Contacts of the strand formed by residues 428 - 432 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273K SER* 3.3 24.8 + - - +
274K PRO* 3.4 8.7 - - - +
303K CYS* 3.6 26.9 - - + -
426K GLY* 3.6 1.4 - - - -
427K LEU* 1.3 82.7 + - + +
429K ALA* 1.3 65.0 + - - +
448K ALA* 3.6 6.7 - - - +
450K THR* 3.3 12.8 - - - +
452K TRP* 3.7 22.4 - - + -
465K PHE* 4.9 1.3 - - + -
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Residues in contact with ALA 429 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273K SER* 4.9 1.1 - - - -
274K PRO* 3.3 26.5 - - + +
428K ALA* 1.3 78.8 - - - +
430K ALA* 1.3 62.4 + - - +
446K LEU* 4.0 23.8 - - + -
448K ALA* 3.8 15.3 - - + -
450K THR 3.0 5.3 + - - +
451K VAL* 3.2 6.6 - - + -
452K TRP* 2.9 28.5 + - - -
456K TYR* 4.6 2.0 + - - -
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Residues in contact with ALA 430 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K PRO 3.0 6.6 + - - +
275K ASN* 3.5 11.4 - - - +
276K ILE* 2.7 35.6 + - - +
429K ALA* 1.3 77.2 - - - +
431K VAL* 1.3 64.1 + - - +
432K PHE* 4.2 1.3 - - + -
446K LEU* 4.7 0.2 - - - +
451K VAL* 4.9 0.4 - - - -
452K TRP* 3.1 12.8 - - + +
455K CYS 4.0 8.3 - - - +
456K TYR* 3.3 34.8 - - + -
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Residues in contact with VAL 431 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276K ILE* 3.3 9.6 - - + +
278K MET* 4.6 1.3 - - + -
430K ALA* 1.3 82.0 - - - +
432K PHE* 1.3 61.5 + - - +
433K THR* 3.7 23.6 - - + -
439K ALA* 4.8 5.4 - - - +
442K LEU* 3.5 50.5 - - + -
443K SER 4.9 0.7 - - - +
446K LEU* 3.6 16.6 - - + -
451K VAL* 4.8 3.8 - - + -
452K TRP 2.9 9.7 + - - +
453K VAL* 3.3 12.3 - - + +
454K ASN* 2.8 31.9 + - - +
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Residues in contact with PHE 432 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275K ASN* 3.5 31.0 - - - -
276K ILE 2.8 8.3 + - - -
277K ILE* 3.8 20.0 - - + -
278K MET* 3.0 25.6 + - - +
281K ALA* 3.3 17.3 - - + +
282K ASP 5.5 0.7 - - - -
285K TRP* 3.7 10.8 - + - -
286K ALA* 3.9 16.2 - - + -
289K GLN* 3.4 38.6 - - + -
430K ALA* 4.2 2.7 - - + -
431K VAL* 1.3 77.8 - - - +
433K THR* 1.3 61.9 + - - +
454K ASN* 3.2 26.5 - - - +
455K CYS* 3.3 34.8 - - - -
456K TYR* 4.9 1.8 - - + -
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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