Contacts of the helix formed by residues 444 - 459 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A SER* 3.9 16.1 + - - -
114A LYS* 4.1 10.0 - - - +
438A THR* 4.8 1.6 - - - -
441A GLY* 3.7 23.3 - - - +
442A VAL 4.2 0.2 + - - -
443A PHE* 1.3 74.2 - - - +
445A ASN* 1.3 65.2 + - - +
446A ASP* 2.4 28.7 + - - -
447A LEU* 3.0 21.3 + - - +
448A ILE* 3.1 15.4 + - - +
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Residues in contact with ASN 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A HIS* 3.5 24.1 + - - -
435A GLU* 5.5 0.5 - - - +
438A THR* 3.9 13.7 - - - +
444A THR* 1.3 73.8 - - - +
446A ASP* 1.3 56.7 + - - +
448A ILE* 3.2 5.3 + - - +
449A GLU* 2.8 49.7 + - + +
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Residues in contact with ASP 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A SER* 2.6 26.4 + - - -
106A ARG* 2.9 26.8 + - - +
444A THR* 2.4 29.9 + - - -
445A ASN* 1.3 76.7 - - - +
447A LEU* 1.3 61.7 + - - +
449A GLU* 4.1 10.1 - - - +
450A THR* 2.7 33.6 + - - -
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.8 28.3 - - + -
105A SER 3.9 11.9 - - - +
106A ARG* 4.0 14.6 - - + -
111A ILE* 3.4 35.2 - - + -
319A PHE* 4.8 5.4 - - + -
378A LEU* 4.5 12.1 - - + -
443A PHE* 3.6 31.4 - - + -
444A THR* 3.0 17.5 + - - +
446A ASP* 1.3 80.3 - - - +
448A ILE* 1.3 58.7 + - + +
450A THR* 3.3 2.9 + - - -
451A TRP* 3.0 31.2 + - + +
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Residues in contact with ILE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A PHE* 4.6 8.5 - - + -
430A LEU* 4.1 16.2 - - + -
434A HIS* 3.7 45.5 - - + +
437A LEU* 4.3 7.4 - - + -
438A THR* 3.9 18.6 - - + -
443A PHE* 4.0 27.1 - - + -
444A THR 3.1 8.9 + - - +
445A ASN* 3.8 7.4 - - - +
447A LEU* 1.3 76.5 - - - +
449A GLU* 1.3 59.6 + - + +
451A TRP* 3.4 7.1 + - - +
452A ILE* 3.0 46.9 + - + +
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Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ASN* 2.8 34.8 + - + +
446A ASP* 4.1 8.5 - - - +
448A ILE* 1.3 74.7 - - + +
450A THR* 1.3 61.2 + - - +
452A ILE* 3.8 11.2 - - + +
453A SER* 2.9 31.8 + - - -
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Residues in contact with THR 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.7 20.4 - - + -
60A GLY* 3.8 24.7 - - - +
61A PHE 5.7 0.2 - - - +
106A ARG* 3.6 17.6 + - - +
446A ASP* 2.7 23.1 + - - +
447A LEU 3.6 4.0 - - - -
449A GLU* 1.3 76.4 - - - +
451A TRP* 1.3 54.3 + - - +
453A SER* 3.5 5.5 - - - -
454A PHE* 2.7 35.5 + - + +
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Residues in contact with TRP 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.4 42.8 - - + +
29A PRO* 4.1 16.4 - - + -
318A ALA 3.0 29.5 + - - -
319A PHE* 3.4 35.4 - + + -
322A PRO* 3.6 12.6 - - + -
375A ASN* 4.7 4.7 - - + -
378A LEU* 3.5 22.0 - - + -
427A ILE* 4.2 8.1 - - + +
430A LEU* 3.9 15.3 - - + -
447A LEU* 3.0 18.4 + - + +
448A ILE* 3.5 6.3 - - - +
450A THR* 1.3 74.3 - - - +
452A ILE* 1.3 65.6 + - - +
454A PHE* 3.3 7.1 + + + +
455A LYS* 3.0 61.6 + - - +
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Residues in contact with ILE 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ILE* 3.7 18.6 - - + +
430A LEU* 3.9 15.3 - - + -
431A GLU* 3.6 39.0 - - + +
434A HIS* 5.7 0.9 - - + -
448A ILE* 3.0 37.3 + - + +
449A GLU* 3.8 10.3 - - + +
451A TRP* 1.3 76.6 - - - +
453A SER* 1.3 59.1 + - - +
455A LYS* 3.4 2.1 + - - +
456A ARG* 3.0 69.4 + - - +
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Residues in contact with SER 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLU 2.9 19.4 + - - -
450A THR* 3.5 6.5 - - - -
452A ILE* 1.3 77.5 - - - +
454A PHE* 1.3 66.3 + - - +
456A ARG* 3.4 5.1 + - - +
457A GLU* 3.1 48.2 + - - +
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Residues in contact with PHE 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 5.8 4.0 - - + -
29A PRO* 3.9 27.1 - - + -
59A ARG* 3.9 41.5 - - + -
60A GLY* 4.8 9.6 - - - -
450A THR* 2.7 26.3 + - + +
451A TRP* 3.8 8.1 - + + +
453A SER* 1.3 72.7 - - - +
455A LYS* 1.3 69.4 + - + +
457A GLU* 5.2 0.2 - - - -
458A ASN* 2.9 73.2 + - + +
459A GLU* 3.4 24.9 - - + -
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Residues in contact with LYS 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO* 5.5 7.7 + - - +
322A PRO* 2.8 34.0 + - - +
323A THR* 4.3 5.5 - - - +
373A SER 5.3 1.0 + - - -
374A GLY* 5.8 0.4 - - - -
423A LEU* 4.4 3.6 - - + -
427A ILE* 4.0 29.8 - - + -
451A TRP* 3.0 54.5 + - - +
452A ILE 3.9 3.4 - - - +
454A PHE* 1.3 84.6 - - + +
456A ARG* 1.3 60.6 + - - +
459A GLU* 2.9 41.9 + - - +
460A ILE* 2.9 30.9 + - + +
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Residues in contact with ARG 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ILE* 3.7 8.1 - - + +
428A ASP* 2.9 36.1 + - - +
431A GLU* 2.9 42.4 + - - -
452A ILE* 3.0 37.2 + - - +
453A SER* 3.9 5.8 - - - +
454A PHE 3.3 0.4 - - - -
455A LYS* 1.3 77.5 - - - +
457A GLU* 1.3 62.5 + - + +
460A ILE* 3.8 22.6 - - + +
461A GLU* 3.0 34.5 + - - +
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Residues in contact with GLU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A SER* 3.1 35.5 + - - +
454A PHE* 5.7 0.3 - - - -
456A ARG* 1.3 78.0 - - + +
458A ASN* 1.3 69.4 + - - +
459A GLU 3.7 0.2 - - - -
461A GLU* 4.5 14.6 - - - +
462A PRO* 3.4 17.2 - - - +
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Residues in contact with ASN 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A PHE* 2.9 64.5 + - + +
457A GLU* 1.3 86.3 + - - +
459A GLU* 1.3 62.1 + - + +
462A PRO* 3.5 16.1 - - - +
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Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO* 5.6 1.0 - - - +
322A PRO 3.5 7.4 - - - +
323A THR* 3.7 18.1 - - - +
324A VAL* 4.2 11.5 + - + +
423A LEU* 3.9 4.0 - - + +
454A PHE* 3.4 16.6 - - + -
455A LYS* 2.9 52.6 + - + +
458A ASN* 1.3 88.2 - - + +
460A ILE* 1.3 70.4 + - - +
461A GLU 3.5 0.7 - - - -
462A PRO* 3.4 2.6 - - - +
463A VAL* 3.2 28.8 + - - +
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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