Contacts of the strand formed by residues 570 - 576 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A TYR* 4.2 20.2 - + - -
438A LEU* 5.1 2.3 - - - +
439A TYR* 2.7 35.3 + + - -
545A PHE 4.7 0.5 - - - +
546A VAL* 2.6 18.1 + - + +
547A LEU* 4.6 12.8 - - + -
548A SER* 3.0 29.3 + - - -
564A PRO* 4.0 7.3 - - - +
565A VAL 4.9 0.2 + - - -
568A ASN 5.2 0.2 - - - -
569A GLY* 1.3 75.9 - - - -
571A GLY* 1.3 60.8 + - - +
585A ILE* 4.3 8.5 - - + -
586A SER 3.3 17.0 - - - +
587A SER* 3.8 14.8 - - - -
594A THR* 3.7 14.4 - - + -
595A SER 2.9 37.5 + - - -
596A SER* 4.2 1.3 - - - -
598A GLU* 5.8 0.2 - - - +
599A PHE* 3.6 33.5 + + + +
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Residues in contact with GLY 571 (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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548A SER* 3.4 6.5 - - - -
562A TYR* 4.3 10.7 - - - +
563A GLY 4.3 5.4 - - - -
564A PRO* 4.1 9.3 - - - +
570A TYR* 1.3 73.2 - - - +
572A ALA* 1.3 62.0 + - - +
584A CYS 3.4 2.1 - - - +
585A ILE* 3.4 6.9 - - - +
586A SER* 3.0 44.6 + - - -
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Residues in contact with ALA 572 (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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431A LEU* 4.7 16.4 - - + -
547A LEU* 4.5 8.1 - - + -
548A SER 2.8 9.7 + - - -
549A THR* 3.1 40.7 - - + -
550A SER 3.2 3.8 + - - +
562A TYR* 3.2 5.1 + - - -
570A TYR* 4.2 0.6 - - + -
571A GLY* 1.3 73.9 - - - +
573A CYS* 1.3 60.3 + - - +
574A TYR* 4.2 4.0 + - + -
583A PHE* 5.5 3.4 - - + -
584A CYS 3.4 4.9 - - - +
585A ILE* 4.6 12.6 - - + -
599A PHE* 4.8 5.4 - - + -
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Residues in contact with CYS 573 (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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550A SER* 3.4 7.0 - - - -
552A VAL* 3.6 34.8 - - - -
560A CYS* 3.4 29.8 - - - +
561A CYS* 4.4 1.3 - - - -
562A TYR* 3.6 29.2 - - + +
571A GLY 4.2 0.2 - - - -
572A ALA* 1.3 73.2 - - - +
574A TYR* 1.3 64.3 + - - +
582A THR 3.8 0.5 - - - +
583A PHE* 3.6 1.5 - - - +
584A CYS* 2.8 44.0 + - + +
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Residues in contact with TYR 574 (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 ASP* 2.6 26.6 + - - -
427A ILE* 3.9 37.0 - - + -
428A GLN* 2.9 33.8 + - - +
431A LEU* 4.2 8.3 - - + -
447A GLU* 3.4 3.6 + - - -
549A THR* 4.6 0.4 - - - -
550A SER 3.2 18.2 + - - -
551A GLN* 3.4 23.5 + - + +
552A VAL 3.0 24.8 + - - +
572A ALA 4.3 5.8 - - - -
573A CYS* 1.3 79.0 - - - +
575A ASN* 1.3 60.6 + - - +
576A PRO* 3.6 16.7 - - + +
581A ILE* 4.3 3.6 - - + -
582A THR 3.1 11.0 - - - +
583A PHE* 3.7 23.1 - + + -
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Residues in contact with ASN 575 (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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552A VAL 3.6 13.5 - - - +
553A PRO* 3.2 5.7 - - - +
554A THR* 3.1 41.0 + - - +
556A MET 4.9 0.6 + - - -
558A MET 3.6 14.3 + - - -
559A PHE* 5.0 7.3 - - + +
560A CYS 6.2 0.2 - - - +
574A TYR* 1.3 73.6 - - - +
576A PRO* 1.3 67.4 - - - +
577A GLN* 3.5 23.9 + - - +
581A ILE* 3.7 1.1 - - - -
582A THR* 2.8 44.0 + - + +
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Residues in contact with PRO 576 (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 LYS* 3.4 30.7 + - + +
423A PRO* 5.1 3.8 - - + -
427A ILE* 3.8 17.7 - - + -
551A GLN* 2.9 36.1 - - + +
553A PRO* 4.6 9.0 - - + +
574A TYR* 3.6 22.0 - - + +
575A ASN* 1.3 89.6 - - - +
577A GLN* 1.3 68.1 + - - +
580A ALA 4.1 2.5 - - - +
581A ILE* 4.3 7.9 - - + -
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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