Contacts of the helix formed by residues 464 - 476 (chain B) in PDB entry 3ZFW
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 LYS 464 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416B GLU* 3.4 25.6 + - + +
419B GLU* 3.3 35.7 - - + +
420B GLU* 5.5 6.5 + - - -
459B TYR* 2.8 26.1 + - + +
462B GLN* 3.6 32.3 + - + +
463B GLY* 1.3 73.7 - - - +
465B LEU* 1.3 52.5 + - - +
466B GLU 3.4 0.4 - - - -
467B ALA* 3.3 9.0 + - + +
468B ALA* 2.8 32.4 + - - +
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Residues in contact with LEU 465 (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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419B GLU* 3.2 2.3 + - - +
460B ARG* 3.3 48.9 - - + +
463B GLY* 3.0 22.8 + - - +
464B LYS* 1.3 73.2 - - - +
466B GLU* 1.3 54.0 + - - +
468B ALA* 3.2 5.5 + - - +
469B HIS* 2.7 54.0 + - + +
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Residues in contact with GLU 466 (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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415B ALA 4.6 0.4 - - - -
418B ARG* 3.2 61.2 + - + +
419B GLU* 2.9 21.7 + - + +
465B LEU* 1.3 75.6 - - - +
467B ALA* 1.4 54.8 + - - +
469B HIS* 3.4 10.6 + - - +
470B THR* 2.7 31.8 + - - -
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Residues in contact with ALA 467 (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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415B ALA* 3.4 38.4 - - - +
416B GLU* 4.4 3.1 - - - +
419B GLU* 3.3 13.3 - - + +
459B TYR* 3.8 24.0 - - + -
464B LYS* 3.3 13.9 + - + +
466B GLU* 1.4 76.3 - - - +
468B ALA* 1.3 61.6 + - - +
470B THR* 3.4 14.9 + - - -
471B LEU* 3.6 9.7 + - - +
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Residues in contact with ALA 468 (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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456B GLY* 3.6 24.9 - - - +
459B TYR* 3.8 6.7 - - + +
460B ARG* 3.8 26.5 - - - +
464B LYS 2.8 17.4 + - - +
465B LEU* 3.2 11.0 + - - +
467B ALA* 1.3 74.5 - - - +
469B HIS* 1.4 64.2 + - - +
471B LEU* 3.4 2.8 + - - +
472B GLU* 3.1 29.8 + - - +
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Residues in contact with HIS 469 (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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460B ARG* 3.3 24.8 + - - -
465B LEU* 2.7 48.3 + - + +
466B GLU* 3.4 12.9 + - - +
468B ALA* 1.4 72.1 - - - +
470B THR* 1.4 54.6 + - - +
472B GLU* 4.2 6.2 - - + +
473B ASP* 2.9 39.2 + - + +
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Residues in contact with THR 470 (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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411B ILE* 4.1 21.3 - - + +
414B HIS* 4.9 2.5 - - + -
415B ALA* 3.8 23.4 - - + +
418B ARG* 3.5 40.8 + - - +
466B GLU 2.7 22.6 + - - -
467B ALA* 3.5 10.0 + - - -
468B ALA 3.3 0.4 - - - -
469B HIS* 1.4 76.7 - - - +
471B LEU* 1.4 58.7 + - - +
473B ASP* 4.1 4.1 - - - +
474B CYS* 3.4 20.3 + - - +
477B ARG* 5.4 1.9 + - - -
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Residues in contact with LEU 471 (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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393B LEU* 4.8 0.4 - - + -
411B ILE* 3.7 31.9 - - + -
412B TRP* 4.3 12.3 - - - +
415B ALA* 4.4 4.0 - - + -
452B LEU* 3.6 33.6 - - + +
455B LEU* 3.7 17.7 - - + -
456B GLY* 3.6 20.6 - - - +
459B TYR* 3.5 26.7 - - + -
467B ALA 3.6 10.1 + - - +
468B ALA 3.4 5.2 + - - +
469B HIS 3.3 0.2 - - - -
470B THR* 1.4 74.9 - - - +
472B GLU* 1.3 58.9 + - - +
473B ASP 3.2 1.6 - - - -
474B CYS* 3.1 6.7 + - - +
475B ALA* 2.9 28.2 + - - +
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Residues in contact with GLU 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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452B LEU 5.3 0.4 - - - -
453B ARG* 4.7 16.5 - - + +
456B GLY* 3.7 24.5 - - - -
457B ALA* 3.9 3.8 + - - -
460B ARG* 2.8 45.5 + - - -
468B ALA 3.1 17.7 + - - +
469B HIS* 4.2 6.5 - - + +
471B LEU* 1.3 74.7 - - - +
473B ASP* 1.4 59.2 + - - +
475B ALA* 3.5 9.1 + - - +
476B SER* 2.8 26.1 + - - -
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Residues in contact with ASP 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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469B HIS* 2.9 19.9 + - + +
470B THR* 4.1 5.4 - - - +
472B GLU* 1.4 73.4 - - - +
474B CYS* 1.3 65.6 + - - +
476B SER* 3.3 20.9 + - - -
477B ARG* 3.1 36.8 + - - +
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Residues in contact with CYS 474 (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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411B ILE* 4.9 4.0 - - + -
441B CYS* 2.0 54.1 - - + -
442B LYS* 3.7 8.8 - - - -
443B VAL 4.6 3.8 + - - +
449B ASN* 4.5 2.3 - - - +
452B LEU* 4.0 15.9 - - + -
470B THR 3.4 14.0 + - - +
471B LEU* 3.1 10.5 + - - +
473B ASP* 1.3 79.8 + - - +
475B ALA* 1.3 61.7 + - - +
477B ARG* 3.1 31.0 + - - +
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Residues in contact with ALA 475 (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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449B ASN* 3.7 33.5 + - - +
452B LEU* 3.9 10.4 - - + +
453B ARG* 3.2 45.7 + - + +
471B LEU 2.9 16.2 + - - +
472B GLU* 3.9 5.6 - - - +
473B ASP 3.4 0.4 - - - -
474B CYS* 1.3 75.2 - - - +
476B SER* 1.4 58.2 + - - +
477B ARG 3.2 4.6 + - - -
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Residues in contact with SER 476 (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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472B GLU 2.8 16.4 + - - -
473B ASP* 3.4 17.4 - - - -
474B CYS 3.1 1.2 - - - -
475B ALA* 1.4 73.6 - - - +
477B ARG* 1.3 61.2 + - - +
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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