Contacts of the helix formed by residues 685 - 703 (chain B) in PDB entry 5QSY
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 685 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B ASP* 1.3 74.8 + - - +
686B ASP* 1.3 66.2 + - - +
687B ASP 3.1 1.8 - - - -
688B ILE* 3.0 31.3 + - - +
689B TYR* 3.2 13.9 + - - +
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Residues in contact with ASP 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B ASP* 3.6 13.4 + - - +
685B ASP* 1.3 77.8 - - - +
687B ASP* 1.3 55.8 + - - +
689B TYR* 3.9 9.8 + - - +
690B ASN* 2.7 37.1 + - - +
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Residues in contact with ASP 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B SER 5.0 1.2 - - - +
675B ASP* 4.3 20.1 - - + +
676B LEU* 3.7 25.6 - - + +
679B GLU* 4.9 4.2 - - - +
684B ASP* 3.1 45.2 + - - +
685B ASP 3.1 0.2 - - - -
686B ASP* 1.3 74.4 - - - +
688B ILE* 1.3 67.8 + - - +
690B ASN* 2.9 26.9 + - - +
691B VAL* 3.3 7.9 + - - +
1001B K0J 3.3 27.3 + - - +
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Residues in contact with ILE 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B LEU* 3.8 20.2 - - + -
684B ASP 3.4 17.9 + - - +
685B ASP* 3.0 24.7 + - - +
687B ASP* 1.3 79.1 - - - +
689B TYR* 1.3 65.5 + - - +
691B VAL* 3.2 4.9 + - - +
692B LEU* 3.1 24.6 + - + +
728B ALA 5.9 0.7 - - - +
730B PRO* 3.8 37.9 - - + -
733B ILE* 3.7 10.0 - - + +
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Residues in contact with TYR 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B LYS 5.2 3.1 + - - -
628B VAL* 3.8 24.9 - - + +
668B ARG* 5.1 4.3 - - - -
685B ASP 3.2 10.5 + - - +
686B ASP* 4.4 9.6 - - - +
688B ILE* 1.3 81.0 - - + +
690B ASN* 1.3 63.3 + - - +
692B LEU* 4.5 7.4 - - + -
693B SER* 2.6 60.6 + - - -
697B ARG* 4.6 5.4 + - - -
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Residues in contact with ASN 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ARG* 2.8 30.4 + - - +
672B SER* 3.5 20.4 - - - +
675B ASP* 5.8 2.6 + - - +
686B ASP* 2.7 26.3 + - - +
687B ASP* 2.9 13.2 + - - +
689B TYR* 1.3 83.3 - - - +
691B VAL* 1.3 53.3 + - - +
693B SER* 3.2 6.5 + - - -
694B THR* 2.4 38.3 + - - +
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Residues in contact with VAL 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B PHE* 4.3 9.0 - - + -
672B SER* 3.3 34.8 - - - +
673B VAL* 4.1 3.4 - - + +
676B LEU* 3.6 25.6 - - + -
687B ASP 3.9 7.0 - - - +
688B ILE 3.2 6.7 + - - +
690B ASN* 1.3 73.2 - - - +
692B LEU* 1.3 57.5 + - - +
694B THR* 3.2 5.1 + - - -
695B LEU* 2.7 40.1 + - + +
719B LEU* 4.1 17.7 - - + -
733B ILE* 3.9 29.4 - - + -
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Residues in contact with LEU 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B VAL* 5.8 2.9 - - + -
688B ILE* 3.1 16.4 + - + +
689B TYR* 4.0 9.4 - - + +
691B VAL* 1.3 80.3 - - - +
693B SER* 1.3 58.3 + - - +
695B LEU* 4.4 1.8 - - + -
696B LYS* 2.8 43.5 + - + +
730B PRO* 5.9 2.5 - - + -
732B GLN* 3.7 48.0 - - + +
733B ILE* 3.8 19.3 - - + +
736B GLN* 4.0 16.8 - - + -
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Residues in contact with SER 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B VAL* 4.1 20.2 - - - +
668B ARG* 4.3 4.5 + - - -
689B TYR* 2.6 51.9 + - - -
690B ASN* 3.2 12.5 + - - -
692B LEU* 1.3 76.7 - - - +
694B THR* 1.3 60.8 + - - +
696B LYS* 3.7 5.7 - - - +
697B ARG* 3.2 44.3 + - - +
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Residues in contact with THR 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B PHE* 4.4 8.0 - - + +
668B ARG* 3.5 45.8 - - + +
669B PHE* 3.6 25.3 - - - +
672B SER* 3.7 1.0 + - - -
690B ASN 2.4 27.8 + - - +
691B VAL* 3.2 10.0 + - - -
693B SER* 1.3 74.6 - - - +
695B LEU* 1.3 63.4 + - - +
697B ARG* 3.3 19.8 + - - +
698B LEU* 3.2 27.8 + - - +
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Residues in contact with LEU 695 (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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669B PHE* 3.9 19.6 - - + -
691B VAL* 2.7 24.4 + - + +
692B LEU* 3.9 3.6 - - - +
694B THR* 1.3 71.9 + - - +
696B LYS* 1.3 49.7 + - - +
698B LEU* 3.2 6.0 + - + -
699B THR* 2.6 50.8 + - - +
716B CYS* 3.9 25.6 - - - -
719B LEU* 4.2 13.9 - - + -
733B ILE* 3.5 33.2 - - + +
736B GLN* 3.8 13.5 - - + -
737B ALA* 3.6 15.7 - - + +
740B CYS* 4.2 7.4 - - + -
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Residues in contact with LYS 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B VAL* 2.7 41.3 + - + +
629B GLU* 4.2 2.0 - - - +
630B SER* 3.5 31.7 + - - +
633B LEU* 3.6 12.1 - - + -
692B LEU* 2.8 29.1 + - + +
693B SER* 3.7 6.3 - - - +
695B LEU* 1.3 76.1 - - - +
697B ARG* 1.3 62.1 + - - +
699B THR* 3.4 1.4 + - - -
700B SER* 3.0 25.1 + - - -
732B GLN* 5.7 6.1 - - - +
736B GLN* 3.7 31.3 - - + +
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Residues in contact with ARG 697 (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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624B VAL* 2.7 24.9 + - + -
625B GLU* 2.8 27.1 + - - +
626B LYS 4.2 3.4 + - - -
627B HIS 3.5 12.2 + - - +
628B VAL* 4.0 13.5 - - - +
633B LEU* 3.9 22.4 - - + -
665B PHE* 3.6 40.4 - - + -
668B ARG* 4.6 8.5 - - - +
689B TYR* 4.6 4.4 + - - -
693B SER* 3.2 37.8 + - - +
694B THR* 3.3 23.7 + - - +
696B LYS* 1.3 77.9 - - - +
698B LEU* 1.3 62.6 + - - +
700B SER* 3.1 18.9 + - - -
701B PHE* 3.1 18.4 - - - -
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Residues in contact with LEU 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B ILE* 4.5 7.4 - - + -
665B PHE* 3.8 28.7 - - + +
666B VAL* 3.7 24.9 - - + -
669B PHE* 3.4 46.4 - - + -
694B THR 3.2 10.0 + - - +
695B LEU* 3.2 8.1 + - + +
697B ARG* 1.3 75.3 - - - +
699B THR* 1.3 61.9 + - - +
701B PHE* 3.3 3.3 + - - -
702B HIS* 2.9 30.6 + - - +
707B LEU* 3.7 15.7 - - + +
712B LEU* 4.2 23.6 - - + -
740B CYS* 4.9 4.7 - - - -
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Residues in contact with THR 699 (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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695B LEU* 2.6 38.8 + - - +
696B LYS 3.8 0.7 - - - -
698B LEU* 1.3 78.4 - - - +
700B SER* 1.3 63.0 + - - +
702B HIS* 3.2 14.0 + - - -
736B GLN* 3.3 32.3 + - - +
739B GLN* 3.9 13.2 - - + -
740B CYS* 3.5 31.3 - - - +
743B TYR* 3.5 22.3 - - + -
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Residues in contact with SER 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B SER* 5.4 1.6 - - - -
633B LEU* 3.4 37.6 - - - +
634B GLU* 4.5 7.3 - - - +
637B SER* 3.6 12.4 + - - -
696B LYS* 3.0 15.8 + - - -
697B ARG 3.1 10.7 + - - -
698B LEU 3.4 0.2 - - - -
699B THR* 1.3 77.2 - - - +
701B PHE* 1.3 71.3 + - - +
703B ASN* 3.9 13.6 + - - +
743B TYR* 5.5 0.7 - - - -
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Residues in contact with PHE 701 (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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624B VAL* 4.1 22.0 - - + -
633B LEU 4.4 2.7 - - - -
636B CYS* 4.1 9.2 - - + -
637B SER* 3.7 34.5 - - - -
640B TYR* 3.8 24.5 - + - -
658B ARG* 5.7 4.5 - - + -
661B LEU* 4.4 15.9 - - + -
662B ILE* 4.4 17.7 - - + -
665B PHE* 4.8 5.2 - + - -
697B ARG 3.1 22.4 + - - +
698B LEU* 3.3 7.3 + - - +
699B THR 3.2 0.8 - - - -
700B SER* 1.3 86.2 + - - +
702B HIS* 1.3 59.6 + - - +
703B ASN 3.0 4.0 + - - -
704B ALA 3.1 3.1 + - - -
705B HIS* 2.8 53.8 + + + +
707B LEU* 4.2 11.7 - - + -
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Residues in contact with HIS 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B LEU 2.9 15.6 + - - +
699B THR* 3.2 8.8 + - - +
701B PHE* 1.3 76.5 - - - +
703B ASN* 1.3 52.9 + - - +
705B HIS 3.4 8.2 + - - +
707B LEU* 3.6 45.5 + - + +
708B THR* 4.2 2.7 - - + -
712B LEU* 3.8 22.2 - - + +
740B CYS* 3.9 15.7 - - - -
743B TYR* 3.6 18.5 - - + +
744B SER* 3.5 33.1 + - - -
747B TRP* 2.7 46.2 + + - -
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Residues in contact with ASN 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B GLU* 6.1 3.2 - - - +
638B LYS* 6.0 1.8 - - - +
699B THR 3.8 0.2 + - - -
700B SER 3.9 12.7 + - - +
702B HIS* 1.3 80.9 - - - +
704B ALA* 1.3 62.9 + - + +
743B TYR* 3.7 46.9 + - + +
747B TRP* 3.5 14.7 + - - -
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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