Contacts of the helix formed by residues 641 - 665 (chain B) in PDB entry 5DO7
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 641 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B LEU* 4.5 22.0 - - + +
533B LEU* 5.9 4.3 - - + -
610B ARG* 6.4 0.2 - - - -
639B PRO* 2.8 3.4 + - + +
640B LEU* 1.3 84.0 - - + +
642B ALA* 1.3 66.1 + - - +
643B ILE 3.2 2.2 - - - -
644B TYR* 3.9 26.2 + + + +
645B LEU* 3.6 18.4 - - + +
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Residues in contact with ALA 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B TYR* 4.6 5.4 - - + -
639B PRO* 2.8 39.9 + - + +
641B TYR* 1.3 78.5 - - - +
643B ILE* 1.3 56.0 + - - +
645B LEU* 2.8 36.4 + - - +
646B ILE* 3.1 21.6 + - + +
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Residues in contact with ILE 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B LEU* 4.8 5.6 - - + -
598B TRP* 3.5 52.0 - - + +
601B GLU* 4.4 13.7 - - + +
602B GLY* 3.5 30.1 - - - +
605B LYS* 4.7 7.4 - - + -
638B TYR* 4.9 5.4 - - + +
639B PRO 3.8 18.8 - - - +
640B LEU 4.0 11.2 - - - +
641B TYR 3.2 1.4 - - - -
642B ALA* 1.3 75.6 - - + +
644B TYR* 1.3 62.2 + - + +
646B ILE* 2.8 34.1 + - + +
647B VAL* 2.8 17.1 + - + +
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Residues in contact with TYR 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B LEU* 2.6 58.9 + - + +
533B LEU* 4.0 12.6 - - + -
534B LEU* 3.5 40.3 - - + +
537B LEU* 3.8 24.3 - - + +
602B GLY* 6.6 0.2 - - - -
606B ILE* 4.2 6.1 - - + +
640B LEU 3.7 20.6 - - - -
641B TYR* 4.0 29.4 - + + +
643B ILE* 1.3 78.3 - - + +
645B LEU* 1.3 64.4 + - + +
647B VAL* 3.4 8.6 + - - +
648B ILE* 2.8 33.5 + - - +
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Residues in contact with LEU 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B TYR* 3.6 16.8 - - + +
642B ALA* 2.8 15.8 + - - +
644B TYR* 1.3 82.8 - - + +
646B ILE* 1.3 57.8 + - + +
648B ILE* 3.0 16.7 - - + +
649B GLY* 2.8 28.6 + - - -
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Residues in contact with ILE 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592B LYS* 4.1 13.2 - - + +
598B TRP* 3.1 63.7 - - + +
638B TYR* 4.8 9.6 - - + -
642B ALA* 3.1 18.0 + - + +
643B ILE* 2.8 26.8 + - + +
645B LEU* 1.3 77.6 - - + +
647B VAL* 1.3 57.3 + - - +
649B GLY* 3.6 1.4 - - - -
650B LEU* 2.8 30.1 + - + +
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Residues in contact with VAL 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B LEU* 4.3 12.1 - - + -
537B LEU* 3.3 42.2 - - + +
538B VAL* 4.4 6.1 - - + +
541B CYS* 4.3 2.9 - - + -
595B PHE* 5.1 8.1 - - + -
598B TRP* 3.7 30.3 - - + -
643B ILE* 2.8 26.0 + - + +
644B TYR* 3.5 10.3 - - - +
646B ILE* 1.3 69.8 - - - +
648B ILE* 1.3 64.1 + - - +
649B GLY 3.0 1.6 - - - -
650B LEU* 3.3 13.0 - - + +
651B SER* 2.8 31.9 + - - -
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Residues in contact with ILE 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B LEU* 4.1 21.8 - - + -
644B TYR 2.8 21.6 + - - +
645B LEU* 3.0 34.1 - - + +
647B VAL* 1.3 75.3 - - - +
649B GLY* 1.3 60.2 + - - +
651B SER* 3.4 19.8 - - - -
652B GLY* 3.4 5.7 + - - -
655B MET* 4.8 4.5 - - + +
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Residues in contact with GLY 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B LEU 2.8 16.7 + - - -
646B ILE* 3.6 1.8 - - - -
648B ILE* 1.3 77.5 - - - +
650B LEU* 1.3 57.4 - - - +
652B GLY* 2.8 26.3 + - - -
653B GLY 3.3 3.3 + - - -
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Residues in contact with LEU 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B CYS* 4.0 8.7 - - - -
592B LYS 5.0 0.4 - - - +
593B VAL* 3.0 59.5 - - + +
595B PHE* 3.8 21.3 - - + +
598B TRP* 3.8 16.6 - - + -
646B ILE* 2.8 22.2 + - + +
647B VAL* 3.3 13.7 - - - +
649B GLY* 1.3 71.0 - - - +
651B SER* 1.3 69.2 + - - +
653B GLY* 2.8 14.4 + - - -
654B PHE* 3.1 23.6 + - + -
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Residues in contact with SER 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B LEU* 4.4 2.4 + - - +
540B PHE* 4.2 7.7 - - - -
541B CYS* 3.3 30.3 + - - +
544B ILE* 4.0 11.1 - - - +
647B VAL 2.8 19.2 + - - -
648B ILE* 3.4 18.3 - - - +
650B LEU* 1.3 68.2 - - - +
652B GLY* 1.3 65.5 + - - +
654B PHE* 2.8 9.2 + - - +
655B MET* 2.8 40.0 + - - +
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Residues in contact with GLY 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B ILE 3.4 6.5 + - - -
649B GLY* 2.8 16.5 + - - -
651B SER* 1.3 74.1 - - - +
653B GLY* 1.3 51.6 + - - -
655B MET* 3.1 15.1 + - - +
656B VAL* 2.8 43.9 + - - +
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Residues in contact with GLY 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B GLY 3.3 4.9 + - - -
650B LEU* 2.8 15.6 + - - -
652B GLY* 1.3 71.0 - - - +
654B PHE* 1.3 60.0 + - - -
656B VAL* 3.4 7.8 + - - +
657B LEU* 3.1 21.8 + - - +
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Residues in contact with PHE 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B CYS* 3.7 25.6 - - - -
544B ILE* 3.6 17.7 - - + +
545B MET* 3.5 43.5 - - + -
548B ALA* 3.6 7.7 - - + +
566B LEU* 4.6 12.1 - - + -
570B PHE* 4.2 25.8 - + - -
593B VAL* 5.9 1.1 - - + -
595B PHE* 4.7 3.4 - + - -
650B LEU* 3.1 40.0 + - + -
651B SER* 2.8 7.9 + - - +
653B GLY* 1.3 69.9 - - - -
655B MET* 1.3 53.7 + - - +
657B LEU* 2.8 15.5 + - + +
658B TYR* 2.8 31.5 + - - +
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Residues in contact with MET 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B PHE* 2.8 34.6 - - + -
497B ILE* 4.0 14.6 - - + -
540B PHE* 4.7 6.1 - - + -
544B ILE* 3.3 29.9 - - + +
648B ILE* 4.8 4.9 - - + +
651B SER* 2.8 33.0 + - - +
652B GLY* 3.2 19.3 - - - +
654B PHE* 1.3 74.4 - - - +
656B VAL* 1.3 58.9 + - + +
658B TYR* 3.1 1.5 + - - -
659B TYR 2.8 25.3 + - - -
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Residues in contact with VAL 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B GLY* 2.8 23.8 + - - +
653B GLY* 3.6 7.4 - - - +
655B MET* 1.3 74.5 - - + +
657B LEU* 1.3 61.6 + - + +
659B TYR* 3.8 9.8 - - + +
660B VAL* 2.8 33.0 + - + +
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Residues in contact with LEU 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ALA* 3.9 19.3 - - + -
549B ALA* 5.0 1.8 - - - +
552B LEU* 3.4 31.4 - - + -
562B PHE* 5.6 8.3 - - + -
653B GLY 3.1 13.4 + - - +
654B PHE* 2.8 17.6 + - + +
656B VAL* 1.3 78.5 - - + +
658B TYR* 1.3 53.2 + - - +
660B VAL* 3.0 10.2 - - + +
661B SER* 2.6 38.1 + - - +
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Residues in contact with TYR 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B CYS* 4.3 5.8 - - - -
477B MET* 4.8 0.2 - - - +
492B TYR* 4.1 4.3 - - - -
493B PHE* 3.3 30.7 - + + -
496B LYS* 2.9 33.4 + - + -
497B ILE* 4.1 14.8 - - + -
544B ILE* 4.9 2.9 - - + -
547B LEU* 3.3 53.6 - - + +
548B ALA* 3.5 11.1 - - - +
551B ALA* 3.4 20.9 - - + -
654B PHE 2.8 14.5 + - - +
655B MET* 3.4 10.3 - - - +
657B LEU* 1.3 69.9 - - - +
659B TYR* 1.3 60.1 + - - +
661B SER* 3.1 1.5 + - - -
662B LEU* 2.8 60.8 + - + +
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Residues in contact with TYR 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B THR* 3.1 26.0 - - + -
489B THR* 3.8 12.5 + - - +
491B PRO* 5.4 0.2 - - + -
493B PHE* 2.9 48.5 - + + -
494B PHE* 5.9 2.2 - + - -
655B MET 2.8 13.3 + - - +
656B VAL* 3.9 9.4 - - + +
658B TYR* 1.3 70.8 - - - +
660B VAL* 1.3 61.3 + - + +
662B LEU* 4.0 2.6 - - - +
663B ARG* 2.5 75.9 + - - +
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Residues in contact with VAL 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B VAL* 2.8 25.9 + - + +
657B LEU* 3.0 29.2 - - + +
659B TYR* 1.3 75.1 - - + +
661B SER* 1.3 80.8 - - - +
663B ARG* 2.8 4.9 + - - -
664B PHE* 2.8 50.5 + - + -
665B ILE* 6.4 0.4 - - + -
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Residues in contact with SER 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ALA 4.5 1.2 + - - -
551B ALA* 4.1 7.5 - - - +
552B LEU* 2.8 53.7 - - - +
657B LEU* 2.6 29.4 + - - +
658B TYR* 3.1 3.3 + - - -
660B VAL* 1.3 75.4 - - - +
662B LEU* 1.3 51.9 + - - +
665B ILE* 2.4 48.9 + - - +
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Residues in contact with LEU 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B MET* 4.8 17.9 - - + -
488B THR* 4.0 18.3 + - + +
492B TYR* 4.0 19.5 - - + -
493B PHE* 4.1 14.1 - - + +
551B ALA* 3.7 22.9 - - + +
658B TYR* 2.8 55.1 + - + +
659B TYR 4.0 0.9 - - - +
661B SER* 1.3 76.8 - - - +
663B ARG* 1.3 64.5 + - - +
664B PHE 4.1 0.2 - - - -
665B ILE 3.2 17.2 + - - +
667B GLN* 5.6 5.6 - - + -
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Residues in contact with ARG 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B THR* 4.0 22.9 + - - -
489B THR* 2.6 46.3 + - - +
659B TYR* 2.5 57.3 + - - +
660B VAL* 2.8 9.7 + - - +
662B LEU* 1.3 73.8 - - - +
664B PHE* 1.3 75.9 + - + +
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Residues in contact with PHE 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B VAL* 2.8 35.2 + - + +
662B LEU 4.1 0.2 - - - -
663B ARG* 1.3 96.1 - - + +
665B ILE* 1.3 73.7 + - + +
666B LYS 4.1 1.0 + - - -
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Residues in contact with ILE 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B ALA 4.6 3.6 - - - +
552B LEU* 4.2 20.4 - - + +
660B VAL* 6.4 0.7 - - + -
661B SER* 2.4 42.4 + - - +
662B LEU* 3.2 14.1 + - - +
664B PHE* 1.3 88.6 - - + +
666B LYS* 1.3 102.4 + - + +
667B GLN 3.8 0.5 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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