Contacts of the helix formed by residues 435 - 446 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280I ASP* 3.3 14.2 + - - +
433I THR* 3.0 7.1 + - - +
434I LYS* 1.3 77.7 - - - +
436I LEU* 1.3 65.1 + - - +
437I ASP* 3.5 10.4 + - - +
438I LYS* 3.0 43.9 + - + +
439I ALA* 3.0 24.6 + - - +
434L LYS* 2.9 33.4 - - - +
435L ASP* 4.6 0.2 - - - +
436L LEU* 3.8 1.8 - - - -
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Residues in contact with LEU 436 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435I ASP* 1.3 69.4 - - - +
437I ASP* 1.3 66.3 + - - +
439I ALA* 3.3 3.1 + - - +
440I ASN* 3.0 46.4 + - - +
493K VAL* 4.4 9.6 - - + -
494K LYS 5.1 0.2 - - - +
433L THR 4.0 4.5 - - - +
434L LYS* 2.8 19.5 + - - +
435L ASP 3.8 1.6 - - - -
436L LEU* 3.1 36.7 - - + +
439L ALA* 3.8 17.3 - - + -
440L ASN* 5.4 3.4 - - - +
453L VAL* 3.7 21.8 - - + -
454L ASN* 3.7 27.1 - - - +
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Residues in contact with ASP 437 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435I ASP* 3.5 10.3 + - - +
436I LEU* 1.3 87.2 - - - +
438I LYS* 1.3 57.6 + - + +
440I ASN* 4.6 1.7 + - - +
441I TYR* 2.9 32.6 + - - +
494K LYS* 4.1 17.5 - - - +
495K VAL* 5.0 0.4 - - - -
496K PRO* 3.9 26.3 - - + +
434L LYS* 4.3 7.8 + - + +
454L ASN* 4.2 12.5 + - - -
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Residues in contact with LYS 438 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278I MET* 4.3 21.9 - - + +
279I SER* 4.8 5.3 + - - -
280I ASP* 3.7 19.5 + - - +
311I GLN* 4.8 7.5 + - - +
413I ILE* 4.2 21.3 - - + -
433I THR* 3.9 17.7 - - + +
435I ASP* 3.0 42.3 + - + +
436I LEU 3.2 0.2 - - - -
437I ASP* 1.3 75.0 - - - +
439I ALA* 1.3 63.3 + - - +
441I TYR* 3.4 2.5 + - - +
442I LEU* 3.0 29.8 + - - +
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Residues in contact with ALA 439 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431I VAL* 4.9 5.2 - - - +
433I THR* 3.9 10.5 - - + +
435I ASP 3.0 16.8 + - - +
436I LEU 3.6 4.7 - - - +
438I LYS* 1.3 78.0 - - - +
440I ASN* 1.3 58.3 + - - +
442I LEU* 3.9 0.7 - - - +
443I SER* 2.9 32.7 + - - -
453I VAL* 3.9 26.2 - - + +
436L LEU* 3.8 23.3 - - + -
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Residues in contact with ASN 440 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436I LEU* 3.0 42.0 + - - +
437I ASP* 4.1 3.2 + - - +
439I ALA* 1.3 76.1 - - - +
441I TYR* 1.3 66.8 + - - +
443I SER* 3.1 19.7 + - - -
444I GLN* 3.2 14.6 + - - +
153J TYR* 4.6 8.0 + - - -
151K PHE* 5.0 10.1 - - - -
493K VAL* 3.9 10.5 - - - +
494K LYS 4.8 1.0 + - - -
495K VAL* 3.8 33.4 - - + +
496K PRO* 4.6 4.3 - - + -
436L LEU* 5.4 2.4 - - - +
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Residues in contact with TYR 441 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413I ILE* 3.6 32.1 - - + -
414I GLU* 4.1 23.8 - - + +
417I VAL* 3.6 28.1 - - + +
437I ASP 2.9 21.2 + - - +
438I LYS* 3.7 5.4 - - - +
440I ASN* 1.3 78.3 - - - +
442I LEU* 1.3 62.5 + - - +
444I GLN* 3.9 4.5 + - - +
445I ALA* 3.0 36.6 + - + +
496K PRO* 4.1 29.1 - - + +
497K GLN* 6.4 1.8 - - + -
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Residues in contact with LEU 442 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I ILE* 4.2 8.5 - - + -
278I MET* 4.1 15.7 - - + -
413I ILE* 3.8 27.8 - - + -
416I VAL* 4.5 6.7 - - + -
417I VAL* 3.3 33.9 - - + -
431I VAL* 3.4 42.4 - - + -
438I LYS 3.0 16.3 + - - +
439I ALA 4.0 1.8 - - - +
441I TYR* 1.3 74.1 - - + +
443I SER* 1.3 65.8 + - - +
444I GLN 3.1 2.2 + - - -
445I ALA* 4.4 0.9 - - - +
446I LEU* 2.8 40.0 + - + +
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Residues in contact with SER 443 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431I VAL* 5.1 0.6 - - - +
439I ALA 2.9 19.7 + - - -
440I ASN* 3.1 17.5 + - - -
442I LEU* 1.3 73.1 - - - +
444I GLN* 1.3 62.2 + - - +
446I LEU 4.1 0.7 - - - +
451I VAL* 3.8 24.4 - - - +
453I VAL* 4.6 6.3 - - - -
153J TYR* 3.9 10.7 + - - -
155J ARG* 5.0 0.8 + - - -
489J LYS* 3.5 23.2 + - - +
491J VAL* 4.0 28.6 - - - +
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Residues in contact with GLN 444 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440I ASN 3.2 14.6 + - - +
441I TYR* 3.9 4.4 + - - +
442I LEU 3.1 0.4 - - - -
443I SER* 1.3 82.0 + - - +
445I ALA* 1.3 63.9 + - - +
72J LEU* 5.5 7.6 - - + +
155J ARG* 3.8 31.3 + - - +
157J GLU* 4.6 0.3 - - - +
489J LYS* 3.3 14.7 + - - -
495K VAL* 5.5 5.6 - - - +
497K GLN 2.6 34.1 + - - +
498K LYS* 3.9 5.7 - - - +
499K ASN* 3.4 38.2 + - + +
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Residues in contact with ALA 445 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417I VAL* 3.7 30.7 - - + +
421I ASN* 3.1 17.6 + - - -
441I TYR* 3.0 28.7 + - + +
442I LEU* 4.0 1.6 - - - +
444I GLN* 1.3 76.2 - - - +
446I LEU* 1.3 63.2 + - - +
447I GLN* 3.3 7.6 + - - +
72J LEU* 4.5 23.0 - - + +
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Residues in contact with LEU 446 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I PRO* 5.8 0.2 - - + -
276I ILE* 4.0 13.9 - - + -
417I VAL* 4.7 11.4 - - - +
420I ALA* 3.7 31.0 - - + -
421I ASN* 3.7 6.7 - - - +
429I ALA* 3.9 27.4 - - + -
430I ALA 4.6 0.7 - - - +
431I VAL* 3.6 31.4 - - + -
442I LEU* 2.8 29.0 + - + +
443I SER 4.1 0.9 - - - +
444I GLN 3.5 0.2 - - - -
445I ALA* 1.3 71.1 - - - +
447I GLN* 1.3 56.2 + - - +
448I ALA 3.2 4.3 + - - +
451I VAL* 4.2 17.5 - - + +
489J LYS* 2.7 33.0 + - - -
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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