Contacts of the helix formed by residues 555 - 574 (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 THR 555 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B TYR* 2.5 20.7 + - - -
554B PRO* 1.3 88.4 + - - +
556B PHE* 1.3 60.5 + - - +
557B HIS* 3.7 11.7 - - + +
558B MET* 2.4 52.4 + - + +
559B ALA 2.8 11.1 + - - -
670B SER* 3.7 12.6 + - - +
672B ASP* 2.8 29.8 - - - +
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Residues in contact with PHE 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A ASN* 3.8 23.3 - - - -
465B LEU* 4.1 26.0 - - + -
468B ILE* 3.6 19.4 - - + +
469B SER* 3.7 29.8 - - - -
472B TYR* 3.2 35.1 - - + -
555B THR* 1.3 70.6 - - - +
557B HIS* 1.3 72.4 + + - +
559B ALA* 3.9 0.7 - - - +
560B SER* 2.8 44.2 + - - -
670B SER* 4.5 1.2 + - - +
672B ASP* 4.2 15.7 - - + -
673B TRP* 3.9 40.2 - + + +
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Residues in contact with HIS 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ASN* 5.2 10.1 - - - -
528A ASN* 3.4 26.1 + - - +
531A ASN* 5.7 7.2 - - + -
555B THR* 2.8 12.4 + - + +
556B PHE* 1.3 87.6 - + - +
558B MET* 1.3 52.9 + - + +
560B SER* 3.3 4.9 - - - -
561B PHE* 2.8 33.5 + - - +
672B ASP* 3.9 24.7 - - + +
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Residues in contact with MET 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B LEU* 3.1 17.7 - - + +
554B PRO* 4.1 23.1 - - + -
555B THR* 2.4 45.7 + - + +
557B HIS* 1.3 74.4 - - + +
559B ALA* 1.3 56.3 + - - +
561B PHE* 2.8 23.5 + - - +
562B PHE* 2.8 13.9 + - - +
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Residues in contact with ALA 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ILE* 4.4 7.4 - - + -
472B TYR* 3.6 31.9 - - + -
549B ALA* 3.7 22.1 - - - +
550B ALA* 3.7 6.5 - - - -
553B LEU* 3.2 14.8 - - + +
555B THR 2.8 8.8 + - - +
556B PHE 4.1 1.8 - - - +
558B MET* 1.3 72.5 - - - +
560B SER* 1.3 51.2 + - - +
562B PHE* 3.8 1.8 - - - +
563B SER* 2.7 43.1 + - - -
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Residues in contact with SER 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ILE* 4.9 4.3 - - - +
465B LEU* 3.7 27.2 - - - +
468B ILE* 4.4 12.0 - - - +
556B PHE* 2.8 34.4 + - - -
557B HIS* 3.3 6.1 - - - -
559B ALA* 1.3 74.1 - - - +
561B PHE* 1.3 58.2 + - - +
563B SER* 4.4 5.8 - - - -
564B ASN* 3.0 28.6 + - - +
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Residues in contact with PHE 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B LEU* 5.7 0.7 - - + -
557B HIS 2.8 12.6 + - - +
558B MET* 2.8 12.2 + - - +
560B SER* 1.3 77.0 - - - +
562B PHE* 1.3 95.0 + + + +
563B SER 2.9 1.6 - - - -
564B ASN* 2.8 15.8 + - + +
565B ALA* 2.8 34.3 + - + -
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Residues in contact with PHE 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ALA* 4.0 24.7 - - + -
552B LEU* 5.6 7.4 - - + -
553B LEU* 3.7 41.3 - - + -
558B MET 2.8 6.2 + - - +
559B ALA 3.8 2.5 - - - +
561B PHE* 1.3 89.9 - + + +
563B SER* 1.3 59.5 + - - +
565B ALA* 3.4 2.1 + - - +
566B LEU* 2.8 58.7 + - + +
657B LEU* 5.6 8.3 - - + -
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Residues in contact with SER 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ILE* 3.6 29.0 - - - +
468B ILE* 4.2 4.7 - - - +
545B MET* 3.5 21.0 - - - +
546B ALA* 4.8 0.7 - - - -
549B ALA* 3.3 20.1 - - - +
559B ALA 2.7 25.9 + - - -
560B SER* 4.4 1.8 - - - -
561B PHE 2.9 0.4 + - - -
562B PHE* 1.3 76.2 - - - +
564B ASN* 1.3 59.6 + - - -
566B LEU* 2.9 6.8 + - - +
567B TYR* 2.8 28.8 + - - +
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Residues in contact with ASN 564 (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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432A TYR* 5.2 9.7 + - - +
461B PHE* 4.7 18.1 - - - +
464B ILE* 4.6 19.8 - - - +
465B LEU* 5.1 7.5 - - - +
560B SER* 3.0 32.4 + - - +
561B PHE* 2.8 10.8 + - + +
563B SER* 1.3 75.1 - - - +
565B ALA* 1.3 54.6 + - - +
567B TYR* 4.0 20.0 - - + +
568B ASN* 2.8 31.4 + - - +
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Residues in contact with ALA 565 (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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399A PHE* 4.0 10.2 - - + -
561B PHE* 2.8 48.7 + - + +
562B PHE 3.6 3.6 - - - +
564B ASN* 1.3 70.3 - - - +
566B LEU* 1.3 52.2 + - - +
567B TYR 3.1 1.3 - - - -
568B ASN* 3.7 4.4 - - - +
569B SER* 2.7 39.3 + - - -
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Residues in contact with LEU 566 (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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545B MET* 3.7 31.9 - - + -
562B PHE* 2.8 53.2 + - + +
563B SER 3.4 3.8 - - - +
565B ALA* 1.3 67.2 - - - +
567B TYR* 1.3 55.9 + - - +
569B SER* 2.3 25.0 + - - +
570B PHE* 3.3 44.5 + - + -
654B PHE* 4.6 9.0 - - + -
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Residues in contact with TYR 567 (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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457B ALA 2.7 23.6 + - - -
458B LEU* 4.1 7.1 + - - -
460B PRO* 3.2 38.4 - - + -
461B PHE* 4.2 18.4 - + + +
464B ILE* 5.3 7.2 - - + -
545B MET* 5.2 7.0 - - + -
563B SER 2.8 18.9 + - - +
564B ASN* 4.0 20.9 - - - +
566B LEU* 1.3 70.5 - - - +
568B ASN* 1.3 80.5 + - + +
569B SER 2.9 1.1 - - - -
570B PHE* 2.8 19.2 + - - +
571B TYR* 2.8 35.0 + + - +
595B PHE* 5.3 5.2 - + + -
596B LEU* 3.8 23.6 - - + -
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Residues in contact with ASN 568 (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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396A MET* 4.3 22.2 - - - +
399A PHE* 3.6 26.5 - - + -
400A LEU* 5.8 0.8 - - - +
425A GLN* 3.3 25.8 + - - +
564B ASN 2.8 24.3 + - - +
565B ALA* 4.0 4.7 - - - +
567B TYR* 1.3 81.3 - - + +
569B SER* 1.3 59.5 - - - +
571B TYR* 3.7 15.5 + - - +
572B LEU* 3.4 26.7 + - - +
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Residues in contact with SER 569 (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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399A PHE* 3.8 14.5 - - - -
403A PHE* 3.2 38.1 - - - -
565B ALA 2.7 18.4 + - - -
566B LEU* 2.3 36.8 + - - +
568B ASN* 1.3 73.3 - - - +
570B PHE* 1.3 60.1 + - - -
573B ALA 3.7 5.2 + - - -
590B ILE* 3.7 16.1 - - - +
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Residues in contact with PHE 570 (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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566B LEU* 3.3 36.5 + - + -
567B TYR* 2.8 14.1 + - - +
569B SER* 1.3 76.4 + - - +
571B TYR* 1.3 60.1 + - - +
573B ALA* 3.4 2.5 + - - +
574B GLY* 2.9 22.2 + - - -
590B ILE* 4.2 13.5 - - + -
593B VAL* 3.7 36.3 - - + -
594B SER* 3.1 42.7 + - - +
595B PHE* 3.4 37.9 - + - -
596B LEU* 3.6 12.9 - - + +
654B PHE* 4.2 12.8 - + - -
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Residues in contact with TYR 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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424A TYR* 4.4 10.6 - + - -
425A GLN* 3.1 40.8 + - - -
453B PHE* 4.0 17.1 - + + -
454B MET* 6.3 2.7 - - + -
457B ALA* 4.1 9.9 - - + -
567B TYR* 2.8 51.1 + + - +
568B ASN* 3.7 10.2 + - - -
569B SER 3.4 0.2 - - - -
570B PHE* 1.3 71.1 - - - +
572B LEU* 1.3 69.2 + - + +
574B GLY* 2.8 23.3 + - - +
577B MET* 3.0 38.9 - - + +
596B LEU* 3.5 16.6 - - + -
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Residues in contact with LEU 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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399A PHE* 4.1 11.0 - - + +
400A LEU* 3.7 33.9 - - + -
403A PHE* 3.5 49.8 - - + -
404A VAL* 6.0 0.9 - - + -
425A GLN* 4.4 16.8 - - + +
568B ASN* 3.4 21.7 + - - +
570B PHE 3.4 0.2 - - - -
571B TYR* 1.3 81.0 - - + +
573B ALA* 1.3 65.6 + - - +
574B GLY 2.9 4.5 - - - +
577B MET* 5.6 7.0 - - + -
578B ILE* 2.8 38.8 + - + +
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Residues in contact with ALA 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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403A PHE* 4.3 4.9 - - + -
569B SER 3.7 12.3 + - - +
570B PHE* 3.4 10.5 + - - +
572B LEU* 1.3 77.8 - - - +
574B GLY* 1.3 64.4 + - - +
575B GLY* 3.5 2.3 + - - -
578B ILE* 4.5 4.6 - - - +
580B LEU* 4.4 6.8 - - - +
583B LEU* 5.2 6.4 - - - +
590B ILE* 3.9 15.7 - - + -
591B SER* 3.7 38.8 - - - -
594B SER* 4.1 7.6 - - - -
597B ARG* 4.1 5.3 - - - +
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Residues in contact with GLY 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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453B PHE* 4.2 10.5 - - - -
570B PHE 2.9 10.2 + - - -
571B TYR* 2.8 22.2 + - - +
572B LEU 2.9 14.4 - - - +
573B ALA* 1.3 70.0 - - - +
575B GLY* 1.3 69.4 + - - +
576B PHE 3.6 1.3 - - - -
577B MET 4.1 0.9 + - - -
578B ILE* 3.6 5.7 + - - +
596B LEU 4.8 0.2 - - - -
597B ARG* 3.6 22.8 - - - +
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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) + - + + + + + -
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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