Contacts of the helix formed by residues 647 - 663 (chain B) in PDB entry 6PUO
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 647 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620B ASP* 4.4 8.8 - - - +
645B SER* 4.2 3.4 + - - -
646B GLN* 1.3 79.2 + - + +
648B CYS* 1.3 64.2 + - - +
649B ILE 3.4 2.0 + - - -
650B ALA* 3.8 7.4 + - + +
651B ALA* 3.4 17.0 + - - +
707B ARG* 3.5 27.9 + - - +
709B SER* 4.0 14.0 - - - -
711B ALA* 4.3 7.4 - - - +
712B TRP* 4.2 17.7 + - - -
1122B LEU* 4.2 11.2 - - + -
1125B GLU* 3.3 12.6 - - - +
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Residues in contact with CYS 648 (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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642B TRP* 3.3 33.8 + - + +
645B SER* 4.3 8.1 - - - +
646B GLN 3.6 2.9 + - - +
647B ASP* 1.3 72.2 - - - +
649B ILE* 1.3 59.0 + - - -
651B ALA* 3.3 3.7 + - - -
652B ALA* 2.9 27.0 + - - +
689B VAL* 3.8 27.8 - - - -
1125B GLU* 2.8 29.5 + - - -
1126B ILE* 6.1 0.2 - - - -
1129B LYS* 3.6 31.9 - - + -
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Residues in contact with ILE 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B ASP 3.4 0.8 - - - -
648B CYS* 1.3 75.2 - - - +
650B ALA* 1.3 65.1 + - - +
652B ALA* 3.3 5.9 + - - +
653B LEU* 3.0 30.8 + - + +
686B ALA* 4.7 15.7 - - + +
689B VAL* 3.8 33.7 - - + -
690B PHE* 4.3 22.9 - - + -
693B CYS* 5.4 1.8 - - + -
704B LEU* 3.8 31.0 - - + -
705B LEU* 6.2 1.6 - - + -
717B CYS* 3.7 19.5 - - - -
729B PHE* 4.7 10.1 - - + -
1125B GLU* 3.6 9.6 + - + +
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Residues in contact with ALA 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B ASP* 3.8 12.6 + - + +
649B ILE* 1.3 78.3 - - - +
651B ALA* 1.3 57.4 + - - +
653B LEU* 3.4 3.5 + - - +
654B ALA* 2.9 31.0 + - - +
707B ARG* 6.2 0.2 - - - +
709B SER* 4.7 10.3 - - - +
712B TRP* 4.2 22.2 - - + -
716B THR 6.3 0.2 - - - -
717B CYS* 3.9 21.8 - - + -
720B LEU* 4.0 10.7 - - + +
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Residues in contact with ALA 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B LEU* 4.5 7.2 - - + -
642B TRP* 4.2 13.9 - - + +
645B SER* 4.2 10.8 - - - +
647B ASP* 3.4 13.4 + - - +
648B CYS* 3.3 11.2 + - - +
649B ILE 3.2 0.6 - - - -
650B ALA* 1.3 78.1 - - - +
652B ALA* 1.3 56.3 + - - +
654B ALA* 3.4 2.1 + - - +
655B CYS* 3.0 34.5 + - - -
712B TRP* 3.6 27.7 - - + +
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Residues in contact with ALA 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B TRP* 4.1 15.0 - - + +
648B CYS 2.9 17.1 + - - +
649B ILE 3.8 0.4 - - - +
651B ALA* 1.3 76.9 - - - +
653B LEU* 1.3 60.2 + - - +
655B CYS* 3.4 2.8 + - - +
656B SER* 3.0 28.2 + - - -
682B TYR* 3.7 39.2 - - + +
685B ARG* 4.8 0.2 - - + -
686B ALA* 3.8 19.7 - - + +
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Residues in contact with LEU 653 (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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649B ILE* 3.0 16.8 + - + +
650B ALA 3.9 3.8 - - - +
652B ALA* 1.3 78.8 - - - +
654B ALA* 1.3 58.1 + - - +
656B SER* 2.8 20.2 + - - +
657B LYS* 3.0 13.9 + - - +
683B GLU* 5.2 4.5 - - - -
686B ALA* 3.9 20.6 - - + -
717B CYS* 3.5 41.5 - - - +
720B LEU* 4.1 17.0 - - + +
721B ALA* 4.1 17.0 - - + +
724B ALA* 4.9 1.4 - - - +
726B ASP* 3.7 20.9 - - - +
729B PHE* 4.2 24.5 - - + -
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Residues in contact with ALA 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B LEU* 4.2 12.7 - - + +
650B ALA 2.9 18.3 + - - +
651B ALA 3.9 1.1 - - - +
653B LEU* 1.3 76.1 - - - +
655B CYS* 1.3 58.7 + - - +
657B LYS* 3.3 6.9 + - - +
658B ILE* 2.9 34.6 + - + +
712B TRP* 3.7 33.9 - - + -
720B LEU* 4.2 14.5 - - + +
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Residues in contact with CYS 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B LEU* 4.0 24.7 - - - -
627B ILE* 5.8 3.1 - - - -
630B ILE* 3.7 33.6 - - + +
651B ALA 3.0 21.4 + - - +
652B ALA 3.8 4.0 - - - +
654B ALA* 1.3 74.6 - - - +
656B SER* 1.3 63.7 + - - +
658B ILE* 3.4 8.9 + - - +
659B LEU* 3.0 31.3 + - + +
682B TYR* 4.3 20.9 - - + -
712B TRP* 5.2 7.0 - - - -
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Residues in contact with SER 656 (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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652B ALA 3.0 16.2 + - - -
653B LEU* 2.8 11.4 + - - -
655B CYS* 1.3 77.0 - - - +
657B LYS* 1.3 60.0 + - - +
660B LYS* 2.9 34.0 + - - +
679B ALA* 3.8 32.0 - - - +
682B TYR* 4.7 1.7 - - - +
683B GLU* 4.5 7.2 - - - -
724B ALA* 4.0 3.3 - - - +
726B ASP* 2.9 29.3 + - - -
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Residues in contact with LYS 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B LEU 3.6 18.9 + - - -
569B LEU* 3.6 32.5 - - + +
570B GLY* 4.7 3.0 - - - +
572B PHE* 5.8 0.9 - - + -
653B LEU 3.0 12.3 + - - +
654B ALA* 3.6 7.4 - - - +
656B SER* 1.3 81.8 + - - +
658B ILE* 1.3 57.4 + - - +
660B LYS* 3.8 2.7 - - + +
661B GLU* 3.0 46.2 + - - +
720B LEU* 4.9 9.6 - - + +
723B GLU* 4.3 21.2 + - + +
724B ALA* 3.8 31.8 - - + +
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Residues in contact with ILE 658 (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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565B LEU* 4.4 19.7 - - + -
568B LEU* 4.7 19.9 - - + +
569B LEU* 3.8 28.7 - - + -
627B ILE* 4.9 18.4 - - + -
630B ILE* 4.4 18.4 - - + -
631B VAL* 4.4 15.3 - - + -
654B ALA* 2.9 23.7 + - + +
655B CYS* 3.8 8.7 - - - +
656B SER 3.3 0.2 - - - -
657B LYS* 1.3 76.0 - - - +
659B LEU* 1.3 60.1 + - + +
661B GLU* 3.2 6.3 + - - +
662B LEU* 2.9 31.6 + - + +
712B TRP* 5.5 2.9 - - + -
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Residues in contact with LEU 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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630B ILE* 3.8 39.9 - - + +
633B ASN* 5.7 0.9 - - - +
655B CYS 3.0 21.2 + - - +
658B ILE* 1.3 78.4 - - + +
660B LYS* 1.3 58.1 + - - +
662B LEU* 3.9 9.3 - - + +
663B SER* 2.9 32.6 + - - -
675B MET* 4.0 30.2 - - + +
678B LEU* 3.7 37.5 - - + +
679B ALA* 3.7 26.7 - - + +
682B TYR* 5.2 2.5 - - + -
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Residues in contact with LYS 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B SER* 2.9 22.7 + - - +
657B LYS* 3.9 5.2 - - + +
659B LEU* 1.3 77.2 - - - +
661B GLU* 1.3 62.1 + - - +
663B SER* 3.9 7.5 + - - -
664B LYS* 3.9 21.5 + - + +
676B LEU* 4.5 18.8 - - + -
679B ALA* 4.2 21.7 + - - +
680B GLU* 5.4 3.8 - - - +
683B GLU* 5.0 3.8 + - - -
724B ALA* 3.4 23.3 + - + +
725B LYS* 4.7 9.4 + - + -
726B ASP* 3.3 25.2 + - - +
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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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567B GLU 5.2 2.0 - - - +
568B LEU* 3.6 41.1 - - + +
657B LYS* 3.0 34.6 + - - +
658B ILE* 3.6 4.9 - - - +
660B LYS* 1.3 78.5 - - - +
662B LEU* 1.3 62.7 + - - +
663B SER 3.4 0.2 + - - -
664B LYS* 3.3 40.0 + - - +
665B GLU* 4.3 14.3 - - - +
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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
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531B LEU* 4.1 33.5 - - + +
532B PHE* 5.1 10.3 - - + +
535B LYS* 4.8 7.0 - - + -
568B LEU* 3.7 33.4 - - + -
631B VAL* 4.2 29.6 - - + +
658B ILE* 2.9 17.1 + - + +
659B LEU* 3.3 11.2 + - + +
661B GLU* 1.3 78.4 - - - +
663B SER* 1.3 63.0 + - - +
664B LYS 3.2 1.4 + - - -
665B GLU* 3.6 10.8 + - - +
666B GLU* 4.2 5.5 + - - +
675B MET* 4.0 29.3 - - + +
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Residues in contact with SER 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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659B LEU 2.9 17.1 + - - -
660B LYS* 3.9 6.3 + - - -
661B GLU 3.3 0.4 - - - -
662B LEU* 1.3 76.3 - - - +
664B LYS* 1.3 61.9 + - - +
665B GLU 3.4 0.4 - - - -
666B GLU* 4.4 7.1 + - - -
672B SER* 3.2 42.4 + - - -
675B MET* 4.1 17.0 - - - -
676B LEU* 4.2 18.5 - - - +
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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) + - + + + + + -
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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