Contacts of the helix formed by residues 435 - 446 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434B LYS* 3.4 29.3 - - - +
436B LEU* 4.3 1.6 - - - -
280C ASP* 3.3 17.8 + - - +
433C THR* 3.2 8.1 + - - +
434C LYS* 1.3 77.9 - - - +
436C LEU* 1.3 64.3 + - - +
437C ASP* 3.3 12.1 + - - +
438C LYS* 2.9 46.1 + - + +
439C ALA* 3.0 25.3 + - - +
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Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A VAL* 4.2 13.9 - - + -
494A LYS 5.0 0.9 - - - +
433B THR 4.2 3.6 - - - +
434B LYS* 2.9 19.4 + - - +
435B ASP 4.3 0.7 - - - -
436B LEU* 3.7 36.4 - - + +
439B ALA* 4.2 16.4 - - + -
440B ASN* 5.6 2.7 - - - +
453B VAL* 3.7 18.6 - - + -
454B ASN* 3.5 28.9 - - - +
435C ASP* 1.3 71.1 - - - +
437C ASP* 1.3 65.6 + - - +
439C ALA* 3.3 2.9 + - - +
440C ASN* 2.9 53.0 + - - +
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Residues in contact with ASP 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LYS* 4.1 27.1 + - - +
495A VAL 5.9 0.2 - - - -
496A PRO* 3.8 21.9 - - + +
434B LYS* 6.0 3.5 - - - +
454B ASN* 4.8 5.7 + - - -
435C ASP* 3.3 10.7 + - - +
436C LEU* 1.3 90.0 - - - +
438C LYS* 1.3 57.3 + - + +
440C ASN* 3.7 3.2 + - - +
441C TYR* 2.8 32.7 + - - +
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Residues in contact with LYS 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C MET* 4.1 23.3 - - + +
279C SER* 5.1 6.5 + - - -
280C ASP* 3.6 23.8 + - - +
311C GLN* 5.4 1.0 + - - +
413C ILE* 3.9 22.2 - - + -
433C THR* 3.9 17.0 - - + +
435C ASP* 2.9 35.6 + - + +
436C LEU 3.3 0.2 - - - -
437C ASP* 1.3 71.9 - - + +
439C ALA* 1.3 67.3 + - - +
441C TYR* 3.6 2.5 - - - +
442C LEU* 3.0 30.2 + - - +
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Residues in contact with ALA 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LEU* 4.3 15.9 - - + -
431C VAL* 4.8 6.1 - - - +
433C THR* 3.8 16.7 - - + +
435C ASP 3.0 17.0 + - - +
436C LEU 3.6 4.3 - - - +
438C LYS* 1.3 77.7 - - - +
440C ASN* 1.3 58.8 + - - +
442C LEU* 3.9 0.7 - - - +
443C SER* 2.9 31.9 + - - -
453C VAL* 4.0 25.6 - - + +
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Residues in contact with ASN 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PHE* 4.6 6.8 - - - -
493A VAL* 4.2 7.9 - - - +
494A LYS 4.9 1.0 + - - -
495A VAL* 3.9 22.4 - - + +
496A PRO* 4.4 4.7 - - + -
3116A EDO 4.1 14.2 - - - -
436B LEU* 5.7 2.2 - - - +
436C LEU* 2.9 46.0 + - - +
437C ASP* 4.0 3.5 + - - +
439C ALA* 1.3 75.5 - - - +
441C TYR* 1.3 63.2 + - - +
443C SER* 3.3 4.9 + - - -
444C GLN* 2.9 46.6 + - - +
153D TYR* 4.5 4.9 + - - -
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Residues in contact with TYR 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A PRO* 3.9 25.0 - - + +
413C ILE* 3.7 34.5 - - + -
414C GLU* 3.7 27.5 - - + +
417C VAL* 3.6 27.5 - - + +
437C ASP 2.8 23.3 + - - +
438C LYS* 3.6 5.6 - - - +
439C ALA 3.3 0.2 - - - -
440C ASN* 1.3 74.2 - - - +
442C LEU* 1.3 62.3 + - + +
444C GLN* 3.6 10.7 + - - +
445C ALA* 3.0 36.1 + - + +
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Residues in contact with LEU 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C ILE* 4.3 12.3 - - + -
278C MET* 4.1 13.5 - - + -
413C ILE* 3.6 33.7 - - + -
416C VAL* 4.3 9.0 - - + -
417C VAL* 3.5 30.7 - - + -
431C VAL* 3.5 39.9 - - + -
438C LYS 3.0 8.9 + - - +
439C ALA 4.2 0.4 - - - +
441C TYR* 1.3 77.9 - - + +
443C SER* 1.3 60.9 + - - +
444C GLN 3.1 1.8 - - - -
445C ALA* 4.4 1.1 - - - +
446C LEU* 2.9 49.2 + - + +
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Residues in contact with SER 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3116A EDO 2.8 28.7 + - - -
431C VAL* 4.9 0.4 - - - +
439C ALA 2.9 21.3 + - - -
440C ASN* 3.3 7.3 + - - -
442C LEU* 1.3 75.7 - - - +
444C GLN* 1.3 52.0 + - - +
451C VAL* 3.9 21.5 - - - +
453C VAL* 4.4 6.7 - - - -
153D TYR* 4.0 2.3 + - - -
489D LYS* 2.8 36.2 + - - +
491D VAL* 4.0 23.4 - - - +
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Residues in contact with GLN 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A VAL* 3.3 31.3 - - - +
496A PRO* 3.8 12.1 + - - +
497A GLN 3.7 21.4 + - - -
498A LYS* 4.9 4.1 - - - +
499A ASN 5.8 0.2 - - - +
3116A EDO 3.1 32.1 - - - +
440C ASN* 2.9 23.8 + - - +
441C TYR* 3.6 9.5 + - - +
442C LEU 3.1 0.4 - - - -
443C SER* 1.3 78.3 - - - +
445C ALA* 1.3 57.9 + - - +
72D LEU* 5.6 3.5 - - - +
155D ARG* 3.7 17.8 + - - +
157D GLU* 4.5 0.7 - - - +
489D LYS* 2.9 18.1 + - - +
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Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C VAL* 4.0 30.2 - - + +
421C ASN* 3.0 21.2 + - - -
441C TYR* 3.0 25.6 + - + +
442C LEU 4.2 1.1 - - - +
444C GLN* 1.3 77.8 - - + +
446C LEU* 1.3 61.1 + - - +
447C GLN* 3.3 6.8 + - - +
72D LEU* 5.3 13.8 - - + +
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Residues in contact with LEU 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C PRO* 4.8 0.7 - - + -
276C ILE* 3.9 14.4 - - + -
417C VAL* 4.9 4.3 - - - +
420C ALA* 3.7 29.6 - - + -
421C ASN* 3.6 9.0 - - - +
429C ALA* 4.1 21.3 - - + -
430C ALA 4.7 0.4 - - - +
431C VAL* 3.6 28.7 - - + -
442C LEU* 2.9 37.2 + - + +
444C GLN 3.5 0.6 - - - -
445C ALA* 1.3 70.4 - - - +
447C GLN* 1.3 60.3 + - - +
448C ALA 3.2 1.4 + - - +
451C VAL* 4.0 22.8 - - + +
489D LYS* 2.7 34.0 + - - -
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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