Contacts of the helix formed by residues 655 - 675 (chain B) in PDB entry 5UO5
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 ASP 655 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A THR* 3.0 20.5 + - - -
627A SER* 3.5 21.2 - - - -
629A LEU* 4.5 5.4 - - + -
594B MET* 4.2 0.7 - - - -
595B GLY* 4.6 1.3 - - - +
643B LEU* 3.7 34.3 - - + +
647B GLN* 6.0 0.8 - - - +
654B VAL* 1.3 79.5 - - - +
656B HIS* 1.3 59.7 + - - +
657B HIS* 2.8 19.1 + - - +
658B SER* 2.8 34.3 + - - -
659B ALA* 3.0 25.6 + - - +
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Residues in contact with HIS 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 3.7 33.5 - - + +
632A ASP* 2.9 27.5 + - - -
594B MET* 3.8 21.6 - - - +
595B GLY* 5.2 0.8 - - - +
596B THR* 3.5 26.4 + - + +
639B ASN* 5.6 0.2 - - + -
643B LEU* 5.4 1.4 - - - +
655B ASP* 1.3 70.8 - - - +
657B HIS* 1.3 70.5 + + - +
659B ALA 4.0 0.4 - - - -
660B THR* 2.7 37.9 + - - +
686B PRO* 3.9 18.6 - - + -
688B MET* 4.1 22.8 - - + +
689B SER* 4.4 0.4 - - - -
693B THR* 4.1 11.6 - - + +
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Residues in contact with HIS 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A THR* 3.9 36.6 - - + -
629A LEU* 4.2 4.9 - - + -
631A LYS* 4.4 15.9 + - + +
632A ASP* 2.8 31.2 + - - -
655B ASP* 2.8 8.7 + - - +
656B HIS* 1.3 96.9 + + - +
658B SER* 1.3 66.2 + - - +
660B THR* 3.1 5.8 + - - -
661B GLU* 3.0 26.6 + - - +
692B ILE* 4.0 31.4 + - + -
693B THR* 3.8 11.0 - - + +
694B PRO* 4.9 2.8 - - - +
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Residues in contact with SER 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A THR* 4.4 6.0 + - - -
654B VAL* 3.6 17.4 - - - +
655B ASP* 2.8 27.1 + - - -
657B HIS* 1.3 73.9 - - - +
659B ALA* 1.3 57.0 + - - +
661B GLU* 3.6 14.9 + - - +
662B SER* 2.9 37.7 + - - -
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Residues in contact with ALA 659 (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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421B VAL* 4.1 16.3 - - + +
422B GLY* 6.3 0.7 - - - -
594B MET* 3.6 24.9 - - - -
654B VAL* 3.6 20.5 - - + +
655B ASP 3.0 17.5 + - - +
656B HIS 4.2 0.7 - - - +
658B SER* 1.3 76.1 - - - +
660B THR* 1.3 58.2 + - - +
662B SER* 3.2 8.2 + - - -
663B PHE* 2.8 28.1 + - - +
801B HEM 5.8 0.9 - - + -
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Residues in contact with THR 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B VAL* 4.3 11.2 - - + -
594B MET* 5.4 1.3 - - - -
656B HIS* 2.7 22.9 + - - +
657B HIS 3.1 5.4 + - - -
659B ALA* 1.3 73.8 - - + +
661B GLU* 1.3 63.1 + - - +
663B PHE* 3.1 9.1 + - - +
664B ILE* 2.9 32.6 + - - +
684B ILE 4.4 1.1 - - - +
686B PRO* 3.5 27.6 - - + -
693B THR* 3.4 15.6 - - - -
694B PRO* 3.5 7.5 - - - +
695B VAL* 3.6 29.4 - - + +
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Residues in contact with GLU 661 (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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657B HIS 3.0 18.1 + - - +
658B SER* 3.6 14.8 + - - +
660B THR* 1.3 77.4 + - - +
662B SER* 1.3 63.8 + - - +
664B ILE* 3.3 6.5 + - - +
665B LYS* 3.2 19.4 + - - +
694B PRO* 3.9 16.1 - - + +
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Residues in contact with SER 662 (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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421B VAL 5.8 0.7 - - - -
424B ILE* 3.7 31.8 - - - +
658B SER* 2.9 22.6 + - - -
659B ALA* 3.4 11.4 - - - -
661B GLU* 1.3 77.4 + - - +
663B PHE* 1.3 57.8 + - - +
665B LYS* 3.2 8.3 + - - +
666B HIS* 2.9 26.9 + - - +
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Residues in contact with PHE 663 (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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420B CYS 3.8 8.5 - - - -
421B VAL* 3.6 35.6 + - + +
423B ARG* 3.4 36.6 - - - -
424B ILE* 5.5 1.3 - - - -
659B ALA 2.8 14.0 + - - +
660B THR* 3.1 7.8 + - - +
662B SER* 1.3 75.1 - - - +
664B ILE* 1.3 61.0 + - - +
666B HIS* 3.1 21.6 + + + +
667B MET* 2.8 56.6 + - + +
677B CYS* 4.6 1.1 - - - -
679B ALA* 3.9 15.7 - - + -
684B ILE* 3.9 27.4 - - + -
695B VAL* 3.9 8.7 - - + -
700B MET* 4.4 3.4 - - + -
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Residues in contact with ILE 664 (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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310B ASN* 4.4 4.7 - - - +
660B THR 2.9 17.6 + - - +
661B GLU* 3.5 9.4 - - - +
663B PHE* 1.3 76.4 - - - +
665B LYS* 1.3 61.9 - - - +
667B MET* 3.3 10.8 + - + +
668B GLU* 3.1 39.6 + - + +
694B PRO* 3.8 28.0 - - + +
695B VAL* 4.0 13.2 - - + -
698B GLN* 3.7 43.5 - - + +
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Residues in contact with LYS 665 (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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424B ILE* 4.6 9.6 - - + -
661B GLU* 3.2 9.3 + - + +
662B SER* 3.2 12.4 + - - +
664B ILE* 1.3 78.0 - - - +
666B HIS* 1.3 58.6 + - - +
668B GLU* 3.3 22.0 + - - +
669B ASN* 2.9 60.1 + - - +
672B ARG* 4.7 6.4 - - - +
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Residues in contact with HIS 666 (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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415B ARG* 5.1 1.7 + - + -
423B ARG* 3.3 41.3 + - + +
424B ILE* 3.5 28.0 + - + +
426B TRP* 3.7 13.4 - + - -
662B SER 2.9 13.0 + - - +
663B PHE* 3.1 27.8 + + - +
665B LYS* 1.3 74.2 - - - +
667B MET* 1.3 65.9 + - - +
669B ASN* 3.1 16.4 + - - +
670B GLU* 2.9 55.9 + - + +
677B CYS* 4.2 9.9 - - - -
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Residues in contact with MET 667 (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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308B VAL* 4.9 1.1 - - + -
317B LEU* 4.4 8.5 - - + -
663B PHE* 2.8 49.2 + - + +
664B ILE* 3.3 12.5 + - - +
666B HIS* 1.3 73.9 - - - +
668B GLU* 1.3 58.0 + - - +
670B GLU* 3.2 1.0 + - - -
671B TYR* 2.8 62.2 + - + +
677B CYS* 4.3 21.3 - - + +
679B ALA* 5.1 1.6 - - + -
698B GLN* 3.7 42.2 - - + +
699B GLU 4.0 8.7 - - - +
700B MET* 4.4 11.2 - - + -
701B LEU 5.9 0.2 - - - +
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Residues in contact with GLU 668 (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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315B VAL* 4.8 15.8 - - + +
317B LEU* 4.7 21.3 - - + -
664B ILE* 3.1 28.8 + - + +
665B LYS* 3.5 24.2 - - + +
666B HIS 3.2 0.2 - - - -
667B MET* 1.3 77.7 - - + +
669B ASN* 1.3 63.6 + - - +
671B TYR* 4.1 5.9 - - - +
672B ARG* 3.2 27.2 + - - +
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Residues in contact with ASN 669 (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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424B ILE* 4.9 10.1 - - - +
665B LYS* 2.9 47.1 + - - +
666B HIS* 3.1 17.5 + - - +
668B GLU* 1.3 76.1 - - - +
670B GLU* 1.3 60.8 + - + +
672B ARG* 2.8 36.2 + - - +
673B CYS* 2.9 33.7 + - - -
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Residues in contact with GLU 670 (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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415B ARG* 2.8 54.7 + - - +
426B TRP* 4.2 4.7 + - - -
666B HIS* 2.9 49.2 + - + +
667B MET 3.7 0.7 - - - +
669B ASN* 1.3 76.5 - - - +
671B TYR* 1.3 59.5 + - - +
673B CYS* 3.9 7.5 - - - -
674B ARG* 2.7 45.1 + - - +
675B GLY 3.2 2.3 + - - -
676B GLY 3.3 16.3 - - - +
677B CYS* 3.7 15.7 - - + -
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Residues in contact with TYR 671 (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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308B VAL* 3.6 22.9 - - + +
317B LEU* 3.5 37.7 - - + -
318B THR 3.2 37.6 - - - +
319B ASP* 3.0 24.1 + - + +
667B MET* 2.8 50.8 + - + +
668B GLU 4.1 3.6 - - - +
670B GLU* 1.3 75.9 - - - +
672B ARG* 1.3 62.8 + - - +
675B GLY* 3.2 17.8 + - - -
676B GLY* 3.6 17.9 - - - +
677B CYS* 3.5 22.0 + - + -
701B LEU* 4.5 6.1 + - - +
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Residues in contact with ARG 672 (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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665B LYS* 4.7 7.1 - - - +
668B GLU* 3.2 13.1 + - - +
669B ASN* 2.8 49.3 + - - +
670B GLU 3.2 0.6 - - - -
671B TYR* 1.3 81.3 - - - +
673B CYS* 1.3 69.4 + - - +
674B ARG 3.7 0.2 + - - -
675B GLY 4.7 0.7 + - - -
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Residues in contact with CYS 673 (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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415B ARG* 3.8 23.3 - - - -
669B ASN* 2.9 22.5 + - - +
670B GLU* 3.9 9.2 - - - -
672B ARG* 1.3 88.9 - - + +
674B ARG* 1.3 60.9 + - - +
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Residues in contact with ARG 674 (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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320B THR* 4.9 0.3 + - - -
321B LEU* 3.7 35.8 - - + +
369B GLN* 5.3 4.6 - - - +
412B HIS* 4.0 16.4 + - - -
415B ARG* 3.5 56.7 + - - +
416B ASN* 2.8 36.5 + - - +
670B GLU* 2.7 28.8 + - - +
673B CYS* 1.3 75.0 - - - +
675B GLY* 1.3 58.8 + - - +
676B GLY 3.6 3.7 + - - +
678B PRO* 4.7 4.9 - - - +
705B LEU* 3.9 18.0 - - - +
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Residues in contact with GLY 675 (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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318B THR 3.6 6.7 - - - +
319B ASP* 3.3 4.0 - - - -
320B THR* 2.7 44.4 + - - -
321B LEU* 3.0 7.3 + - - -
670B GLU 3.2 2.6 + - - -
671B TYR 3.2 14.9 + - - -
672B ARG 4.7 0.4 + - - -
673B CYS 3.9 0.4 - - - -
674B ARG* 1.3 78.5 - - - +
676B GLY* 1.3 57.1 + - - +
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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
------------------------------------------------------------
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