Contacts of the strand formed by residues 430 - 438 (chain A) in PDB entry 1YC0
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 SER 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A TYR* 3.7 5.7 - - - +
427A ILE* 2.8 37.8 + - - -
428A GLY 4.2 0.7 - - - +
429A ASP* 1.3 84.3 + - - +
431A PHE* 1.3 64.0 + - - +
550A TYR* 4.5 0.9 - - - -
262I SER 3.3 13.5 - - - -
263I PHE* 3.1 44.4 - - - -
264I PRO* 3.7 3.5 + - - +
265I ARG* 5.6 0.3 + - - -
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A ALA* 3.7 11.9 - - + -
425A ILE 3.4 25.8 - - - -
426A TYR* 3.7 24.7 - + + -
427A ILE* 4.9 1.8 - - - -
430A SER* 1.3 76.2 - - - +
432A CYS* 1.3 88.5 + - - +
433A ALA* 4.4 1.3 - - + -
467A PHE* 3.6 30.3 - + + -
540A TRP* 3.6 36.3 - + + -
550A TYR* 3.5 29.1 + + + +
596A GLY* 3.6 23.3 - - - -
261I GLY* 4.1 0.2 - - - -
262I SER* 2.9 33.1 + - - -
263I PHE* 4.7 0.5 - - - -
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Residues in contact with CYS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A ILE* 2.9 33.4 + - + +
427A ILE* 4.2 8.9 - - + +
431A PHE* 1.3 96.4 - - - +
433A ALA* 1.3 64.4 + - - +
444A SER* 4.4 1.8 - - - +
448A CYS* 2.0 55.0 - - + -
596A GLY 4.6 2.7 - - - -
598A SER* 3.5 7.9 - - - +
261I GLY* 3.9 15.5 - - - -
263I PHE* 4.3 5.6 - - - -
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A LEU* 4.0 10.8 - - + -
423A ALA 3.1 13.2 - - - +
425A ILE* 3.3 6.0 - - - +
431A PHE* 4.4 4.7 - - + -
432A CYS* 1.3 72.9 - - - +
434A GLY* 1.3 55.5 + - - +
444A SER* 2.7 28.2 + - - -
538A ALA 5.3 2.2 - - - +
539A GLY* 5.6 1.8 - - - -
540A TRP* 4.7 11.2 - - + -
596A GLY 4.7 1.7 + - - +
597A ASP* 4.4 5.8 - - - +
598A SER 2.7 8.8 + - - +
599A GLY* 3.2 9.8 - - - -
600A GLY* 3.7 20.9 - - - +
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Residues in contact with GLY 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A LEU* 3.2 13.2 - - - +
423A ALA* 2.9 32.1 + - - -
425A ILE* 4.0 3.3 - - - +
433A ALA* 1.3 76.1 - - - +
435A SER* 1.3 64.7 + - - -
442A VAL* 3.8 11.9 - - - -
443A VAL 3.3 6.7 - - - -
599A GLY 3.2 11.1 + - - -
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A TRP* 3.4 5.4 - - - -
434A GLY* 1.3 70.6 - - - -
436A LEU* 1.3 63.7 + - - +
437A VAL* 3.3 3.3 + - - +
442A VAL* 3.2 6.8 - - - +
443A VAL 2.9 32.9 + - - -
520A ILE* 4.0 14.4 - - - -
599A GLY 4.3 1.0 + - - -
601A PRO* 3.1 37.8 - - - +
612A LEU* 3.7 25.0 - - - +
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A PRO 5.1 0.2 - - - +
421A TRP* 2.9 18.1 + - - +
423A ALA* 4.9 0.8 - - - +
435A SER* 1.3 71.4 - - - +
437A VAL* 1.3 58.0 + - - +
438A HIS 3.1 28.7 - - - +
439A THR* 4.2 4.7 - - - +
441A TRP 3.6 7.2 - - - +
442A VAL* 4.2 10.5 - - + +
462A LEU* 3.8 26.7 - - + -
503A LEU* 4.4 2.7 - - + -
511A ALA* 4.1 12.1 - - + -
517A VAL* 4.0 23.6 - - + -
518A GLN 3.9 9.6 - - - +
519A PRO* 3.2 24.4 - - + +
520A ILE* 2.9 29.3 + - - +
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Residues in contact with VAL 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A SER 3.3 4.0 + - - +
436A LEU* 1.3 77.1 - - - +
438A HIS* 1.3 62.4 + - - +
441A TRP* 3.0 24.8 + - + +
443A VAL* 3.7 33.9 - - + -
500A LEU* 6.2 0.2 - - + -
519A PRO* 3.9 11.9 - - - +
520A ILE* 3.9 18.6 - - + +
522A LEU* 4.0 19.9 - - + +
612A LEU* 3.8 18.8 - - + -
641A ILE* 4.9 3.1 - - + -
645A ILE* 4.1 15.8 - - + +
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Residues in contact with HIS 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A LEU* 3.1 16.2 - - - +
437A VAL* 1.3 79.8 - - - +
439A THR* 1.3 90.6 + - + +
440A CYS* 2.8 27.9 + - + -
441A TRP* 2.9 38.4 + + + -
519A PRO* 4.1 6.8 - - - +
645A ILE* 3.4 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