Contacts of the helix formed by residues 414 - 421 (chain B) in PDB entry 3D0G
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 THR 414 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU 3.5 13.9 - - - +
411B SER 2.9 22.4 + - - +
413B ALA* 1.3 76.7 - - - +
415B PRO* 1.3 72.3 - - - +
416B LYS* 3.8 11.0 - - - +
417B HIS* 3.0 21.3 + - - +
418B LEU* 2.8 15.2 + - - +
438B PHE* 3.9 7.8 - - + -
540B HIS 4.2 16.8 - - - +
541B LYS* 4.9 3.4 - - - -
542B CYS 3.7 20.9 - - - +
543B ASP* 4.0 4.4 - - - +
587B TYR* 6.0 0.4 - - - +
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Residues in contact with PRO 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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291B ILE* 3.7 22.9 - - + -
413B ALA 3.5 1.3 - - - +
414B THR* 1.3 83.8 - - - +
416B LYS* 1.3 63.6 + - - +
418B LEU* 3.1 11.3 + - + +
419B LYS* 2.8 30.6 + - - +
424B LEU* 3.7 16.1 - - + +
428B PHE* 4.0 16.4 - - + -
430B GLU* 4.5 12.1 - - + +
434B THR* 5.5 3.4 - - - +
438B PHE* 3.8 29.4 - - + -
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Residues in contact with LYS 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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536A GLU* 6.0 2.0 - - - +
414B THR* 3.8 8.7 - - - +
415B PRO* 1.3 78.5 - - - +
417B HIS* 1.3 60.3 + - - +
419B LYS* 3.4 9.7 - - - +
420B SER* 3.3 19.2 + - - -
430B GLU* 4.3 24.1 + - - +
535B HIS* 4.8 8.5 + - - -
541B LYS* 3.3 30.9 + - + +
542B CYS* 4.7 0.6 - - - +
543B ASP* 3.5 35.9 + - - +
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Residues in contact with HIS 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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310B GLU* 6.2 1.2 - - - +
314B PHE* 3.6 22.7 - + + +
369B PHE* 4.6 0.4 - + - -
373B HIS* 4.6 6.3 + - - -
411B SER 3.5 4.5 + - - +
412B ALA* 3.4 33.3 - - + +
414B THR* 3.0 21.0 + - - +
416B LYS* 1.3 75.7 - - - +
418B LEU* 1.3 66.9 + - - +
420B SER* 3.0 21.2 + - - -
421B ILE* 3.0 38.3 + - + +
543B ASP* 2.7 25.5 + - - +
545B SER* 3.1 20.0 + - - -
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Residues in contact with LEU 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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291B ILE* 4.9 4.7 - - + +
293B VAL* 3.7 23.8 - - + -
366B MET* 4.1 15.3 - - + -
369B PHE* 4.1 9.6 - - + -
412B ALA 3.3 20.4 - - - +
413B ALA 3.1 18.8 - - - +
414B THR 2.8 32.4 + - - +
415B PRO* 3.1 10.1 + - + +
417B HIS* 1.3 75.6 - - - +
419B LYS* 1.3 61.6 + - - +
421B ILE* 3.4 19.2 + - + -
422B GLY 2.9 4.3 + - - -
423B LEU* 2.8 28.5 + - + +
424B LEU* 3.7 23.1 - - + +
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Residues in contact with LYS 419 (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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536A GLU* 2.8 45.5 + - - +
415B PRO 2.8 17.9 + - - +
416B LYS* 3.4 12.6 - - - +
418B LEU* 1.3 76.5 - - - +
420B SER* 1.3 57.7 + - - +
422B GLY* 2.9 20.6 + - - -
424B LEU* 3.4 24.6 - - + +
425B SER 3.4 19.1 - - - +
426B PRO* 2.9 27.0 + - + +
428B PHE* 3.1 32.8 + - + +
430B GLU* 3.9 10.1 - - - -
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Residues in contact with SER 420 (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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313B LYS* 5.9 1.0 + - - -
416B LYS 3.3 9.8 + - - -
417B HIS* 3.0 18.2 + - - -
419B LYS* 1.3 80.9 - - - +
421B ILE* 1.3 60.0 + - - +
422B GLY* 3.4 0.7 + - - -
543B ASP* 5.8 0.2 - - - -
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Residues in contact with ILE 421 (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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300B GLN* 5.4 1.0 + - - -
302B TRP* 3.5 16.2 - - + -
306B ARG* 4.3 11.6 + - - +
310B GLU* 3.2 43.1 - - + +
313B LYS* 5.9 2.9 - - - +
369B PHE* 3.3 35.7 - - + -
417B HIS* 3.0 33.3 + - + +
418B LEU* 3.9 15.9 - - + +
420B SER* 1.3 74.4 + - - +
422B GLY* 1.3 59.7 + - - +
423B LEU* 3.7 9.4 + - + +
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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