Contacts of the helix formed by residues 435 - 446 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434E LYS* 3.4 26.0 - - - +
436E LEU* 4.2 2.0 - - - -
280H ASP* 3.4 17.4 + - - +
433H THR* 3.1 6.3 + - - +
434H LYS* 1.3 77.7 - - - +
436H LEU* 1.3 67.1 + - - +
437H ASP* 3.5 11.9 + - - +
438H LYS* 3.2 41.6 + - + +
439H ALA* 3.0 23.7 + - - +
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Residues in contact with LEU 436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433E THR 4.1 4.5 - - - +
434E LYS* 2.9 21.7 + - - +
435E ASP 4.3 0.2 - - - -
436E LEU* 3.7 33.5 - - + +
439E ALA* 4.3 16.8 - - + -
440E ASN* 5.8 1.8 - - - +
453E VAL* 3.7 20.4 - - + -
454E ASN* 3.6 27.6 - - - +
493F VAL* 4.2 12.6 - - + -
494F LYS 5.1 0.2 - - - +
435H ASP* 1.3 71.9 - - - +
437H ASP* 1.3 65.4 + - - +
439H ALA* 3.3 2.4 + - - +
440H ASN* 3.0 51.2 + - - +
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Residues in contact with ASP 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434E LYS* 6.0 4.0 - - - +
454E ASN* 4.8 6.8 + - - -
494F LYS* 4.0 17.3 - - - +
495F VAL* 4.9 0.6 - - - -
496F PRO* 3.8 25.4 - - + +
435H ASP* 3.4 9.6 + - - +
436H LEU* 1.3 87.8 - - - +
438H LYS* 1.3 61.4 + - + +
440H ASN* 4.5 1.4 + - - +
441H TYR* 2.8 33.2 + - - +
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Residues in contact with LYS 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H MET* 4.2 22.4 - - + +
279H SER* 5.3 4.8 + - - -
280H ASP* 3.4 23.5 + - - +
311H GLN* 5.8 1.0 + - - -
413H ILE* 4.0 21.8 - - + -
433H THR* 3.9 16.6 - - + +
435H ASP* 3.2 32.7 + - + +
436H LEU 3.3 0.4 - - - -
437H ASP* 1.3 74.4 - - + +
439H ALA* 1.3 59.0 + - - +
441H TYR* 3.4 2.5 + - - +
442H LEU* 2.9 36.5 + - + +
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Residues in contact with ALA 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E LEU* 4.1 16.6 - - + -
431H VAL* 4.8 5.2 - - - +
433H THR* 3.9 12.2 - - + +
435H ASP 3.0 18.5 + - - +
436H LEU 3.6 4.3 - - - +
438H LYS* 1.3 76.0 - - - +
440H ASN* 1.3 58.6 + - - +
442H LEU* 3.8 1.2 - - - +
443H SER* 2.9 33.5 + - - -
453H VAL* 3.9 31.1 - - + +
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Residues in contact with ASN 440 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E LEU* 5.8 1.9 - - - +
151F PHE* 4.7 6.6 - - - -
493F VAL* 4.1 9.1 - - - +
494F LYS 4.8 1.4 + - - -
495F VAL* 4.0 31.5 - - + +
496F PRO* 4.5 6.3 - - + -
153G TYR* 4.3 6.2 + - - -
3123G EDO 4.0 16.4 - - - -
436H LEU* 3.0 43.9 + - - +
437H ASP* 4.0 3.5 + - - +
439H ALA* 1.3 75.5 - - - +
441H TYR* 1.3 66.4 + - - +
443H SER* 3.3 7.1 + - - -
444H GLN* 3.2 24.4 + - - +
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Residues in contact with TYR 441 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496F PRO* 4.2 28.4 - - + +
497F GLN* 5.7 2.9 - - + -
72G LEU* 6.5 1.1 - - + -
413H ILE* 3.6 37.5 - - + -
414H GLU* 4.1 24.7 - - - +
417H VAL* 3.8 26.6 - - + +
437H ASP 2.8 23.3 + - - +
438H LYS* 3.7 4.3 - - - +
440H ASN* 1.3 72.7 - - - +
442H LEU* 1.3 63.0 + - + +
444H GLN* 4.0 8.1 + - - +
445H ALA* 3.0 36.5 + - + +
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Residues in contact with LEU 442 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H ILE* 4.4 9.0 - - + -
278H MET* 4.0 15.7 - - + -
413H ILE* 3.7 29.6 - - + -
416H VAL* 4.5 6.5 - - + -
417H VAL* 3.3 33.7 - - + -
431H VAL* 3.5 41.1 - - + -
438H LYS 2.9 17.0 + - - +
439H ALA 4.0 1.6 - - - +
441H TYR* 1.3 74.6 - - + +
443H SER* 1.3 66.2 + - - +
444H GLN 3.1 1.3 - - - -
445H ALA* 4.4 0.7 - - - +
446H LEU* 2.9 41.0 + - + +
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Residues in contact with SER 443 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G TYR* 3.9 2.9 + - - -
489G LYS* 3.1 28.4 + - - +
491G VAL* 3.8 23.1 - - - -
3123G EDO 2.7 34.1 + - - -
431H VAL* 5.0 0.2 - - - +
439H ALA 2.9 20.9 + - - -
440H ASN* 3.3 8.0 + - - -
442H LEU* 1.3 73.1 - - - +
444H GLN* 1.3 56.9 + - - +
446H LEU 4.1 1.7 - - - +
451H VAL* 4.0 21.7 - - - +
453H VAL* 4.6 5.4 - - - -
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Residues in contact with GLN 444 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495F VAL* 5.9 2.7 - - - +
497F GLN 2.7 30.1 + - - +
498F LYS* 3.8 5.1 - - - +
499F ASN* 2.9 45.4 + - + +
500F SER 6.0 0.2 - - - +
72G LEU* 5.2 8.5 - - + +
155G ARG* 3.5 28.2 + - - +
157G GLU* 4.3 0.9 - - - +
489G LYS* 3.1 16.1 + - - -
3123G EDO 4.1 9.4 - - - -
440H ASN 3.2 17.2 + - - +
441H TYR* 4.0 6.9 + - - +
442H LEU 3.1 0.4 - - - -
443H SER* 1.3 79.3 + - - +
445H ALA* 1.3 63.0 + - - +
447H GLN* 6.0 0.3 - - - +
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Residues in contact with ALA 445 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G LEU* 4.5 22.5 - - + +
417H VAL* 3.9 30.9 - - + +
421H ASN* 3.0 19.9 + - - -
441H TYR* 3.0 28.1 + - + +
442H LEU 3.2 1.5 + - - +
444H GLN* 1.3 79.3 - - - +
446H LEU* 1.3 63.0 + - - +
447H GLN* 3.4 7.6 + - - +
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Residues in contact with LEU 446 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489G LYS* 2.7 32.1 + - - -
274H PRO* 5.1 0.7 - - + -
276H ILE* 3.9 14.1 - - + -
417H VAL* 4.9 4.9 - - + +
420H ALA* 3.7 29.4 - - + -
421H ASN* 3.5 9.2 - - - +
429H ALA* 4.2 20.9 - - + -
430H ALA 4.7 0.4 - - - +
431H VAL* 3.5 30.5 - - + -
442H LEU* 2.9 31.3 + - + +
444H GLN 3.4 0.2 - - - -
445H ALA* 1.3 74.2 - - - +
447H GLN* 1.3 57.3 + - - +
448H ALA 3.2 3.7 + - - -
451H VAL* 4.1 21.9 - - + +
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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