Contacts of the helix formed by residues 615 - 632 (chain B) in PDB entry 1XYZ
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 ARG 615 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614B ASN* 1.3 74.1 - - - +
616B ASP* 1.3 67.7 + - - +
618B LEU* 3.9 0.5 - - - -
619B LEU* 3.0 45.1 + - + +
662B VAL* 3.7 21.4 + - - +
663B ILE* 2.8 45.3 + - - +
664B GLY* 4.6 1.2 - - - -
666B ASP* 2.9 37.6 + - - -
670B TYR* 3.5 24.0 + - - -
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Residues in contact with ASP 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B ASN* 3.2 9.1 + - - +
615B ARG* 1.3 87.9 + - - +
617B SER* 1.3 62.8 + - - +
619B LEU* 3.5 10.6 + - - +
620B ALA* 3.2 21.8 + - - +
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Residues in contact with SER 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ASN 4.5 1.2 + - - -
613B TRP* 3.7 21.0 - - - -
614B ASN* 3.0 40.4 + - - -
616B ASP* 1.3 74.9 - - - +
618B LEU* 1.3 63.7 + - - +
620B ALA* 3.4 8.0 + - - +
621B VAL* 3.2 24.3 + - - +
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Residues in contact with LEU 618 (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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608B LEU* 3.9 23.6 - - + -
613B TRP* 4.0 22.9 - - + -
614B ASN 3.0 17.2 + - - +
617B SER* 1.3 75.4 + - - +
619B LEU* 1.3 64.2 + - - +
621B VAL* 3.2 7.2 + - + +
622B MET* 3.0 21.7 + - - +
658B ILE* 3.7 20.2 - - + +
659B TRP* 3.8 32.5 - - + -
662B VAL* 3.6 31.6 - - + -
663B ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B ARG* 3.0 47.7 + - + +
616B ASP* 3.8 10.5 - - - +
617B SER 3.3 0.2 - - - -
618B LEU* 1.3 77.9 - - - +
620B ALA* 1.3 55.7 + - - +
622B MET* 3.3 11.5 + - - +
623B LYS* 2.9 29.5 + - - +
663B ILE* 3.9 26.9 - - + +
667B TYR 5.3 0.4 - - - +
670B TYR* 3.7 46.4 - - + -
674B TYR* 3.9 15.8 - - - +
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Residues in contact with ALA 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B ASP 3.2 14.9 + - - +
617B SER* 3.6 10.8 - - - +
618B LEU 3.3 0.2 - - - -
619B LEU* 1.3 73.9 - - - +
621B VAL* 1.3 64.8 + - + +
623B LYS* 3.5 7.6 + - - +
624B ASN* 3.1 24.8 + - - +
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Residues in contact with VAL 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B PHE* 4.4 9.4 - - + -
568B GLN* 5.2 2.0 + - - +
571B GLN* 4.2 12.8 - - - +
607B TRP* 4.0 22.7 - - + -
608B LEU* 4.0 16.8 - - + -
613B TRP* 3.6 30.5 - - + -
617B SER 3.2 13.1 + - - +
618B LEU* 3.2 11.4 + - + +
620B ALA* 1.3 76.0 - - + +
622B MET* 1.3 64.9 + - - +
624B ASN* 3.4 5.8 + - - +
625B HIS* 3.0 22.9 + - - +
659B TRP* 4.5 4.3 - - + -
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Residues in contact with MET 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B ILE* 4.1 13.0 - - + -
618B LEU 3.0 12.9 + - - +
619B LEU* 3.4 11.2 - - - +
621B VAL* 1.3 76.3 - - - +
623B LYS* 1.3 64.8 + - - +
625B HIS* 3.4 3.0 + - - +
626B ILE* 3.0 44.2 + - + +
659B TRP* 3.9 32.3 - - + -
663B ILE* 3.9 15.9 - - + -
667B TYR* 4.1 24.2 - - + +
670B TYR* 4.4 3.1 - - - -
671B ALA* 3.8 33.7 - - + -
674B TYR* 4.1 12.3 - - + -
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Residues in contact with LYS 623 (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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619B LEU 2.9 16.8 + - - +
620B ALA* 3.8 7.9 - - - +
621B VAL 3.3 0.2 - - - -
622B MET* 1.3 78.2 - - - +
624B ASN* 1.3 58.9 + - - +
626B ILE* 4.0 0.3 - - - +
627B THR* 2.8 53.0 + - - +
674B TYR* 3.7 48.4 + - + +
677B GLU* 4.0 17.5 + - - +
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Residues in contact with ASN 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B GLN* 4.4 4.9 + - - +
572B ASN* 3.1 36.8 + - - +
574B PHE* 3.8 13.3 - - - -
620B ALA 3.1 18.3 + - - +
621B VAL* 3.8 5.8 - - - +
622B MET 3.3 0.2 - - - -
623B LYS* 1.3 76.0 - - - +
625B HIS* 1.3 59.6 + - - +
627B THR* 4.8 2.5 - - - -
628B THR* 2.9 49.3 + - - -
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Residues in contact with HIS 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B LYS 5.4 0.2 - - - -
564B PHE* 3.5 48.1 - + + -
567B LEU* 4.1 15.9 - - + +
568B GLN* 3.1 42.3 + - + +
574B PHE* 3.9 6.2 - + - -
597B THR 5.5 0.4 + - - -
598B LEU* 4.0 26.6 + - + +
599B ILE* 5.4 1.3 - - + -
621B VAL 3.0 16.8 + - - +
622B MET* 3.9 3.6 - - - +
624B ASN* 1.3 78.6 - - - +
626B ILE* 1.3 66.9 + - + +
628B THR* 4.0 0.3 - - - -
629B VAL* 3.0 48.1 + - + +
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Residues in contact with ILE 626 (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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598B LEU* 4.2 26.5 - - + -
599B ILE* 4.2 12.3 - - + -
622B MET* 3.0 39.6 + - + +
623B LYS 4.1 2.0 - - - +
625B HIS* 1.3 79.1 - - + +
627B THR* 1.3 58.9 + - - +
629B VAL* 4.1 0.2 - - - -
630B MET* 3.0 42.9 + - - +
642B VAL* 4.9 1.6 - - + -
671B ALA* 3.7 29.6 - - + +
674B TYR* 4.1 11.4 - - + +
675B ALA* 3.8 31.6 - - + +
678B ALA* 4.9 0.2 - - + -
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Residues in contact with THR 627 (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 LYS* 2.8 45.7 + - - +
624B ASN* 4.2 2.7 - - - -
626B ILE* 1.3 76.1 - - - +
628B THR* 1.3 61.1 + - - +
631B THR* 2.8 47.8 + - + +
674B TYR* 4.7 6.4 + - - +
678B ALA* 4.1 16.6 - - + +
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Residues in contact with THR 628 (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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574B PHE* 3.7 41.5 - - + -
576B PHE* 4.1 10.0 - - + -
624B ASN* 2.9 39.8 + - - -
627B THR* 1.3 73.4 - - - +
629B VAL* 1.3 62.9 + - - +
631B THR* 3.2 15.1 + - - -
632B HIS* 3.3 13.5 + - - +
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Residues in contact with VAL 629 (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 LEU* 3.8 31.9 - - + -
574B PHE* 4.2 15.5 - - + -
576B PHE* 4.3 9.2 - - + -
598B LEU* 4.0 10.1 - - + -
625B HIS* 3.0 36.2 + - + +
626B ILE 4.1 1.3 - - - +
628B THR* 1.3 76.6 - - - +
630B MET* 1.3 63.0 + - - +
632B HIS* 3.3 10.6 + - - +
633B TYR* 3.4 24.0 - - + -
640B TRP* 3.6 26.9 - - + -
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Residues in contact with MET 630 (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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598B LEU* 3.9 16.8 - - + -
626B ILE* 3.0 27.2 + - - +
629B VAL* 1.3 76.0 - - - +
631B THR* 1.3 57.5 + - - +
633B TYR 3.2 3.8 + - - -
634B LYS* 2.9 26.9 + - - +
640B TRP* 3.7 46.9 + - + +
675B ALA* 3.5 44.9 - - - +
678B ALA* 3.8 11.2 - - + -
679B ASP* 4.0 18.9 - - + +
682B ALA* 4.2 2.0 - - + -
684B LEU* 4.0 16.6 - - + -
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Residues in contact with THR 631 (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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627B THR* 2.8 45.6 + - + +
628B THR* 3.2 7.8 + - - -
630B MET* 1.3 72.8 - - - +
632B HIS* 1.3 67.9 + - - +
634B LYS* 3.2 25.1 + - + +
678B ALA* 4.0 20.0 - - + +
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Residues in contact with HIS 632 (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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576B PHE* 3.6 45.6 - + + -
580B ASP* 2.8 41.8 + - - -
583B LEU* 6.0 0.2 - - - +
628B THR 3.3 9.8 + - - +
629B VAL 3.3 10.8 + - - +
631B THR* 1.3 81.3 + - - +
633B TYR* 1.3 66.7 + + - +
634B LYS 3.8 0.5 + - - -
636B LYS* 4.9 7.6 + - - -
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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
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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