Contacts of the helix formed by residues 565 - 579 (chain B) in PDB entry 6WG4
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 SER 565 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563B VAL* 3.3 6.7 + - - +
564B ASP* 1.3 83.1 - - - +
566B ASP* 1.3 63.1 + - - +
567B GLU* 3.4 12.4 + - - +
568B VAL* 3.2 28.2 + - - +
569B SER* 3.1 22.0 + - - -
589B PRO* 3.6 7.4 - - - -
591B ASN* 3.1 25.8 - - - -
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Residues in contact with ASP 566 (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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626A ARG* 2.8 41.7 + - - +
630A PHE* 3.7 11.2 - - + +
652A ILE* 3.6 22.2 - - + -
565B SER* 1.3 71.2 - - - +
567B GLU* 1.3 62.6 + - - +
569B SER* 3.2 8.5 + - - -
570B THR* 2.9 34.6 + - - +
589B PRO* 3.8 2.1 - - + +
591B ASN* 3.5 11.7 + - - -
592B LYS* 3.6 33.2 - - + -
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Residues in contact with GLU 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A ARG* 4.9 12.6 - - - +
527B HIS* 3.5 33.3 + - + +
565B SER* 3.3 10.3 + - - +
566B ASP* 1.3 85.8 + - - +
568B VAL* 1.3 57.4 + - - +
570B THR* 3.3 7.8 + - - +
571B LYS* 3.0 31.5 + - + +
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Residues in contact with VAL 568 (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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527B HIS* 3.9 29.8 - - + +
528B VAL* 4.1 24.2 - - - +
531B GLY* 4.0 15.3 - - - +
563B VAL* 3.8 24.9 - - + -
564B ASP* 4.4 3.1 - - + -
565B SER* 3.2 28.3 + - - +
566B ASP 3.2 0.2 - - - -
567B GLU* 1.3 73.6 - - - +
569B SER* 1.3 66.2 + - - +
571B LYS* 3.4 1.7 + - - +
572B ILE* 3.0 34.6 + - + +
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Residues in contact with SER 569 (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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652A ILE* 3.9 20.7 - - - +
563B VAL* 3.4 14.6 - - - +
565B SER 3.1 14.0 + - - -
566B ASP* 3.2 10.0 + - - -
568B VAL* 1.3 80.3 - - - +
570B THR* 1.3 58.6 + - - +
572B ILE* 3.3 2.9 + - - +
573B LEU* 2.9 31.2 + - - +
587B PHE* 3.6 36.0 - - - +
589B PRO* 4.1 1.2 - - - +
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Residues in contact with THR 570 (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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622A VAL* 3.7 33.5 - - + +
623A GLU* 4.0 12.0 + - - -
626A ARG* 4.1 6.9 - - - -
644A THR* 4.8 5.8 - - + -
646A PHE* 3.7 23.8 - - + -
652A ILE* 4.8 1.3 - - + -
566B ASP 2.9 17.0 + - - +
567B GLU* 3.3 9.2 + - - -
569B SER* 1.3 80.4 - - - +
571B LYS* 1.3 58.5 + - - +
573B LEU* 3.7 7.0 - - - +
574B MET* 2.8 30.1 + - - +
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Residues in contact with LYS 571 (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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519B PHE* 4.3 8.9 - - + -
525B ASN* 3.7 35.1 + - - +
527B HIS* 4.5 11.4 - - + +
528B VAL* 3.7 21.8 - - + -
567B GLU* 3.0 20.5 + - + +
568B VAL 3.8 0.4 - - - +
570B THR* 1.3 74.9 + - - +
572B ILE* 1.3 66.5 - - - +
574B MET* 3.4 25.8 + - - +
575B GLU* 3.4 26.7 + - - +
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Residues in contact with ILE 572 (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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512B ILE* 3.9 28.3 - - + -
515B VAL* 4.1 20.7 - - + +
516B LEU* 5.0 6.1 - - + -
519B PHE* 4.9 0.9 - - - -
528B VAL* 3.6 21.1 - - + -
532B TYR* 3.9 28.9 - - + -
568B VAL* 3.0 33.0 + - + +
569B SER 3.6 4.0 - - - +
571B LYS* 1.3 77.8 - - - +
573B LEU* 1.3 58.1 + - + +
575B GLU* 3.3 2.3 + - - +
576B PHE* 2.8 28.5 + - + +
587B PHE* 3.9 21.5 - - + -
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Residues in contact with LEU 573 (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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622A VAL* 6.4 1.1 - - + -
644A THR* 3.7 35.2 - - + +
652A ILE* 4.4 7.0 - - + -
653A SER 4.2 3.8 - - - +
654A GLY* 4.2 9.0 - - - +
655A GLY* 3.8 24.7 - - - +
569B SER 2.9 17.8 + - - +
570B THR* 3.8 6.1 - - - +
571B LYS 3.2 0.2 - - - -
572B ILE* 1.3 73.9 - - - +
574B MET* 1.3 60.6 + - - +
576B PHE* 3.4 15.0 - - + +
577B ASN* 2.9 41.8 + - - +
585B VAL* 3.8 17.9 - - + -
587B PHE* 4.0 21.3 - - + -
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Residues in contact with MET 574 (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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622A VAL* 6.6 0.4 - - + -
623A GLU* 6.4 2.0 - - + -
570B THR 2.8 17.9 + - - +
571B LYS* 3.8 30.3 - - - +
572B ILE 3.3 0.4 - - - -
573B LEU* 1.3 77.8 - - - +
575B GLU* 1.3 58.2 + - - +
577B ASN* 4.0 3.2 - - - +
578B LYS* 3.0 29.9 + - + +
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Residues in contact with GLU 575 (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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515B VAL* 3.9 18.2 - - + -
518B HIS* 3.7 12.9 + - + -
519B PHE* 3.9 34.1 - - + -
524B ILE* 6.0 0.3 - - - +
571B LYS* 3.4 11.7 + - - +
572B ILE 3.3 2.0 + - - +
573B LEU 3.3 0.2 - - - -
574B MET* 1.3 78.9 - - + +
576B PHE* 1.3 66.3 + - - +
578B LYS* 3.6 28.7 + - - +
579B MET* 3.1 57.7 + - + +
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Residues in contact with PHE 576 (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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655A GLY* 3.8 21.5 - - - -
508B GLY* 4.0 4.0 - - - -
511B SER* 3.4 25.8 - - - -
512B ILE* 4.0 15.9 - - + -
515B VAL* 3.9 11.5 - - + +
572B ILE* 2.8 20.0 + - + +
573B LEU* 3.4 13.9 - - + +
575B GLU* 1.3 77.0 - - - +
577B ASN* 1.3 72.6 + - - +
579B MET 3.5 0.5 + - - -
580B ASN 3.4 2.6 + - - -
581B LEU* 3.2 52.0 + - + +
582B PRO 3.4 21.5 - - - -
583B GLY 4.2 6.1 - - - -
585B VAL* 3.8 33.7 - - + -
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Residues in contact with ASN 577 (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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642A ASP* 3.9 24.7 + - + +
644A THR* 4.3 8.3 + - - -
655A GLY* 3.9 1.8 - - - +
656A ALA* 2.9 47.8 + - + +
657A SER 4.7 1.0 + - - +
573B LEU* 2.9 26.0 + - - +
574B MET* 4.2 3.5 - - - +
576B PHE* 1.3 84.4 - - - +
578B LYS* 1.3 67.5 + - - +
579B MET 3.2 0.4 - - - -
580B ASN* 3.2 19.0 + - - +
581B LEU 5.0 0.4 - - - +
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Residues in contact with LYS 578 (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 MET* 3.0 22.5 + - + +
575B GLU* 3.3 33.0 + - - +
577B ASN* 1.3 78.6 - - - +
579B MET* 1.3 59.6 + - + +
580B ASN* 3.3 13.9 + - - -
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Residues in contact with MET 579 (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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514B LYS* 5.6 3.1 - - - +
515B VAL* 4.6 6.7 - - - -
518B HIS* 4.0 31.9 - - + +
575B GLU* 3.1 47.3 + - + +
576B PHE 3.5 0.2 + - - -
578B LYS* 1.3 78.1 - - + +
580B ASN* 1.3 71.4 + - - +
581B LEU* 3.3 36.7 + - + +
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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
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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