Contacts of the helix formed by residues 646 - 665 (chain B) in PDB entry 5OF4
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 ILE 646 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644B PHE* 2.9 13.7 + - + +
645B GLN* 1.3 87.9 - - + +
647B ARG* 1.3 74.0 + - - +
648B GLU* 3.0 13.0 + - - +
649B ASN* 4.0 4.5 + - - +
650B ASP* 3.9 11.1 + - + +
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Residues in contact with ARG 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ASP* 4.5 6.3 + - - +
466B ILE* 4.4 17.5 - - - +
637B LEU* 3.7 16.0 - - + +
640B LEU* 3.8 33.6 - - + +
641B ARG* 4.9 2.0 - - - +
644B PHE* 3.3 63.0 - - + +
645B GLN 3.4 2.7 - - - +
646B ILE* 1.3 98.5 - - - +
648B GLU* 1.3 63.7 + - + +
649B ASN 3.1 1.1 - - - -
650B ASP* 3.0 43.1 + - - -
651B PHE* 3.0 21.1 + - + +
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Residues in contact with GLU 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 3.4 38.6 - - + +
638B GLU* 3.9 19.0 - - - +
641B ARG* 4.2 19.3 + - + +
645B GLN 4.0 16.7 - - - +
646B ILE 3.0 4.4 + - - +
647B ARG* 1.3 76.9 - - + +
649B ASN* 1.3 58.3 + - + +
652B LEU* 3.7 9.7 - - - +
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Residues in contact with ASN 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B ILE 4.0 3.5 + - - +
648B GLU* 1.3 77.3 - - - +
650B ASP* 1.3 60.7 + - - +
651B PHE 3.4 2.0 - - - -
652B LEU* 3.4 18.1 + - - +
653B THR* 3.0 34.6 + - - -
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Residues in contact with ASP 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ILE* 3.3 27.8 - - - +
646B ILE* 3.9 9.9 + - + +
647B ARG* 3.0 35.1 + - - +
649B ASN* 1.3 76.1 - - - +
651B PHE* 1.3 61.9 + - - +
653B THR* 3.3 6.2 + - - -
654B PHE* 2.9 24.1 + - - +
690B ARG* 2.4 36.2 + - - +
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Residues in contact with PHE 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ASP* 3.3 24.0 - - - -
466B ILE* 3.9 16.2 - - + -
469B LYS* 4.1 20.4 - - + -
636B ARG* 3.3 34.8 - - + -
637B LEU* 3.7 29.4 - - + -
640B LEU* 5.1 10.8 - - + -
647B ARG* 3.0 17.0 + - + +
650B ASP* 1.3 76.7 + - - +
652B LEU* 1.3 64.9 + - + +
654B PHE* 3.4 32.7 - + - +
655B ASP* 2.9 39.0 + - + +
658B ARG* 4.4 2.9 - - - -
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Residues in contact with LEU 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B TYR* 4.7 7.5 - - + +
626B VAL* 4.5 10.3 - - + +
628B THR* 3.8 30.3 - - + +
633B LEU* 4.1 26.2 - - + -
637B LEU* 4.2 17.0 - - + -
647B ARG 4.5 0.2 + - - -
648B GLU 3.7 22.2 - - - +
649B ASN* 3.4 18.8 + - - +
650B ASP 3.2 0.4 - - - -
651B PHE* 1.3 79.0 - - + +
653B THR* 1.3 64.3 + - - +
655B ASP* 2.7 25.4 - - - +
656B ALA* 3.0 14.0 + - - +
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Residues in contact with THR 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B ASN* 3.0 24.4 + - - -
650B ASP* 3.8 7.1 - - - -
652B LEU* 1.3 76.7 - - - +
654B PHE* 1.3 56.2 + - - +
656B ALA* 3.5 6.0 + - - +
657B MET* 3.0 35.0 + - + +
686B ARG* 6.1 4.3 - - - -
687B GLY* 4.3 20.2 - - - -
690B ARG* 3.6 26.7 - - - +
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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
----------------------------------------------------------
237B HIS 5.4 1.3 - - - -
461B LEU* 3.9 25.6 - - + -
463B PRO* 3.5 31.2 - - + -
466B ILE* 3.7 38.1 - - + -
469B LYS* 6.2 0.4 - - + -
650B ASP 2.9 14.3 + - - +
651B PHE* 3.4 37.2 - + - +
652B LEU 3.2 0.4 - - - -
653B THR* 1.3 77.0 - - - +
655B ASP* 1.3 60.8 + - - +
657B MET* 3.2 4.0 + - - +
658B ARG* 3.0 64.0 + - + +
690B ARG* 4.6 9.8 - - - +
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Residues in contact with ASP 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B TYR* 5.2 0.2 - - - -
626B VAL* 3.4 33.7 + - - +
636B ARG* 5.3 3.6 + - - -
651B PHE* 2.9 25.7 + - + +
652B LEU* 2.7 38.2 - - - +
654B PHE* 1.3 78.6 - - + +
656B ALA* 1.3 60.5 + - - +
658B ARG* 3.4 36.4 + - - +
659B HIS* 2.4 38.4 + - + -
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Residues in contact with ALA 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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623B VAL* 4.4 7.6 - - + -
624B PRO* 3.2 32.7 - - - +
625B TYR* 3.8 17.0 - - + +
652B LEU 3.0 15.1 + - - +
653B THR* 3.6 7.4 - - - +
655B ASP* 1.3 83.5 + - - +
657B MET* 1.3 70.1 + - + +
660B ALA* 3.0 22.5 + - - +
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Residues in contact with MET 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B THR* 4.3 0.2 - - - +
463B PRO* 5.4 4.5 - - + -
623B VAL* 5.1 2.2 - - + -
653B THR* 3.0 27.9 + - + +
654B PHE* 3.2 5.4 + - - +
656B ALA* 1.3 93.5 - - + +
658B ARG* 1.3 65.1 + - - +
660B ALA* 3.5 5.9 - - - +
661B ALA* 2.9 26.3 + - - +
683B ARG 5.8 0.2 - - - +
684B PHE* 3.5 29.8 - - + -
687B GLY* 3.4 31.9 - - - +
688B ASP* 3.5 19.5 - - - +
690B ARG* 4.2 7.9 - - - -
691B GLY* 3.7 24.9 - - - +
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Residues in contact with ARG 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B HIS* 3.7 26.6 + - + +
238B ASN* 3.9 14.5 - - - +
240B ASP* 2.8 47.4 + - - +
241B ASN* 3.0 20.7 + - - +
460B THR* 3.4 18.9 - - + +
461B LEU* 5.8 2.7 - - + -
636B ARG* 3.8 3.6 - - - +
651B PHE* 4.4 0.6 - - - -
654B PHE* 3.0 46.7 + - + +
655B ASP* 3.4 34.6 + - - +
657B MET* 1.3 78.0 - - - +
659B HIS* 1.4 67.0 + - - +
662B GLN* 3.0 34.4 + - - +
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Residues in contact with HIS 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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238B ASN* 4.1 15.2 + - - -
241B ASN* 4.5 9.4 + - - -
600B ALA* 5.1 5.8 - - + -
601B ARG* 3.5 33.0 - - + +
624B PRO* 3.7 27.6 + - + +
626B VAL* 4.2 19.5 - - + +
655B ASP* 2.4 48.5 + - + +
658B ARG* 1.4 83.3 - - - +
660B ALA* 1.3 65.2 + - - +
662B GLN* 3.8 8.6 - - - +
663B CYS* 2.9 31.9 + - - +
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Residues in contact with ALA 660 (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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620B MET* 3.8 9.4 - - + -
624B PRO* 3.6 19.3 - - + +
656B ALA 3.0 19.3 + - - +
657B MET* 3.2 14.3 + - - +
659B HIS* 1.3 78.1 - - - +
661B ALA* 1.3 58.1 + - - +
663B CYS* 3.7 0.7 - - - +
664B VAL* 2.9 34.9 + - - +
679B PHE* 5.0 9.0 - - + -
684B PHE* 4.5 11.9 - - + -
688B ASP* 5.3 1.8 - - - +
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Residues in contact with ALA 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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459B GLY 5.1 1.9 - - - +
460B THR* 3.1 36.8 + - + +
657B MET 2.9 10.4 + - - +
660B ALA* 1.3 74.7 - - - +
662B GLN* 1.3 61.5 + - - +
664B VAL* 4.4 2.9 - - - +
665B GLY* 2.9 31.8 + - - +
679B PHE* 6.2 0.9 - - - -
691B GLY 4.5 11.2 - - - +
692B LYS* 5.4 6.7 - - + -
693B LEU* 5.5 2.7 - - + -
696B TRP* 6.0 4.9 - - + -
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Residues in contact with GLN 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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75B ARG* 4.3 1.4 - - - +
237B HIS* 3.8 25.1 + - + +
238B ASN* 2.6 39.8 + - - +
460B THR* 3.1 11.3 + - - +
605B SER* 4.6 12.1 + - - +
606B GLU* 2.4 40.9 + - - +
658B ARG 3.0 22.2 + - - +
659B HIS* 3.8 12.1 - - - +
661B ALA* 1.3 77.5 - - - +
663B CYS* 1.3 62.2 + - - +
665B GLY 4.5 1.2 + - - -
666B ARG* 3.8 23.1 + - - +
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Residues in contact with CYS 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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538B PHE* 3.1 40.6 - - + -
600B ALA* 3.2 45.8 - - - -
605B SER* 4.0 17.5 - - - -
618B VAL* 4.3 2.1 - - - +
620B MET* 3.8 5.4 - - + -
659B HIS* 2.9 21.5 + - - +
660B ALA 3.7 3.1 - - - +
662B GLN* 1.3 79.2 - - - +
664B VAL* 1.3 64.5 + - - +
666B ARG* 3.8 13.2 + - - +
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Residues in contact with VAL 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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538B PHE* 4.6 0.4 - - + -
618B VAL* 3.9 23.6 - - + +
620B MET* 3.8 26.7 - - + +
660B ALA 2.9 19.3 + - - +
661B ALA* 4.6 2.2 - - - +
663B CYS* 1.3 74.8 - - - +
665B GLY* 1.3 58.0 + - - +
666B ARG 2.9 11.0 + - - -
667B ALA* 3.4 18.5 + - - +
677B MET* 3.5 40.7 - - + +
679B PHE* 3.6 30.5 - - + -
692B LYS* 5.3 0.7 - - - +
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Residues in contact with GLY 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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42B MET* 5.4 2.4 - - - +
44B SER* 3.4 31.2 - - - -
459B GLY* 5.5 3.6 - - - +
460B THR* 5.7 0.2 - - - -
661B ALA* 2.9 20.4 + - - +
662B GLN 4.8 0.9 - - - -
664B VAL* 1.3 77.4 - - - +
666B ARG* 1.3 62.2 + - - +
667B ALA 3.3 2.2 - - - -
668B ILE 5.3 0.2 - - - +
677B MET* 4.8 6.5 - - - -
696B TRP* 5.0 9.6 - - - -
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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