Contacts of the strand formed by residues 430 - 435 (chain A) in PDB entry 5Y7K
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 ASN 430 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A ILE* 3.2 9.5 - - - +
419A SER 3.2 30.5 + - - +
422A TYR* 3.4 28.4 - - + +
428A GLY 5.3 0.5 - - - -
429A ARG* 1.3 76.7 + - - +
431A LEU* 1.3 58.6 + - - +
432A TYR* 3.5 23.1 - - + +
444A CYS* 3.9 0.2 - - - -
446A SER* 2.7 34.8 + - - +
447A CYS* 3.4 16.1 + - - +
454A CYS 5.2 0.8 + - - -
455A GLN* 4.4 9.7 + - - +
457A TYR* 3.2 21.2 - - - -
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Residues in contact with LEU 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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408A GLU* 4.7 0.7 - - + -
416A TYR* 4.2 11.0 - - + -
417A TYR 3.3 26.2 - - - +
418A ILE* 4.2 12.1 - - + -
430A ASN* 1.3 71.9 - - - +
432A TYR* 1.3 66.9 + - - +
444A CYS* 3.4 9.0 - - - -
445A LEU* 2.9 43.0 + - + -
446A SER* 2.8 16.3 + - - +
457A TYR* 4.6 2.3 - - + +
459A VAL* 3.8 19.3 - - + -
461A PHE* 4.1 8.7 - - + -
468A TYR* 3.8 22.0 - - + -
470A LEU* 3.8 28.5 - - + -
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Residues in contact with TYR 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 3.2 5.6 - - - +
417A TYR* 2.7 64.9 + + + +
419A SER* 3.2 27.8 - - - -
421A GLU* 3.7 19.2 + - - +
422A TYR* 3.4 26.3 + - - +
430A ASN* 3.5 27.1 - - + -
431A LEU* 1.3 78.7 - - - +
433A LYS* 1.3 60.6 + - - +
434A ILE 4.3 0.4 - - - -
442A VAL* 4.2 9.4 - - + -
443A THR 3.3 7.2 - - - +
444A CYS* 3.4 35.0 - - + -
445A LEU* 4.5 2.0 - - - +
447A CYS* 3.4 13.0 - - - -
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Residues in contact with LYS 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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414A TYR* 3.4 47.4 + - + -
415A LEU 3.6 5.2 - - - +
416A TYR* 3.6 31.3 + - + -
432A TYR* 1.3 74.7 - - - +
434A ILE* 1.3 59.9 + - - +
435A GLN 4.2 0.2 - - - -
441A LYS 3.9 1.6 - - - +
442A VAL* 3.5 3.5 - - - -
443A THR* 2.8 54.2 + - - +
445A LEU* 3.4 27.4 - - + -
485A SER 3.9 7.5 + - - -
486A VAL 5.5 1.4 + - - -
488A ASP* 3.2 24.9 + - - +
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Residues in contact with ILE 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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397A ILE* 3.3 54.3 - - + +
398A THR* 4.4 5.2 - - + -
414A TYR* 3.4 3.2 - - - -
415A LEU* 3.0 52.3 + - + +
417A TYR* 3.9 17.5 - - + -
432A TYR 4.3 0.2 - - - -
433A LYS* 1.3 72.8 - - - +
435A GLN* 1.3 73.7 + - - +
436A LEU* 3.4 2.9 + - + +
439A TYR* 3.8 20.4 - - + +
441A LYS 3.9 3.4 - - - -
442A VAL* 4.1 16.8 - - + +
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Residues in contact with GLN 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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413A ASP* 3.4 13.5 - - + +
414A TYR* 3.7 27.4 + - + -
434A ILE* 1.3 71.5 - - - +
436A LEU* 1.3 66.5 + - - +
437A SER* 2.7 28.3 + - - +
438A ASP* 3.0 43.4 + - - +
439A TYR* 3.5 9.7 - - - -
441A LYS* 3.2 45.6 + - + +
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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