Contacts of the strand formed by residues 659 - 671 (chain A) in PDB entry 6X70
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 LYS 659 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A GLN* 3.8 33.0 + - - +
620A ARG 4.8 3.6 + - - +
654A LEU* 2.6 43.1 + - + +
655A ASN* 5.0 1.6 - - - +
657A ILE* 3.4 26.6 - - + +
658A ASN* 1.3 85.6 - - - +
660A THR* 1.3 60.9 + - - +
702A ASN* 5.0 1.8 - - - +
735A LEU* 4.4 21.7 + - + +
736A VAL 3.2 13.0 - - - +
737A ASP* 3.0 31.1 + - - +
738A VAL* 4.2 3.5 - - - +
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Residues in contact with THR 660 (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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654A LEU* 4.1 3.9 - - - +
659A LYS* 1.3 75.6 - - - +
661A THR* 1.3 60.0 + - - +
700A PRO* 3.3 20.6 - - - +
701A THR* 3.6 33.0 - - - +
702A ASN* 4.1 10.5 - - + +
735A LEU* 3.1 7.4 - - - +
736A VAL* 2.7 44.6 + - - +
737A ASP 4.6 1.4 + - - -
738A VAL* 3.9 19.3 - - + +
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Residues in contact with THR 661 (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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654A LEU* 4.3 4.3 - - + -
660A THR* 1.3 78.2 - - - +
662A SER* 1.3 59.9 + - - +
663A GLN 3.3 16.1 + - - -
664A ILE* 4.3 8.5 - - + -
697A LEU* 3.7 9.4 - - + +
700A PRO* 3.5 3.1 - - - +
701A THR 3.0 33.6 + - - +
707A ILE* 3.7 21.5 - - + -
732A PHE* 3.4 34.6 - - + +
734A LYS 2.8 18.1 + - - -
735A LEU* 4.4 2.7 - - - -
736A VAL 4.7 0.2 - - - +
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Residues in contact with SER 662 (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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661A THR* 1.3 73.4 - - - +
663A GLN* 1.3 60.8 + - - +
696A ARG* 3.6 7.8 + - - +
697A LEU* 2.7 38.7 + - - +
700A PRO* 4.4 12.6 - - - -
734A LYS* 3.0 31.3 + - - +
736A VAL* 4.2 17.5 - - - +
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Residues in contact with GLN 663 (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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661A THR* 3.3 8.0 + - - -
662A SER* 1.3 82.7 + - - +
664A ILE* 1.3 64.6 + - - +
694A SER* 3.9 14.4 + - - -
695A SER 3.3 16.3 - - - +
696A ARG* 3.0 34.6 - - - +
697A LEU* 4.3 1.4 - - - +
733A ASN* 2.7 56.3 + - - +
734A LYS* 3.5 30.3 + - + +
5P T 3.4 17.4 + - - -
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Residues in contact with ILE 664 (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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661A THR* 4.3 5.8 - - + -
663A GLN* 1.3 78.7 - - - +
665A THR* 1.3 59.9 + - - +
694A SER* 3.1 4.7 - - - -
695A SER* 2.9 39.1 + - - +
697A LEU* 3.9 23.8 - - + -
707A ILE* 3.9 10.8 - - + +
710A GLU* 3.7 34.3 - - + -
711A MET* 3.8 28.7 - - + +
714A LEU* 4.1 9.7 - - + +
731A GLN 3.2 8.5 - - - +
732A PHE* 3.8 22.9 - - + -
733A ASN* 3.1 5.8 - - - -
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Residues in contact with THR 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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664A ILE* 1.3 71.8 - - - +
666A LEU* 1.3 69.4 + - - +
667A LYS* 4.4 1.6 - - + +
692A SER* 3.7 21.5 - - - +
693A ARG 3.4 15.3 - - - +
694A SER* 3.2 15.8 - - - -
711A MET* 3.2 11.1 - - - +
714A LEU* 4.4 0.4 - - - -
729A ALA 4.0 0.5 - - - +
730A LEU* 3.7 0.7 - - - -
731A GLN* 2.9 56.4 + - - +
733A ASN* 2.6 26.0 + - - -
7P T 6.2 0.7 - - + -
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Residues in contact with LEU 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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643A ILE* 4.2 8.1 - - + -
665A THR* 1.3 76.0 - - - +
667A LYS* 1.3 72.7 + - - +
668A LEU* 4.2 5.8 - - + -
692A SER* 3.5 1.7 - - - -
693A ARG 3.1 30.9 + - - +
711A MET* 3.7 24.7 - - - +
714A LEU* 3.9 18.6 - - + +
715A TYR* 4.1 20.4 - - + -
718A LEU* 3.7 23.4 - - + +
728A LEU* 4.0 17.0 - - + -
729A ALA 3.5 8.1 - - - +
730A LEU* 3.6 21.8 - - + -
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Residues in contact with LYS 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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626A ASP* 4.5 6.7 + - - -
628A ASN* 4.7 8.5 - - - +
665A THR* 4.2 4.2 - - + -
666A LEU* 1.3 77.0 - - - +
668A LEU* 1.3 93.3 + - - +
669A MET* 4.4 12.5 - - - +
690A SER* 3.7 18.6 + - - +
691A PHE 3.3 18.6 - - - +
692A SER* 4.1 12.3 - - - +
728A LEU* 3.5 8.0 - - - +
729A ALA* 2.7 56.6 + - + +
731A GLN* 5.4 5.8 - - - +
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Residues in contact with LEU 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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666A LEU* 4.2 0.9 - - + -
667A LYS* 1.3 90.4 - - - +
669A MET* 1.3 70.7 + - - +
670A ARG* 4.1 1.3 - - + +
690A SER* 3.5 3.3 - - - -
691A PHE* 3.0 52.9 + - + +
715A TYR* 3.9 21.8 - - + -
718A LEU* 3.8 33.2 - - + -
720A CYS* 3.8 36.6 - - + -
725A LEU* 3.6 6.7 - - + -
727A GLY 3.2 13.2 - - - +
728A LEU* 4.1 4.7 - - + -
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Residues in contact with MET 669 (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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628A ASN* 3.2 23.3 - - - +
667A LYS* 4.4 9.9 - - + +
668A LEU* 1.3 77.7 - - - +
670A ARG* 1.3 60.9 + - - +
685A MET* 3.6 27.8 - - + -
688A CYS* 3.8 27.8 - - + +
689A ASP 3.5 3.1 - - - +
690A SER* 2.9 32.8 - - - +
725A LEU* 3.5 7.3 - - - +
726A ARG 2.9 26.6 + - - +
727A GLY* 2.9 17.9 + - - +
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Residues in contact with ARG 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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668A LEU* 4.1 6.1 - - + -
669A MET* 1.3 74.3 - - - +
671A ARG* 1.3 80.9 + - - +
672A CYS* 3.2 0.5 + - - -
688A CYS* 3.2 4.5 - - - -
689A ASP* 2.9 37.3 + - + +
691A PHE* 4.2 22.0 - - + -
718A LEU 5.2 2.0 + - - -
719A GLY 3.7 11.3 + - - -
720A CYS* 3.8 19.8 - - - +
721A PRO* 3.5 33.4 - - - +
724A GLU* 3.4 28.8 + - + +
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Residues in contact with ARG 671 (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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670A ARG* 1.3 84.0 + - - +
672A CYS* 1.3 87.5 + - - +
673A LYS* 3.2 24.8 + - - +
675A ALA* 2.7 42.2 + - + +
676A PRO 3.9 8.3 - - - +
677A ILE* 3.3 35.0 - - - +
685A MET 5.4 1.1 - - - +
687A ARG 3.9 6.5 - - - +
688A CYS* 4.2 4.3 - - - -
689A ASP* 4.5 1.9 - - - +
724A GLU* 2.7 53.4 + - - +
726A ARG* 4.0 22.2 - - + +
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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