Contacts of the helix formed by residues 435 - 446 (chain A) in PDB entry 1ZUM
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 ASP 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A ASP* 3.4 18.7 + - - +
433A THR* 3.0 7.7 + - - +
434A LYS* 1.3 78.7 - - - +
436A LEU* 1.3 59.7 + - - +
437A ASP* 3.4 12.8 + - - +
438A LYS* 3.0 42.3 + - + +
439A ALA* 3.0 30.8 + - - +
434D LYS* 3.5 26.4 - - - +
436D LEU* 4.3 1.8 - - - -
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LYS 3.7 2.4 + - - -
435A ASP* 1.3 70.9 - - - +
437A ASP* 1.3 70.8 + - - +
439A ALA* 3.2 3.8 + - - +
440A ASN* 3.0 46.0 + - - +
493C VAL* 4.3 12.6 - - + -
494C LYS 4.9 0.9 - - - +
433D THR 4.1 4.5 - - - +
434D LYS* 2.8 23.8 + - - +
435D ASP 4.3 0.2 - - - -
436D LEU* 3.7 30.9 - - + +
439D ALA* 4.2 15.7 - - + -
440D ASN* 5.6 2.0 - - - +
453D VAL* 3.8 18.8 - - + -
454D ASN* 3.4 28.9 - - - +
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Residues in contact with ASP 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ASP* 3.4 11.3 + - - +
436A LEU* 1.3 89.0 - - - +
438A LYS* 1.3 57.7 + - + +
440A ASN* 4.8 1.2 + - - -
441A TYR* 2.9 32.8 + - - +
494C LYS* 4.2 15.1 - - - +
495C VAL* 5.0 0.2 - - - -
496C PRO* 3.8 29.9 - - + +
434D LYS* 4.7 4.3 + - - +
454D ASN* 4.8 5.3 + - - -
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Residues in contact with LYS 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A MET* 3.9 25.8 - - + +
279A SER* 4.7 8.7 + - - -
280A ASP* 2.8 35.8 + - - +
311A GLN* 5.3 0.8 - - - +
413A ILE* 4.2 17.7 - - + -
433A THR* 3.7 20.2 - - + +
435A ASP* 3.0 24.1 + - + +
436A LEU 3.3 0.2 - - - -
437A ASP* 1.3 75.7 - - + +
439A ALA* 1.3 62.9 + - - +
441A TYR* 3.7 2.0 - - - +
442A LEU* 3.1 31.8 + - + +
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Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A VAL* 4.9 4.2 - - - +
433A THR* 3.9 11.4 - - + +
435A ASP 3.0 18.6 + - - +
436A LEU 3.5 4.5 - - - +
438A LYS* 1.3 76.9 - - - +
440A ASN* 1.3 58.8 + - - +
442A LEU* 4.1 1.0 - - - +
443A SER* 3.0 31.0 + - - -
453A VAL* 4.0 30.5 - - + +
436D LEU* 4.0 17.5 - - + -
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Residues in contact with ASN 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU* 3.0 41.0 + - - +
437A ASP* 4.1 2.8 + - - +
439A ALA* 1.3 76.1 - - - +
441A TYR* 1.3 66.0 + - - +
443A SER* 3.1 19.8 + - - -
444A GLN* 3.1 31.7 + - - +
153B TYR* 4.3 10.7 + - - -
151C PHE* 4.8 8.9 - - - -
493C VAL* 4.1 8.1 - - - +
494C LYS 4.7 1.2 + - - -
495C VAL* 3.6 28.3 - - + +
496C PRO* 4.5 3.8 - - + -
436D LEU* 5.9 0.9 - - - +
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Residues in contact with TYR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 3.6 35.0 - - + -
414A GLU* 4.2 22.9 - - + +
417A VAL* 3.7 28.3 - - + +
437A ASP 2.9 20.1 + - - +
438A LYS* 3.7 4.9 - - - +
440A ASN* 1.3 76.6 - - - +
442A LEU* 1.3 60.7 + - - +
444A GLN* 3.5 11.3 + - - +
445A ALA* 3.0 36.5 + - + +
496C PRO* 4.2 24.1 - - + +
497C GLN 5.8 0.7 - - - -
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE* 4.2 23.1 - - + -
278A MET* 4.3 14.4 - - + -
413A ILE* 3.7 30.5 - - + -
416A VAL* 4.4 3.1 - - + -
417A VAL* 3.5 29.6 - - + -
431A VAL* 3.2 42.0 - - + -
438A LYS 3.1 15.4 + - - +
439A ALA 4.2 0.7 - - - +
441A TYR* 1.3 73.6 - - + +
443A SER* 1.3 59.9 + - - +
444A GLN 3.1 1.6 - - - -
445A ALA* 4.4 1.6 - - - +
446A LEU* 2.8 41.8 + - + +
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Residues in contact with SER 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A VAL* 4.9 0.6 - - - +
439A ALA 3.0 16.9 + - - -
440A ASN* 3.1 19.9 + - - -
442A LEU* 1.3 77.8 - - - +
444A GLN* 1.3 59.1 + - - +
446A LEU 4.1 1.7 - - - +
451A VAL* 3.9 22.3 - - - +
453A VAL* 4.6 5.4 - - - -
153B TYR* 4.0 10.6 + - - -
155B ARG* 5.9 0.4 - - - -
489B LYS* 2.8 27.7 + - - +
491B VAL* 3.9 29.2 - - - +
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Residues in contact with GLN 444 (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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440A ASN* 3.1 24.0 + - - +
441A TYR* 3.8 9.6 + - - +
442A LEU 3.1 0.4 - - - -
443A SER* 1.3 82.3 + - - +
445A ALA* 1.3 59.5 + - - +
447A GLN* 5.9 0.3 - - - +
72B LEU* 6.0 0.9 - - - +
153B TYR* 6.1 0.2 - - - +
155B ARG* 3.8 25.5 + - - +
157B GLU* 5.7 0.5 - - - -
489B LYS* 2.9 19.1 + - - +
151C PHE* 5.3 2.8 - - - +
495C VAL* 3.6 32.0 - - - +
496C PRO* 4.5 7.5 + - - +
497C GLN 3.7 22.6 + - - -
498C LYS* 5.0 4.4 - - - +
499C ASN 5.6 2.0 - - - +
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Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A VAL* 3.9 29.3 - - + +
421A ASN* 3.1 18.8 + - - -
441A TYR* 3.0 28.0 + - + +
442A LEU* 4.1 1.3 - - - +
444A GLN* 1.3 77.5 - - - +
446A LEU* 1.3 64.5 + - - +
447A GLN* 3.3 7.3 + - - +
72B LEU* 5.0 14.8 - - + +
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Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A PRO* 5.7 0.2 - - + -
276A ILE* 3.7 26.7 - - + -
417A VAL* 4.8 5.8 - - + -
420A ALA* 3.8 20.9 - - + -
421A ASN* 3.5 8.5 - - - +
429A ALA* 4.0 21.1 - - + -
430A ALA 4.6 0.4 - - - +
431A VAL* 3.5 31.4 - - + -
442A LEU* 2.8 32.2 + - + +
445A ALA* 1.3 69.6 - - - +
447A GLN* 1.3 59.1 + - - +
448A ALA 3.2 5.1 + - - -
451A VAL* 4.0 22.7 - - + +
489B LYS* 3.0 26.2 + - - -
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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