Contacts of the strand formed by residues 428 - 432 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273L SER* 3.3 23.8 + - - +
274L PRO* 3.4 7.8 - - - +
303L CYS* 3.7 19.1 - - + -
426L GLY* 3.6 2.0 - - - -
427L LEU* 1.3 82.1 + - - +
429L ALA* 1.3 66.7 + - - +
448L ALA* 3.6 6.4 - - - +
450L THR* 3.2 13.0 - - - +
452L TRP* 3.5 29.8 - - + -
465L PHE* 4.8 1.6 - - + -
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Residues in contact with ALA 429 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273L SER* 4.9 1.1 - - - -
274L PRO* 3.3 27.1 - - + +
428L ALA* 1.3 80.0 - - - +
430L ALA* 1.3 62.2 + - - +
446L LEU* 3.9 23.1 - - + -
448L ALA* 3.9 14.8 - - + -
450L THR 3.0 4.2 + - - +
451L VAL* 3.3 6.8 - - + -
452L TRP* 2.9 28.8 + - - -
456L TYR* 4.5 1.8 - - - -
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Residues in contact with ALA 430 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274L PRO 2.9 8.3 + - - +
275L ASN* 3.4 14.1 - - - +
276L ILE* 2.8 26.8 + - - +
429L ALA* 1.3 74.2 - - - +
431L VAL* 1.3 71.3 + - - +
432L PHE* 4.2 0.9 - - + -
446L LEU* 4.5 0.5 - - - +
451L VAL* 5.0 0.2 - - - -
452L TRP* 3.2 10.8 - - + +
455L CYS 3.9 9.2 - - - +
456L TYR* 3.2 35.7 - - + -
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Residues in contact with VAL 431 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276L ILE* 3.3 11.2 - - + +
278L MET* 4.7 1.3 - - + -
430L ALA* 1.3 81.9 - - - +
432L PHE* 1.3 67.3 + - - +
433L THR* 3.7 23.1 - - + -
439L ALA* 4.7 6.1 - - - +
442L LEU* 3.6 41.1 - - + -
443L SER 5.1 0.4 - - - +
446L LEU* 3.6 25.1 - - + -
451L VAL* 4.9 2.9 - - + -
452L TRP 2.9 9.8 + - - +
453L VAL* 3.3 11.7 - - + +
454L ASN* 2.8 26.3 + - - +
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Residues in contact with PHE 432 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275L ASN* 3.3 35.0 - - - -
276L ILE 2.8 10.5 + - - +
277L ILE* 3.7 16.2 - - + -
278L MET* 3.1 26.2 + - - +
281L ALA* 3.5 17.1 - - + +
282L ASP 5.6 0.7 - - - -
285L TRP* 3.9 11.7 - + - -
286L ALA* 3.9 15.7 - - + -
289L GLN* 3.4 38.8 - - + -
430L ALA* 4.2 2.7 - - + -
431L VAL* 1.3 75.2 - - - +
433L THR* 1.3 64.0 + - - +
454L ASN* 3.2 25.8 - - - -
455L CYS* 3.4 31.4 - - - -
456L TYR* 4.9 2.5 - + + -
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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