Contacts of the helix formed by residues 404 - 417 (chain B) in PDB entry 4I6J
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 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373B CYS* 4.7 1.1 - - - -
399B PRO* 4.2 8.5 - - - -
403B TYR* 1.3 74.7 - - - +
405B LEU* 1.3 68.9 + - - +
406B GLU* 3.0 7.7 + - - +
407B GLN* 2.7 45.0 + - - +
408B ILE* 3.4 10.5 + - - +
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Residues in contact with LEU 405 (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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373B CYS* 4.1 10.5 - - - -
394B GLU* 3.8 41.5 - - + +
397B LEU* 3.7 38.4 - - + +
399B PRO* 4.4 15.7 - - + +
404B SER* 1.3 72.8 - - - +
406B GLU* 1.3 65.0 + - - +
408B ILE* 3.0 32.4 - - + +
409B HIS* 4.4 2.6 + - - -
422B PRO* 4.8 6.1 - - + -
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Residues in contact with GLU 406 (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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301A PRO* 3.7 31.9 - - + +
303A SER* 3.9 11.8 + - - -
404B SER* 3.0 8.5 + - - +
405B LEU* 1.3 83.4 - - - +
407B GLN* 1.3 61.0 + - + +
409B HIS* 3.4 31.0 + - - +
410B TRP* 3.7 9.1 + - - +
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Residues in contact with GLN 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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402B LYS 3.3 19.5 + - - +
403B TYR* 3.3 13.0 - - + -
404B SER* 2.7 46.8 + - - +
406B GLU* 1.3 76.2 - - + +
408B ILE* 1.3 62.5 + - - +
409B HIS 3.5 0.4 - - - -
410B TRP* 3.3 19.7 + - - +
411B GLU* 3.4 12.1 + - - +
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Residues in contact with ILE 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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373B CYS* 3.8 28.9 - - + +
376B PHE* 5.4 2.9 - - + -
377B VAL* 3.8 27.6 - - + -
397B LEU* 3.7 30.1 - - + -
403B TYR* 4.2 9.6 - - + -
404B SER 3.4 6.0 + - - +
405B LEU* 3.0 30.5 - - + +
407B GLN* 1.3 71.3 - - - +
409B HIS* 1.3 77.3 + - + +
410B TRP 3.0 2.0 - - - -
411B GLU* 2.9 4.6 + - - +
412B VAL* 2.7 40.3 + - + +
420B TRP* 4.8 2.0 - - + -
422B PRO* 4.5 15.9 - - + -
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Residues in contact with HIS 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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405B LEU 4.8 1.8 - - - -
406B GLU* 3.4 35.9 + - - +
408B ILE* 1.3 82.9 - - + +
410B TRP* 1.3 108.9 + + - +
413B SER* 2.6 38.6 + - - -
419B VAL* 5.9 0.6 - - - +
420B TRP* 3.3 26.2 + - - +
421B PHE* 3.2 45.1 - + + -
422B PRO* 4.4 6.1 - - + -
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Residues in contact with TRP 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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406B GLU* 3.7 20.7 + - - +
407B GLN* 3.3 10.2 + - + +
408B ILE 3.0 0.6 - - - -
409B HIS* 1.3 110.3 + + - +
411B GLU* 1.3 63.2 + - + +
413B SER* 3.7 7.5 - - - -
414B LYS* 3.1 27.8 + - - +
419B VAL* 6.4 2.2 - - + -
421B PHE* 6.1 1.1 - + - -
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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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377B VAL* 4.2 13.4 - - + +
381B LYS* 3.9 7.6 + - - -
403B TYR* 3.4 39.5 - - + +
407B GLN 3.4 7.0 + - - +
408B ILE 2.9 6.2 + - - +
410B TRP* 1.3 74.7 - - + +
412B VAL* 1.3 66.6 + - - +
414B LYS* 3.2 36.0 + - - +
415B HIS* 2.9 54.1 + - - -
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Residues in contact with VAL 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 PHE* 3.5 29.2 - - + -
377B VAL* 4.9 5.6 - - + -
380B VAL* 4.2 15.9 - - + +
390B LEU* 3.8 13.9 - - + -
408B ILE* 2.7 32.0 + - + +
411B GLU* 1.3 71.9 - - - +
413B SER* 1.3 61.9 + - - +
415B HIS* 3.2 3.9 + - - +
416B LEU* 2.9 40.4 + - + +
420B TRP* 3.5 31.6 - - + -
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Residues in contact with SER 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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409B HIS* 2.6 25.3 + - - -
410B TRP* 3.7 10.4 - - - -
412B VAL* 1.3 77.7 - - - +
414B LYS* 1.3 56.7 + - - +
416B LEU* 4.4 1.6 - - - -
417B GLY* 2.8 28.2 + - - -
418B ARG 3.2 23.9 + - - -
419B VAL* 3.7 4.7 - - - +
420B TRP* 2.9 27.0 + - - -
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Residues in contact with LYS 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 TRP* 3.1 17.2 + - - +
411B GLU* 3.2 39.8 + - - +
413B SER* 1.3 77.8 - - - +
415B HIS* 1.3 72.7 + - + +
417B GLY* 3.6 8.4 + - - -
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Residues in contact with HIS 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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377B VAL* 4.6 7.6 - - + -
380B VAL* 3.5 30.1 - - + +
381B LYS* 3.5 48.6 + - + +
384B GLY* 3.4 17.8 - - - -
385B GLY* 3.6 3.8 + - - -
411B GLU* 2.9 44.8 + - - -
412B VAL* 3.2 3.3 + - - +
414B LYS* 1.3 88.3 - - + +
416B LEU* 1.3 63.2 + - - +
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Residues in contact with LEU 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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380B VAL* 4.1 9.6 - - + -
384B GLY 3.6 21.7 - - - +
385B GLY* 4.5 6.8 - - - -
387B LEU* 4.1 13.0 - - + +
390B LEU* 3.7 13.9 - - + -
412B VAL* 2.9 27.2 + - + +
413B SER 3.7 2.7 - - - +
415B HIS* 1.3 81.4 - - - +
417B GLY* 1.3 60.6 + - - +
418B ARG* 3.7 41.8 + - + +
420B TRP* 3.4 46.7 - - + -
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Residues in contact with GLY 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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413B SER 2.8 9.7 + - - -
414B LYS* 3.6 6.9 + - - -
415B HIS 3.4 1.6 - - - -
416B LEU* 1.3 78.4 - - - +
418B ARG* 1.3 62.2 + - - +
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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