Contacts of the strand formed by residues 428 - 432 (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 ALA 428 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273H SER* 3.2 23.4 + - - +
274H PRO* 3.3 7.1 - - - +
303H CYS* 3.8 19.3 - - + -
426H GLY* 3.5 2.5 - - - -
427H LEU* 1.3 84.1 + - - +
429H ALA* 1.3 64.9 + - - +
448H ALA* 3.6 6.2 - - - +
450H THR* 3.2 14.6 - - - +
452H TRP* 3.7 28.9 - - + -
465H PHE* 4.6 2.2 - - + -
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Residues in contact with ALA 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H SER* 4.9 1.3 - - - -
274H PRO* 3.3 26.2 - - + +
428H ALA* 1.3 78.5 - - - +
430H ALA* 1.3 62.5 + - - +
446H LEU* 4.2 24.7 - - + -
448H ALA* 4.0 13.5 - - + -
450H THR 3.0 5.5 + - - +
451H VAL* 3.2 8.8 - - + -
452H TRP* 2.9 27.9 + - - -
456H TYR* 4.8 1.6 - - - -
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Residues in contact with ALA 430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H PRO 3.0 7.3 + - - +
275H ASN* 3.4 12.3 - - - +
276H ILE* 2.9 26.7 + - - +
429H ALA* 1.3 77.2 - - - +
431H VAL* 1.3 69.4 + - - +
432H PHE* 4.2 0.9 - - + -
446H LEU* 4.7 0.5 - - - +
451H VAL* 4.7 0.2 - - - -
452H TRP* 3.2 13.2 - - + +
455H CYS 3.9 9.9 - - - +
456H TYR* 3.4 33.0 - - + -
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Residues in contact with VAL 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H ILE* 3.3 9.9 - - + +
278H MET* 4.5 2.7 - - + -
430H ALA* 1.3 81.3 - - - +
432H PHE* 1.3 66.7 + - - +
433H THR* 4.0 21.3 - - + -
439H ALA* 4.8 5.2 - - - +
442H LEU* 3.5 39.5 - - + -
443H SER 5.0 0.4 - - - +
446H LEU* 3.5 26.9 - - + -
451H VAL* 4.5 7.4 - - + -
452H TRP 2.9 7.7 + - - +
453H VAL* 3.3 11.8 - - + +
454H ASN* 2.8 25.3 + - - +
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Residues in contact with PHE 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H ASN* 3.4 32.1 - - - -
276H ILE 2.8 8.7 + - - -
277H ILE* 3.9 21.3 - - + -
278H MET* 3.0 27.9 + - - +
281H ALA* 3.5 16.3 - - + +
282H ASP 5.6 0.7 - - - -
285H TRP* 3.6 18.6 - + - -
286H ALA* 3.9 12.6 - - + -
289H GLN* 3.4 35.0 - - + -
290H ALA 5.6 0.2 - - - -
430H ALA* 4.2 3.1 - - + -
431H VAL* 1.3 76.7 - - - +
433H THR* 1.3 63.3 + - - +
454H ASN* 3.2 26.0 - - - +
455H CYS 3.3 33.9 - - - -
456H TYR* 4.8 2.2 - + + -
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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
------------------------------------------------------------
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