Contacts of the helix formed by residues 435 - 446 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A LYS* 3.3 28.9 - - - +
436A LEU* 4.3 2.0 - - - -
280D ASP* 3.4 19.6 + - - +
433D THR* 2.9 8.2 + - - +
434D LYS* 1.3 78.6 - - - +
436D LEU* 1.3 66.9 + - - +
437D ASP* 3.5 12.0 + - - +
438D LYS* 3.0 41.7 + - + +
439D ALA* 3.0 24.3 + - - +
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Residues in contact with LEU 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A THR 4.1 4.0 - - - +
434A LYS* 2.9 21.1 + - - +
435A ASP 4.3 0.4 - - - -
436A LEU* 3.7 30.9 - - + +
439A ALA* 4.0 17.9 - - + -
440A ASN* 5.9 1.6 - - - +
453A VAL* 3.7 18.2 - - + -
454A ASN* 3.3 30.1 - - - +
493B VAL* 4.2 13.2 - - + -
494B LYS 4.6 0.9 - - - +
434D LYS 3.6 2.4 + - - -
435D ASP* 1.3 70.3 - - - +
437D ASP* 1.3 70.1 + - - +
439D ALA* 3.3 4.7 + - - +
440D ASN* 3.1 43.2 + - - +
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Residues in contact with ASP 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A LYS* 4.7 1.5 + - - +
454A ASN* 4.5 6.0 + - - -
494B LYS* 4.1 24.8 - - - +
495B VAL* 4.9 0.6 - - - -
496B PRO* 3.2 27.1 - - + +
435D ASP* 3.4 11.0 + - - +
436D LEU* 1.3 87.0 - - - +
438D LYS* 1.3 58.0 + - + +
440D ASN* 3.4 0.6 + - - -
441D TYR* 2.8 32.2 + - - +
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Residues in contact with LYS 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D MET* 4.3 21.4 - - + +
279D SER* 5.3 4.9 + - - -
280D ASP* 3.0 29.7 + - - +
311D GLN* 5.7 1.0 + - - -
413D ILE* 4.2 20.9 - - + -
433D THR* 3.9 14.4 - - + +
435D ASP* 3.0 36.7 + - + +
437D ASP* 1.3 75.2 - - + +
439D ALA* 1.3 57.5 + - - +
441D TYR* 3.7 1.4 - - - +
442D LEU* 3.0 36.8 + - + +
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Residues in contact with ALA 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU* 4.2 17.0 - - + -
431D VAL* 4.8 6.2 - - - +
433D THR* 3.8 15.7 - - + +
435D ASP 3.0 16.2 + - - +
436D LEU 3.5 4.9 - - - +
438D LYS* 1.3 77.6 - - - +
440D ASN* 1.3 61.0 + - - +
442D LEU* 3.8 1.6 - - - +
443D SER* 2.9 32.3 + - - -
453D VAL* 4.1 24.4 - - + +
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Residues in contact with ASN 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU* 5.6 1.6 - - - +
151B PHE* 4.8 8.8 - - - -
493B VAL* 3.9 9.3 - - - +
494B LYS 4.4 1.4 + - - -
495B VAL* 3.4 39.5 - - + +
496B PRO* 4.1 2.9 - - + -
153C TYR* 4.7 7.4 + - - -
3113C EDO 4.1 7.6 - - - -
436D LEU* 3.1 38.6 + - - +
437D ASP* 4.0 3.1 - - - +
439D ALA* 1.3 80.0 - - - +
441D TYR* 1.3 66.4 + - - +
443D SER* 3.2 18.9 + - - -
444D GLN* 3.2 14.7 + - - +
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Residues in contact with TYR 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B PRO* 3.8 27.2 - - + +
497B GLN* 5.3 7.4 - - + -
413D ILE* 3.3 35.0 - - + -
414D GLU* 3.9 28.0 - - + +
417D VAL* 3.7 26.1 - - + +
437D ASP 2.8 22.8 + - - +
438D LYS* 3.7 4.9 - - - +
440D ASN* 1.3 74.0 - - - +
442D LEU* 1.3 60.9 + - - +
444D GLN* 3.9 4.0 + - - +
445D ALA* 3.0 34.3 + - + +
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Residues in contact with LEU 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D ILE* 4.3 21.8 - - + -
278D MET* 4.0 20.2 - - + -
413D ILE* 3.9 23.3 - - + -
416D VAL* 4.5 2.5 - - + -
417D VAL* 3.4 31.9 - - + -
431D VAL* 3.4 40.4 - - + -
438D LYS 3.0 17.8 + - - +
439D ALA 4.0 1.3 - - - +
441D TYR* 1.3 73.7 - - + +
443D SER* 1.3 66.1 + - - +
444D GLN 3.1 1.6 - - - -
445D ALA* 4.5 1.1 - - - +
446D LEU* 2.9 35.1 + - + +
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Residues in contact with SER 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C TYR* 4.0 2.1 + - - -
489C LYS* 2.9 29.8 + - - +
491C VAL* 3.9 24.0 - - - -
3113C EDO 2.9 28.2 + - - -
431D VAL* 5.0 0.4 - - - +
439D ALA 2.9 21.0 + - - -
440D ASN* 3.2 9.5 + - - -
441D TYR 3.4 0.2 - - - -
442D LEU* 1.3 76.5 - - - +
444D GLN* 1.3 58.9 + - - +
446D LEU 4.1 1.0 - - - +
451D VAL* 3.8 19.5 - - - +
453D VAL* 4.6 5.6 - - - -
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Residues in contact with GLN 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B VAL* 5.8 2.5 - - - +
497B GLN 2.6 29.0 + - - -
498B LYS* 3.6 7.2 - - - +
499B ASN* 2.8 50.3 + - + +
72C LEU* 5.7 3.6 - - + +
155C ARG* 3.4 28.6 + - - +
157C GLU* 4.5 2.6 - - - +
489C LYS* 3.2 17.0 + - - +
3113C EDO 4.1 12.9 - - - -
440D ASN 3.2 13.7 + - - +
441D TYR* 3.9 4.7 + - - +
442D LEU 3.1 0.6 - - - -
443D SER* 1.3 82.6 + - - +
445D ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LEU* 4.3 18.5 - - + +
417D VAL* 3.8 29.6 - - + -
421D ASN* 2.9 20.8 + - - -
441D TYR* 3.0 26.7 + - + +
442D LEU 4.3 1.1 - - - +
444D GLN* 1.3 78.1 - - - +
446D LEU* 1.3 61.5 + - - +
447D GLN* 3.3 5.9 + - - +
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Residues in contact with LEU 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C LYS* 2.7 32.6 + - - -
274D PRO* 5.1 0.2 - - + -
276D ILE* 3.7 24.5 - - + -
417D VAL* 4.7 7.9 - - - -
420D ALA* 3.8 20.0 - - + -
421D ASN* 3.5 7.0 - - - +
429D ALA* 4.0 25.8 - - + -
430D ALA 4.6 0.2 - - - +
431D VAL* 3.5 30.1 - - + -
442D LEU* 2.9 31.1 + - + +
444D GLN 3.5 0.6 - - - -
445D ALA* 1.3 73.9 - - - +
447D GLN* 1.3 57.7 + - - +
448D ALA 3.2 4.0 + - - +
451D VAL* 4.2 18.4 - - + -
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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