Contacts of the strand formed by residues 664 - 670 (chain A) in PDB entry 5JZU
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 GLN 664 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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629A THR* 4.5 3.6 - - + -
631A TRP* 3.1 16.8 - - - +
632A GLN* 3.9 15.2 - - + +
633A GLN* 5.6 0.6 - - - +
657A THR 5.8 1.3 - - - -
663A GLY* 1.3 89.9 + - - +
665A ILE* 1.3 65.0 + - - +
666A LYS* 2.7 46.2 + - + +
686A ARG* 4.0 5.1 - - - +
688A ARG* 2.8 16.0 + - - -
739A ILE* 3.8 2.6 - - - +
741A ASP* 2.7 39.5 + - - +
758A ILE* 4.5 9.5 + - - -
102B LYS* 3.6 37.7 + - + +
103B ASP* 3.7 2.1 - - - +
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Residues in contact with ILE 665 (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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629A THR* 3.6 0.2 - - - -
630A LEU* 2.7 33.4 + - + -
631A TRP* 2.9 46.6 + - + +
651A LEU* 3.6 17.5 - - + -
657A THR* 3.3 42.8 - - + +
658A THR* 4.1 7.4 - - + -
664A GLN* 1.3 75.7 - - - +
666A LYS* 1.3 65.7 + - - +
738A PHE* 3.5 30.7 - - + -
739A ILE 3.3 7.0 - - - +
740A VAL* 4.3 5.8 - - + -
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Residues in contact with LYS 666 (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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627A GLN* 3.5 29.7 + - + +
628A PHE 3.2 14.8 - - - +
629A THR* 3.6 18.8 - - - +
630A LEU* 4.4 0.9 - - - +
664A GLN* 2.7 33.4 + - + +
665A ILE* 1.3 78.3 - - - +
667A TYR* 1.3 63.4 + - - +
688A ARG* 4.0 7.2 - - - +
738A PHE* 4.0 7.2 - - - -
739A ILE* 2.8 61.7 + - + +
102B LYS* 4.5 4.6 - - - +
103B ASP* 2.7 36.2 + - - -
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Residues in contact with TYR 667 (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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597A ILE* 2.6 33.0 + - + +
600A GLU* 4.0 3.1 - - - +
601A GLY* 3.6 24.2 + - - -
612A PHE* 3.8 21.1 - - + -
627A GLN* 3.2 6.8 - - - +
628A PHE* 2.8 65.5 + + - +
630A LEU* 4.2 5.4 - - + -
644A ALA* 4.1 10.0 - - + +
647A THR* 3.2 21.1 + - - +
666A LYS* 1.3 73.9 - - - +
668A SER* 1.3 58.6 + - - +
669A ILE 4.3 0.4 - - - -
693A LEU* 3.6 25.4 - - + -
736A LEU* 4.3 6.3 - - + -
737A ILE 3.5 4.5 - - - -
738A PHE* 3.7 24.0 - + - -
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Residues in contact with SER 668 (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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625A TRP* 2.9 19.1 + - - -
626A SER 3.6 4.3 - - - -
627A GLN* 3.8 5.9 + - - -
666A LYS 3.8 0.2 + - - -
667A TYR* 1.3 75.5 - - - +
669A ILE* 1.3 59.2 + - - +
735A ARG* 3.2 8.7 + - - -
736A LEU* 3.6 3.0 - - - +
737A ILE* 2.9 36.0 + - - -
739A ILE* 3.6 19.1 - - - -
802A OGA 2.5 30.3 + - - -
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Residues in contact with ILE 669 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605A MET* 3.4 42.6 - - + -
612A PHE* 3.7 19.5 - - + -
624A ASP 4.1 0.5 - - - +
625A TRP* 3.4 4.4 - - - -
626A SER* 3.0 46.0 + - - +
668A SER* 1.3 73.2 - - - +
670A MET* 1.3 64.2 + - - +
671A HIS* 3.6 33.8 - - + +
734A PHE* 3.7 13.7 - - + -
735A ARG* 3.3 10.8 - - - +
736A LEU* 3.9 10.5 - - + +
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Residues in contact with MET 670 (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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624A ASP 3.5 4.5 - - - +
625A TRP* 3.7 28.7 - - + -
669A ILE* 1.3 75.6 - - - +
671A HIS* 1.3 65.2 + - - +
674A THR* 3.6 32.1 - - + -
676A VAL* 3.8 10.5 - - + -
727A VAL* 3.7 27.4 - - + -
728A TRP 4.6 0.7 - - - -
729A GLN* 2.9 36.2 + - + +
735A ARG* 2.9 37.6 + - - +
802A OGA 3.2 27.6 - - - +
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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