Residues in contact with ILE 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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322B VAL* 5.1 6.1 - - + -
324B VAL* 4.6 5.8 - - + -
376B PRO* 4.5 9.2 - - + -
379B LEU* 3.7 26.9 - - + -
380B LEU* 3.5 28.3 - - + -
390B PHE* 4.0 25.7 - - + -
396B VAL* 5.4 2.9 - - + -
412B ASP 3.1 19.6 + - - +
413B MET* 3.6 22.9 - - + +
414B ARG 3.1 0.2 - - - -
415B ARG* 1.3 74.9 - - - +
417B MET* 1.3 74.7 - - + +
418B THR 3.1 2.0 + - - -
419B HIS* 3.1 16.0 + - - +
422B MET* 3.4 17.6 - - + +
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Residues in contact with MET 417 (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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396B VAL* 3.5 33.0 - - + -
398B LEU* 4.6 12.1 - - + -
413B MET* 2.8 31.9 + - + +
414B ARG 4.2 0.2 - - - +
416B ILE* 1.3 78.9 - - - +
418B THR* 1.3 60.9 + - - +
422B MET* 3.7 20.1 - - + +
426B HIS* 3.8 30.5 + - + +
428B THR* 4.0 15.7 - - + +
446B PHE* 3.6 42.8 - - + +
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Residues in contact with THR 418 (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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414B ARG* 2.8 33.4 + - + +
415B ARG* 4.1 2.2 - - - +
417B MET* 1.3 77.6 - - - +
419B HIS* 1.3 71.0 + - - +
420B VAL* 3.4 2.6 + - - +
422B MET* 4.8 0.2 - - - -
446B PHE* 4.8 5.7 - - - -
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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