Contacts of the helix formed by residues 444 - 459 (chain B) in PDB entry 3ZXR
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 444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B SER* 3.9 16.9 + - - -
114B LYS* 4.0 8.9 - - - +
438B THR* 4.7 1.6 - - - -
441B GLY* 3.7 20.9 - - - +
442B VAL 4.2 0.4 + - - -
443B PHE* 1.3 77.3 - - - +
445B ASN* 1.3 66.2 + - - +
446B ASP* 2.6 27.6 + - - -
447B LEU* 3.1 20.9 + - - +
448B ILE* 3.2 14.9 + - - +
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Residues in contact with ASN 445 (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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434B HIS* 3.5 23.4 + - - -
435B GLU* 5.5 0.9 - - - +
438B THR* 3.9 13.5 - - - +
444B THR* 1.3 74.1 - - - +
446B ASP* 1.3 57.6 + - - +
448B ILE* 3.4 6.1 + - - +
449B GLU* 2.8 48.6 + - - +
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Residues in contact with ASP 446 (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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105B SER* 2.7 27.7 + - - -
106B ARG* 2.8 26.6 + - - +
444B THR* 2.6 28.2 + - - -
445B ASN* 1.3 75.1 - - - +
447B LEU* 1.3 64.8 + - - +
449B GLU* 4.2 9.3 - - - +
450B THR* 2.8 31.2 + - - -
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Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.8 29.2 - - + -
105B SER 4.0 11.9 - - - +
106B ARG* 4.0 13.2 - - + +
111B ILE* 3.5 35.7 - - + -
319B PHE* 4.7 6.1 - - + -
378B LEU* 4.5 11.0 - - + -
443B PHE* 3.6 29.8 - - + -
444B THR* 3.1 16.8 + - - +
446B ASP* 1.3 82.3 - - - +
448B ILE* 1.3 56.9 + - + +
450B THR* 3.3 2.3 + - - -
451B TRP* 3.0 31.1 + - + +
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Residues in contact with ILE 448 (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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319B PHE* 4.6 8.3 - - + -
430B LEU* 4.1 15.5 - - + -
434B HIS* 3.8 44.4 - - + +
437B LEU* 4.3 7.6 - - + -
438B THR* 3.9 12.8 - - + -
443B PHE* 3.9 35.0 - - + -
444B THR 3.2 9.2 + - - +
445B ASN* 3.9 8.3 - - - +
447B LEU* 1.3 75.8 - - - +
449B GLU* 1.3 59.2 + - + +
451B TRP* 3.4 6.8 + - - +
452B ILE* 3.0 46.5 + - + +
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Residues in contact with GLU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ASN* 2.8 39.5 + - + +
446B ASP* 4.2 7.3 - - - +
448B ILE* 1.3 72.1 - - + +
450B THR* 1.3 59.6 + - - +
452B ILE* 3.5 11.0 + - + +
453B SER* 2.9 31.2 + - - -
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Residues in contact with THR 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.7 19.3 - - + -
60B GLY* 3.8 24.5 - - - +
106B ARG* 3.5 18.2 + - - +
446B ASP 2.8 23.2 + - - -
447B LEU 3.7 3.4 - - - -
449B GLU* 1.3 74.6 - - - +
451B TRP* 1.3 55.4 + - - +
453B SER* 3.6 5.3 - - - -
454B PHE* 2.7 35.9 + - + +
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Residues in contact with TRP 451 (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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28B LEU* 3.3 46.0 - - + +
29B PRO* 4.1 14.4 - - + -
318B ALA 2.9 29.0 + - - -
319B PHE* 3.4 34.5 - + + -
322B PRO* 3.7 13.0 - - + -
375B ASN* 4.7 4.9 - - + -
378B LEU* 3.6 19.3 - - + -
427B ILE* 4.1 8.3 - - + +
430B LEU* 3.9 14.8 - - + -
447B LEU* 3.0 18.7 + - + +
448B ILE* 3.6 6.3 - - - +
449B GLU 3.3 0.2 - - - -
450B THR* 1.3 73.8 - - - +
452B ILE* 1.3 65.7 + - - +
454B PHE* 3.3 6.5 + + + +
455B LYS* 3.0 61.5 + - - +
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Residues in contact with ILE 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ILE* 3.7 21.0 - - + +
430B LEU* 4.0 15.5 - - + -
431B GLU* 3.6 39.0 - - + +
434B HIS* 5.7 0.9 - - + -
448B ILE* 3.0 38.9 + - + +
449B GLU* 3.8 9.9 - - + +
451B TRP* 1.3 75.4 - - - +
453B SER* 1.3 64.1 + - - +
455B LYS* 3.5 2.1 + - - +
456B ARG* 3.1 61.0 + - - +
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Residues in contact with SER 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B GLU 2.9 20.3 + - - -
450B THR* 3.6 6.3 - - - -
452B ILE* 1.3 76.4 - - - +
454B PHE* 1.3 65.1 + - - +
456B ARG* 3.3 6.3 + - - +
457B GLU* 3.1 49.3 + - - +
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Residues in contact with PHE 454 (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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28B LEU* 5.8 3.6 - - + -
29B PRO* 3.9 27.6 - - + -
59B ARG* 3.9 41.1 - - + -
60B GLY* 4.8 8.5 - - - -
450B THR* 2.7 28.0 + - + +
451B TRP* 3.3 8.0 + + + +
453B SER* 1.3 72.4 + - - +
455B LYS* 1.3 67.5 + - + +
457B GLU* 5.2 0.2 - - - -
458B ASN* 2.9 72.5 + - + +
459B GLU* 3.3 25.6 - - + -
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Residues in contact with LYS 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PRO* 5.4 7.0 + - - +
322B PRO* 2.8 38.0 + - - +
323B THR* 4.3 4.9 - - - +
373B SER 5.3 0.8 + - - -
423B LEU* 4.4 3.1 - - + -
427B ILE* 3.9 29.4 - - + -
451B TRP* 3.0 54.1 + - - +
452B ILE 3.9 3.1 - - - +
454B PHE* 1.3 87.0 - - + +
456B ARG* 1.3 59.8 + - - +
459B GLU* 2.9 40.5 + - - +
460B ILE* 2.9 31.9 + - + +
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Residues in contact with ARG 456 (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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427B ILE* 3.7 7.7 - - + +
428B ASP* 2.9 36.8 + - - +
431B GLU* 2.9 42.6 + - - +
452B ILE* 3.1 36.4 + - - +
453B SER* 3.7 6.1 - - - +
455B LYS* 1.3 76.8 - - - +
457B GLU* 1.3 62.7 + - + +
458B ASN 3.7 0.2 + - - -
460B ILE* 3.9 21.9 - - + +
461B GLU* 3.0 34.4 + - - +
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Residues in contact with GLU 457 (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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453B SER* 3.1 36.2 + - - +
454B PHE* 5.8 0.2 - - - -
456B ARG* 1.3 78.8 - - + +
458B ASN* 1.3 69.3 + - - +
461B GLU* 4.6 13.8 - - - +
462B PRO* 3.4 17.3 - - - +
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Residues in contact with ASN 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B PHE* 2.9 64.6 + - + +
457B GLU* 1.3 85.6 + - - +
459B GLU* 1.3 62.9 + - + +
462B PRO* 3.4 16.4 - - - +
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Residues in contact with GLU 459 (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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29B PRO* 5.6 0.7 - - - +
322B PRO 3.5 9.7 - - - +
323B THR* 3.7 18.3 - - - +
324B VAL* 4.3 13.4 + - + -
423B LEU* 3.9 3.5 - - + +
454B PHE* 3.3 20.4 - - + -
455B LYS* 2.9 46.4 + - - +
458B ASN* 1.3 88.0 - - + +
460B ILE* 1.3 70.1 + - - +
461B GLU 3.5 0.9 - - - -
462B PRO* 3.3 2.9 - - - +
463B VAL* 3.1 28.0 + - + +
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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