Contacts of the helix formed by residues 466 - 473 (chain B) in PDB entry 4TVJ
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 MET 466 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B SER 5.3 0.4 - - - +
389B THR* 3.4 39.9 - - - +
390B HIS 4.2 1.1 - - - +
391B ALA* 3.5 28.0 - - + +
392B PRO* 4.7 2.5 - - + -
427B TRP* 3.7 3.4 - - - -
464B ALA* 3.4 5.9 - - - +
465B ASP* 1.3 87.2 - - - +
467B SER* 1.3 69.0 + - - +
468B SER* 4.6 1.8 - - - +
469B LYS* 3.1 27.7 + - + +
470B SER 3.4 7.6 + - - -
521B MET 5.3 0.7 - - - +
522B ALA* 4.9 0.2 - - - -
523B PRO* 3.8 25.4 - - + -
541B ALA* 3.8 23.8 - - + +
556B TYR* 4.1 28.5 - - + -
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Residues in contact with SER 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LEU* 2.8 36.2 + - - -
389B THR* 3.1 26.8 + - - -
390B HIS 3.5 1.4 + - - -
399B MET* 3.5 9.9 - - - +
427B TRP* 3.5 30.8 - - - +
466B MET* 1.3 72.6 - - - +
468B SER* 1.3 58.8 + - - +
470B SER* 3.3 5.0 + - - -
471B ALA* 2.9 26.7 + - - +
485B LEU* 4.3 3.7 - - - +
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Residues in contact with SER 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B THR 4.0 0.3 + - - -
390B HIS* 3.7 28.7 - - - -
391B ALA* 2.8 22.5 + - - +
394B HIS* 2.6 29.1 + - - -
397B TYR* 3.2 14.9 + - - -
399B MET* 4.2 1.1 - - - -
466B MET* 4.6 0.2 - - - +
467B SER* 1.3 76.5 + - - +
469B LYS* 1.3 66.6 + - - +
471B ALA* 4.1 3.1 - - - +
472B ASN* 3.0 29.5 + - - -
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Residues in contact with LYS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B HIS* 3.6 17.8 + - + -
464B ALA* 3.8 11.9 - - + -
466B MET* 3.1 19.4 + - + +
468B SER* 1.3 82.7 + - - +
470B SER* 1.3 60.9 + - - +
472B ASN* 3.7 7.7 - - - +
473B TYR* 3.2 27.2 - - + -
554B LEU* 4.4 7.1 - - - +
556B TYR* 3.0 33.4 + - + +
557B ASN 3.0 28.2 + - - +
558B GLU* 2.7 29.0 + - - +
601B 09L 4.0 16.6 - - + -
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Residues in contact with SER 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B TRP* 3.1 38.6 + - - +
428B HIS 4.0 0.9 - - - -
429B GLY* 3.3 28.1 - - - -
464B ALA* 3.3 10.9 - - - +
466B MET 3.4 1.0 + - - -
467B SER 3.3 5.5 + - - -
468B SER 3.2 0.2 - - - -
469B LYS* 1.3 75.2 - - - +
471B ALA* 1.3 59.2 + - - +
472B ASN 3.2 2.7 - - - -
473B TYR* 2.9 20.1 + - - +
485B LEU* 4.1 2.7 - - - -
601B 09L 2.8 26.9 + - - -
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Residues in contact with ALA 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B TYR* 3.6 13.0 - - - +
399B MET* 3.6 29.6 - - + -
467B SER 2.9 20.6 + - - +
468B SER 3.2 0.4 + - - -
470B SER* 1.3 72.9 - - - +
472B ASN* 1.3 51.9 + - - +
474B CYS* 3.0 23.7 + - - +
485B LEU* 3.8 9.8 - - + +
577B PHE* 3.7 11.1 - - + -
602B GOL 2.7 24.9 + - - -
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Residues in contact with ASN 472 (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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394B HIS* 3.3 38.0 + - - +
396B ASP* 5.1 0.6 - - - +
397B TYR* 2.6 35.9 + - - -
468B SER 3.0 17.0 + - - +
469B LYS* 3.7 8.3 + - - +
471B ALA* 1.3 76.3 - - - +
473B TYR* 1.3 61.8 + - + +
475B PHE* 3.2 21.0 + - - -
602B GOL 2.9 30.8 + - - +
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Residues in contact with TYR 473 (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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332B GLN* 4.2 21.3 - - - -
429B GLY 3.6 3.4 - - - +
430B SER* 3.3 20.2 - - - -
431B ARG* 3.5 1.4 + - - +
456B MET* 6.0 2.4 - - - +
469B LYS* 3.2 33.8 - - + -
470B SER 2.9 10.2 + - - +
472B ASN* 1.3 77.6 - - + +
474B CYS* 1.3 58.8 + - - +
475B PHE* 3.2 25.6 - + - -
558B GLU* 5.8 0.2 + - - -
601B 09L 3.3 72.7 - + + +
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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
------------------------------------------------------------
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