Contacts of the helix formed by residues 412 - 422 (chain B) in PDB entry 4X2Q
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 412 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B PHE* 3.3 20.2 - - - -
411B LYS* 1.3 102.2 - - + +
413B MET* 1.3 63.0 + - - +
414B ASP* 3.5 10.4 + - - +
415B GLU* 3.0 32.1 + - + +
416B VAL* 3.4 4.3 - - - +
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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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278B PHE* 3.8 28.0 - - + -
412B THR* 1.3 71.3 - - - +
414B ASP* 1.3 69.7 + - - +
415B GLU 3.1 2.9 + - - -
416B VAL* 3.2 18.6 - - - +
417B ILE* 3.4 24.4 + - + +
437B ASN 5.4 0.2 - - - -
438B LYS* 3.7 35.0 - - + +
441B THR* 3.3 33.2 - - + -
442B VAL* 3.9 13.2 - - + -
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Residues in contact with ASP 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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412B THR* 3.4 8.0 - - - +
413B MET* 1.3 81.6 - - - +
415B GLU* 1.3 61.6 + - - +
417B ILE* 4.2 9.6 - - - +
418B GLU* 3.1 30.4 + - - +
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Residues in contact with GLU 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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409B ARG 4.6 0.5 - - - +
410B PHE* 3.6 2.1 - - - -
411B LYS* 2.7 41.3 + - - +
412B THR* 3.0 20.9 + - - +
413B MET 3.1 0.2 - - - -
414B ASP* 1.3 74.4 - - - +
416B VAL* 1.3 65.0 - - - +
417B ILE 3.2 0.9 + - - -
418B GLU* 3.2 6.3 + - - +
419B ARG* 3.0 60.6 + - + +
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Residues in contact with VAL 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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276B ILE* 4.2 21.3 - - + -
278B PHE* 4.6 5.4 - - + -
309B PHE* 3.8 24.7 - - + -
410B PHE* 3.4 49.4 - - + -
412B THR 3.4 13.0 - - - +
413B MET* 3.2 22.0 - - + +
415B GLU* 1.3 76.0 - - - +
417B ILE* 1.3 52.7 + - + +
419B ARG* 3.7 6.0 - - - +
420B ALA* 2.6 40.2 + - + +
442B VAL* 6.0 0.7 - - + -
446B MET* 5.3 0.4 - - - -
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Residues in contact with ILE 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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72A LEU* 5.0 4.7 - - + -
276B ILE* 6.1 0.2 - - + -
413B MET* 3.4 41.4 + - + +
414B ASP* 4.2 10.8 - - - +
415B GLU 3.2 0.8 + - - -
416B VAL* 1.3 76.6 - - + +
418B GLU* 1.3 63.3 + - - +
420B ALA* 4.2 0.5 - - - +
421B ASN* 2.9 49.1 + - - +
441B THR* 4.5 11.2 - - + +
442B VAL* 4.3 14.4 - - + -
445B ALA* 3.9 21.5 - - + +
446B MET* 4.2 20.8 - - + +
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Residues in contact with GLU 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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72A LEU* 5.2 9.5 - - - +
414B ASP* 3.1 21.4 + - - +
415B GLU* 3.2 8.8 + - - +
417B ILE* 1.3 86.6 - - - +
419B ARG* 1.3 64.6 + - + +
421B ASN* 3.4 8.8 + - - +
422B ASN* 3.2 23.1 + - - +
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Residues in contact with ARG 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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272B LYS* 4.2 9.2 + - - -
307B ARG* 4.3 3.6 + - - -
309B PHE* 3.7 26.3 - - + -
389B VAL 5.4 1.6 + - - -
390B THR* 5.5 1.2 - - - +
391B ASP* 3.1 45.6 + - - +
408B LEU* 4.4 5.3 - - - +
409B ARG 2.4 31.7 + - - +
410B PHE* 3.3 20.6 - - - +
415B GLU* 3.0 46.2 + - + +
416B VAL* 3.7 4.7 - - - +
418B GLU* 1.3 76.8 - - + +
420B ALA* 1.3 61.5 + - - +
422B ASN* 3.4 19.6 + - - +
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Residues in contact with ALA 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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272B LYS* 4.5 9.7 - - - -
274B PRO* 3.7 33.9 - - + +
276B ILE* 4.5 5.8 - - + -
307B ARG* 4.6 5.6 - - - +
309B PHE* 4.5 6.5 - - + -
416B VAL 2.6 23.4 + - - +
419B ARG* 1.3 70.4 - - - +
421B ASN* 1.3 63.4 + - - +
422B ASN 3.2 1.1 + - - -
427B LEU* 3.4 19.1 - - - +
446B MET* 3.9 17.9 - - + -
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Residues in contact with ASN 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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72A LEU* 4.1 13.5 - - - +
417B ILE* 2.9 29.8 + - - +
418B GLU* 3.6 10.1 + - - +
420B ALA* 1.3 75.9 - - - +
422B ASN* 1.3 51.4 + - - +
423B SER* 2.7 25.7 + - - +
427B LEU* 4.4 7.8 - - - +
445B ALA 3.4 17.4 + - - +
446B MET* 3.9 6.3 - - - +
447B GLN* 3.0 54.7 + - - +
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Residues in contact with ASN 422 (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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272B LYS* 2.8 25.6 + - - +
391B ASP* 5.9 1.3 + - - +
418B GLU 3.2 12.4 + - - +
419B ARG* 3.5 15.1 - - - +
420B ALA 3.2 2.6 - - - -
421B ASN* 1.3 71.4 - - - +
423B SER* 1.3 55.6 + - - +
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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