Contacts of the helix formed by residues 601 - 619 (chain B) in PDB entry 4WGK
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 HIS 601 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B VAL* 4.0 19.4 - - + +
439B LEU* 3.8 35.8 - - + +
445B SER* 3.0 32.6 + - - -
446B LYS 3.8 15.9 - - - +
447B THR* 4.4 5.6 - - + -
498B CYS 5.8 0.4 - - - -
583B TYR* 3.6 31.9 - + - -
598B TYR 4.8 0.6 + - - -
599B GLY 3.2 1.2 - - - -
600B PRO* 1.3 90.5 - - + +
602B THR* 1.3 63.6 + - - +
603B LEU 3.3 2.7 - - - -
604B SER* 3.4 8.9 + - - +
605B ALA* 3.0 25.1 + - - +
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Residues in contact with THR 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B MET* 4.3 1.6 - - + -
447B THR* 4.6 4.7 - - - -
579B TYR 5.2 0.7 - - - +
580B ILE* 4.1 12.8 - - + -
596B THR* 3.4 16.4 - - + +
597B ILE 5.6 0.4 - - - +
598B TYR* 3.1 39.6 + - + +
599B GLY 2.6 24.2 + - - -
600B PRO 3.4 1.4 - - - -
601B HIS* 1.3 78.4 - - - +
603B LEU* 1.3 62.6 + - - +
605B ALA* 3.4 6.8 + - - +
606B TYR* 3.1 46.6 + - + -
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Residues in contact with LEU 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B PHE* 3.5 32.8 - - + -
545B SER* 3.6 32.1 - - - +
548B ARG* 4.2 17.3 - - - +
580B ILE* 3.8 11.1 - - + +
581B THR 3.5 17.1 + - - +
582B THR* 3.7 27.1 - - + -
583B TYR 5.0 1.6 - - - +
600B PRO 4.8 2.6 + - - +
601B HIS* 3.3 0.6 - - - +
602B THR* 1.3 76.7 - - - +
604B SER* 1.3 63.2 + - - +
606B TYR* 3.1 3.9 + - - +
607B ILE* 2.9 48.2 + - + +
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Residues in contact with SER 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B VAL* 3.5 24.3 - - - +
438B TRP 5.6 1.8 - - - -
439B LEU* 4.5 13.2 - - - +
583B TYR* 5.8 4.5 - - - +
600B PRO 5.6 0.2 + - - -
601B HIS* 3.4 12.7 + - - +
603B LEU* 1.3 79.3 - - - +
605B ALA* 1.3 57.1 + - - +
607B ILE* 3.6 12.9 + - - +
608B GLN* 3.1 28.4 + - - +
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Residues in contact with ALA 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B MET* 4.2 10.3 - - + -
435B VAL* 3.9 12.3 - - + -
437B VAL* 3.7 21.2 - - + +
447B THR* 3.8 14.8 - - + -
601B HIS 3.0 18.6 + - - +
602B THR 3.5 5.8 - - - +
603B LEU 3.1 0.2 - - - -
604B SER* 1.3 76.9 - - - +
606B TYR* 1.3 57.2 + - - +
608B GLN* 3.2 6.3 + - - +
609B LEU* 2.8 34.1 + - - +
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Residues in contact with TYR 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B MET* 3.6 33.9 - - + +
522B VAL* 3.9 9.0 - - + +
524B VAL* 4.1 17.0 - - + -
538B PRO* 3.7 23.5 - - + +
541B PHE* 3.9 20.0 - + + -
549B LEU* 3.9 13.9 - - + -
577B THR* 3.7 11.1 + - - -
580B ILE* 3.7 18.4 - - + -
598B TYR* 4.0 6.3 - + - -
602B THR* 3.1 37.0 + - + -
603B LEU 3.1 6.8 + - - +
605B ALA* 1.3 75.9 - - - +
607B ILE* 1.3 57.7 + - - +
609B LEU* 4.2 2.7 - - + -
610B PHE* 2.7 57.6 + + + +
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Residues in contact with ILE 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ARG* 4.0 27.4 - - + -
549B LEU* 3.9 21.5 - - + +
552B ALA* 3.6 25.8 - - + -
553B VAL* 5.2 0.7 - - - +
603B LEU* 2.9 44.1 + - + +
604B SER* 3.8 10.3 - - - +
606B TYR* 1.3 75.6 - - - +
608B GLN* 1.3 57.4 + - - +
610B PHE* 4.3 0.3 - - - +
611B ARG* 2.9 45.6 + - - +
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Residues in contact with GLN 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B VAL* 4.1 15.3 - - - +
436B THR 3.3 25.4 + - - +
437B VAL* 4.0 3.8 - - - +
438B TRP* 3.7 27.7 + - - +
604B SER 3.1 15.4 + - - +
605B ALA* 3.3 8.3 + - - +
607B ILE* 1.3 77.0 - - - +
609B LEU* 1.3 68.2 + - + +
611B ARG* 3.5 9.8 - - - +
612B ASN* 3.2 22.6 + - + +
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Residues in contact with LEU 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B GLN* 4.7 8.5 - - - +
430B VAL* 3.7 42.6 - - + -
432B MET* 3.8 19.7 - - - -
435B VAL* 4.7 12.6 - - + -
524B VAL* 4.2 20.6 - - + -
605B ALA 2.8 23.7 + - - +
606B TYR* 3.7 9.0 - - + +
608B GLN* 1.3 81.0 - - + +
610B PHE* 1.3 60.6 + - - +
612B ASN* 3.4 8.6 + - + +
613B LEU* 3.2 29.7 + - - +
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Residues in contact with PHE 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B VAL* 3.7 28.3 - - + -
525B GLN 3.5 25.6 - - - -
526B ILE* 3.5 26.8 - - + +
535B THR* 3.9 17.9 - - + -
536B ALA 3.3 22.2 - - - -
537B ILE* 3.9 15.5 - - + -
538B PRO* 4.6 1.8 - - + -
549B LEU* 3.9 11.7 - - + -
553B VAL* 3.9 17.4 - - + +
606B TYR* 2.7 48.2 + + + +
607B ILE 4.3 0.9 - - - +
609B LEU* 1.3 73.3 - - - +
611B ARG* 1.3 60.0 + - - +
613B LEU* 3.3 7.5 + - + -
614B ALA* 3.0 26.0 + - - +
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Residues in contact with ARG 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B ALA* 3.5 37.1 + - + +
553B VAL* 4.3 3.3 - - + +
555B ALA* 4.9 4.9 - - - +
556B GLU* 2.9 46.9 + - + +
607B ILE* 2.9 41.7 + - + +
608B GLN* 3.5 8.9 - - - +
610B PHE* 1.3 77.4 - - - +
612B ASN* 1.3 56.5 + - - +
614B ALA* 3.2 3.0 + - - -
615B LYS* 2.9 25.8 + - - +
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Residues in contact with ASN 612 (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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428B GLN* 4.8 8.9 + - - +
608B GLN 3.2 10.9 + - - +
609B LEU* 3.5 12.8 - - + +
610B PHE 3.3 0.2 - - - -
611B ARG* 1.3 77.7 - - - +
613B LEU* 1.3 57.8 + - - +
615B LYS* 3.2 19.2 + - - +
616B ALA* 2.8 29.0 + - - +
625B LEU* 3.3 27.2 - - - +
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Residues in contact with LEU 613 (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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426B ALA* 4.0 18.5 - - + +
428B GLN* 4.1 25.6 - - + +
524B VAL* 3.5 37.0 - - + +
525B GLN* 3.6 21.1 - - - +
526B ILE* 3.8 13.0 - - + +
609B LEU 3.2 17.1 + - - +
610B PHE* 3.5 12.1 - - + +
612B ASN* 1.3 80.7 - - + +
614B ALA* 1.3 56.8 + - - +
616B ALA* 3.1 8.4 + - - +
617B ILE* 2.9 33.6 + - - +
625B LEU* 4.2 16.8 - - + -
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Residues in contact with ALA 614 (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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526B ILE* 3.8 4.6 - - + +
553B VAL* 4.1 9.9 - - + -
556B GLU* 4.0 12.1 - - + -
557B PHE* 3.5 43.2 - - + -
610B PHE 3.0 13.6 + - - +
611B ARG* 3.5 8.3 - - - +
613B LEU* 1.3 75.1 - - - +
615B LYS* 1.3 57.6 + - - +
617B ILE* 3.3 1.8 + - - -
618B ALA* 2.9 30.8 + - - +
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Residues in contact with LYS 615 (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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556B GLU* 3.3 28.4 - - - +
560B HIS* 3.7 26.9 - - + +
611B ARG 2.9 9.6 + - - +
612B ASN* 3.4 20.6 + - - +
614B ALA* 1.3 76.8 - - - +
616B ALA* 1.3 51.8 + - - +
618B ALA* 4.6 4.7 - - - +
619B THR* 2.8 49.5 + - + +
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Residues in contact with ALA 616 (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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612B ASN* 2.8 14.0 + - - +
613B LEU 3.1 9.2 + - - +
615B LYS* 1.3 76.6 - - - +
617B ILE* 1.3 60.3 + - - +
620B ASP* 3.2 1.0 + - - -
621B THR* 2.8 41.4 + - - +
622B VAL* 3.4 15.7 + - + +
625B LEU* 3.7 35.2 - - + -
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Residues in contact with ILE 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ALA* 3.8 23.6 - - + +
425B SER* 4.4 5.2 - - - +
426B ALA* 3.7 28.5 - - + +
526B ILE* 3.9 35.9 - - + +
528B THR* 4.1 14.6 - - + +
557B PHE* 4.3 14.1 - - + -
562B MET* 4.5 8.7 - - + +
613B LEU 2.9 17.6 + - - +
614B ALA 3.6 6.3 - - - +
616B ALA* 1.3 76.0 - - - +
618B ALA* 1.3 64.4 + - - +
620B ASP* 3.3 14.4 + - - +
622B VAL* 3.8 10.0 - - + +
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Residues in contact with ALA 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B PHE* 4.3 8.1 - - + +
560B HIS* 3.6 38.9 - - + +
562B MET* 3.7 25.0 - - + +
614B ALA 2.9 16.9 + - - +
615B LYS* 3.9 2.2 - - - +
617B ILE* 1.3 79.5 - - - +
619B THR* 1.3 59.3 + - - +
620B ASP* 3.2 2.7 + - - +
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Residues in contact with THR 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B HIS* 3.5 32.5 - - + -
615B LYS* 2.8 35.4 + - + +
616B ALA 3.8 0.2 + - - -
618B ALA* 1.3 75.1 - - - +
620B ASP* 1.3 69.1 + - - +
621B THR* 2.8 36.9 + - - +
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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