Contacts of the strand formed by residues 570 - 576 (chain B) in PDB entry 1Q6X
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 TYR 570 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435B TYR* 4.2 21.8 - + - -
438B LEU* 5.1 1.9 - - - +
439B TYR* 2.7 36.3 + + - -
545B PHE 4.8 0.5 - - - +
546B VAL* 2.6 16.0 + - + +
547B LEU* 4.6 12.6 - - + -
548B SER* 3.0 28.7 + - - -
564B PRO* 4.0 7.1 - - - +
565B VAL 5.0 0.2 + - - -
568B ASN 5.2 0.2 - - - -
569B GLY* 1.3 77.4 - - - -
571B GLY* 1.3 61.6 + - - +
572B ALA* 4.2 0.4 - - + -
585B ILE* 4.2 9.0 - - + -
586B SER 3.3 17.3 - - - -
587B SER* 3.8 13.9 - - - -
594B THR* 3.7 13.9 - - + -
595B SER 2.9 31.2 + - - -
596B SER* 4.2 1.1 - - - -
598B GLU* 5.8 0.2 - - - +
599B PHE* 3.6 39.6 + + + +
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Residues in contact with GLY 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B SER* 3.4 7.0 - - - -
562B TYR* 4.3 10.4 - - - +
563B GLY 4.3 13.7 - - - -
564B PRO* 4.1 1.2 - - - +
570B TYR* 1.3 74.6 - - - +
572B ALA* 1.3 59.6 + - - +
584B CYS 3.4 2.3 - - - +
585B ILE* 3.3 7.3 - - - +
586B SER* 3.0 42.8 + - - -
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Residues in contact with ALA 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B LEU* 4.7 16.8 - - + -
547B LEU* 4.6 8.7 - - + -
548B SER 2.8 10.5 + - - -
549B THR* 3.2 40.4 - - + -
550B SER 3.3 5.2 + - - +
562B TYR* 3.7 3.7 - - - -
570B TYR* 4.2 0.6 - - + -
571B GLY* 1.3 73.6 - - - +
573B CYS* 1.3 61.1 + - - +
574B TYR* 4.3 4.0 - - + -
583B PHE* 5.5 3.6 - - + -
584B CYS 3.4 4.7 - - - +
585B ILE* 4.6 11.7 - - + -
599B PHE* 4.8 5.2 - - + -
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Residues in contact with CYS 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B SER* 3.4 7.0 - - - -
552B VAL* 3.6 34.5 - - - -
560B CYS* 3.4 28.9 - - - +
561B CYS* 4.4 2.2 - - - -
562B TYR* 3.6 28.7 - - + +
571B GLY 4.2 0.4 - - - -
572B ALA* 1.3 73.8 - - - +
574B TYR* 1.3 63.7 + - - +
582B THR 3.8 0.5 - - - +
583B PHE* 3.6 1.9 - - - -
584B CYS* 2.8 41.9 + - + +
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Residues in contact with TYR 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ASP* 2.6 26.2 + - - -
427B ILE* 3.9 38.4 - - + -
428B GLN* 2.9 33.7 + - - +
431B LEU* 4.2 8.3 - - + -
447B GLU* 3.4 3.6 + - - -
549B THR* 4.6 0.7 - - - -
550B SER 3.2 17.8 + - - -
551B GLN* 3.5 23.4 + - + +
552B VAL 3.0 24.3 + - - -
572B ALA* 4.3 6.1 - - + -
573B CYS* 1.3 77.2 - - - +
575B ASN* 1.3 60.3 + - - +
576B PRO* 3.6 16.1 - - + +
581B ILE* 4.3 3.6 - - + -
582B THR 3.1 9.9 - - - +
583B PHE* 3.7 23.1 - + + -
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Residues in contact with ASN 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B VAL 3.7 13.7 - - - +
553B PRO* 3.2 5.4 - - - +
554B THR* 3.1 41.9 + - - +
556B MET 4.9 0.2 + - - -
558B MET 3.6 13.9 + - - -
559B PHE* 5.0 7.9 - - + +
574B TYR* 1.3 73.6 - - - +
576B PRO* 1.3 68.4 - - - +
577B GLN* 3.5 22.7 + - - +
581B ILE* 3.7 1.1 - - - -
582B THR* 2.8 43.6 + - + +
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Residues in contact with PRO 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B LYS* 3.4 30.4 + - + +
423B PRO* 5.1 3.8 - - + -
427B ILE* 3.8 18.2 - - + -
551B GLN* 2.9 36.1 - - + +
553B PRO* 4.6 9.6 - - + +
574B TYR* 3.6 21.1 - - + +
575B ASN* 1.3 88.8 - - - +
577B GLN* 1.3 69.3 + - - +
580B ALA 4.1 2.7 - - - +
581B ILE* 4.3 8.3 - - + -
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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