Contacts of the helix formed by residues 559 - 574 (chain B) in PDB entry 6WCZ
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 GLU 559 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391B ARG* 5.8 5.5 + - - +
392B PRO* 4.9 14.3 - - + +
393B ARG* 6.0 2.2 - - - -
394B VAL* 5.9 4.7 - - + -
557B GLN 5.2 2.3 - - - +
558B MET* 1.3 78.4 - - - +
560B GLU* 1.3 57.0 + - - +
561B GLY 3.7 0.7 - - - -
562B HIS* 3.2 20.1 + - + +
563B ARG* 2.4 34.7 + - - +
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Residues in contact with GLU 560 (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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558B MET 5.3 0.4 - - - +
559B GLU* 1.3 76.0 + - - +
561B GLY* 1.3 60.6 + - - +
563B ARG* 3.0 25.3 + - - +
564B THR* 2.9 29.3 + - - +
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Residues in contact with GLY 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B LEU* 4.3 2.9 - - - +
560B GLU* 1.3 79.7 - - - +
562B HIS* 1.3 56.8 + - - +
564B THR* 2.3 33.8 + - - -
565B LEU* 2.9 19.1 + - - +
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Residues in contact with HIS 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PRO* 5.0 1.5 - - + +
393B ARG 3.1 25.9 + - - -
394B VAL* 3.4 26.6 - - + +
488B GLU* 4.0 12.7 + - - -
489B ALA 3.7 18.1 + - - -
492B PHE* 4.6 5.6 - + - -
558B MET* 3.4 41.8 - - + +
559B GLU* 3.3 26.1 + - + +
560B GLU 3.2 0.4 - - - -
561B GLY* 1.3 76.8 - - - +
563B ARG* 1.3 55.6 + - - +
565B LEU* 3.3 24.7 - - + +
566B ALA* 2.9 31.4 + - - +
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Residues in contact with ARG 563 (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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555B THR* 2.3 47.7 + - - +
556B ASN* 4.0 8.4 + - - +
557B GLN 4.0 2.6 - - - -
558B MET* 2.4 46.2 + - + +
559B GLU 2.4 27.8 + - - +
560B GLU* 3.0 31.8 + - - +
562B HIS* 1.3 69.1 + - - +
564B THR* 1.3 58.4 + - + +
567B LEU* 2.8 45.5 + - + +
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Residues in contact with THR 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B HIS 4.7 1.0 - - - +
444B LEU* 3.3 21.4 - - - +
560B GLU 2.9 13.9 + - - +
561B GLY* 2.3 32.5 + - - -
563B ARG* 1.3 77.3 - - + +
565B LEU* 1.3 49.1 + - - +
567B LEU* 4.4 4.0 - - - +
568B ALA* 2.7 38.6 + - - +
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Residues in contact with LEU 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ARG* 5.8 4.7 - - - +
443B HIS* 5.7 1.3 - - - +
444B LEU* 3.7 33.0 - - + -
488B GLU* 3.6 28.0 - - - +
489B ALA* 3.7 22.6 - - + +
561B GLY 2.9 14.5 + - - +
562B HIS* 3.3 31.4 - - + +
564B THR* 1.3 81.3 + - - +
566B ALA* 1.3 72.3 + - + +
568B ALA* 3.4 5.1 - - - +
569B VAL* 2.9 30.7 + - - +
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Residues in contact with ALA 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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489B ALA 3.7 22.7 - - - +
490B LEU* 3.7 9.2 - - + -
555B THR* 5.4 0.4 - - - -
558B MET* 3.7 23.8 - - + -
562B HIS* 2.9 18.2 + - + +
565B LEU* 1.3 76.6 - - - +
567B LEU* 1.3 61.4 + - - +
569B VAL* 3.3 11.4 - - - +
570B ILE* 3.0 33.6 + - - +
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Residues in contact with LEU 567 (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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552B ALA* 5.9 2.2 - - + -
555B THR* 3.8 34.1 - - + +
563B ARG* 2.8 29.8 + - + +
564B THR* 4.4 3.1 - - - +
566B ALA* 1.3 74.2 - - - +
568B ALA* 1.3 67.0 + - - +
570B ILE* 3.3 16.9 - - + +
571B LYS* 3.0 32.4 + - + +
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Residues in contact with ALA 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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443B HIS* 3.7 16.6 - - + +
564B THR 2.7 25.3 + - - +
565B LEU* 3.4 7.0 - - - +
566B ALA 3.2 0.2 - - - -
567B LEU* 1.3 80.0 - - - +
569B VAL* 1.3 57.3 + - - +
571B LYS* 3.0 8.3 + - - +
572B TYR* 2.9 57.6 + - + +
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Residues in contact with VAL 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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443B HIS* 4.8 17.9 - - + +
451B CYS* 5.2 3.8 - - - -
482B ALA* 5.7 2.5 - - + +
485B LEU* 4.8 17.7 - - + +
486B GLU* 5.0 5.4 - - + +
489B ALA* 3.7 23.8 - - + -
490B LEU* 4.1 8.1 - - + -
565B LEU 2.9 16.7 + - - +
566B ALA* 3.3 11.9 - - - +
568B ALA* 1.3 76.3 - - - +
570B ILE* 1.3 61.8 + - + +
572B TYR* 4.0 8.7 - - + +
573B THR* 2.9 44.4 + - + +
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Residues in contact with ILE 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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490B LEU* 4.1 20.4 - - + -
548B LEU 5.3 3.4 - - - +
552B ALA* 3.9 24.7 - - + +
555B THR* 5.5 2.0 - - + -
566B ALA 3.0 21.7 + - - +
567B LEU* 3.3 20.4 - - + +
569B VAL* 1.3 78.4 - - + +
571B LYS* 1.3 59.3 + - - +
574B TYR* 3.3 29.8 - - + +
575B GLN* 2.9 60.4 + - + +
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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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274B ASN* 5.6 6.1 - - - +
277B ILE* 4.3 24.1 - - + +
567B LEU* 3.0 22.7 + - + +
568B ALA* 3.2 12.6 - - - +
570B ILE* 1.3 80.6 - - - +
572B TYR* 1.3 74.2 + - + +
575B GLN* 3.3 24.9 - - + +
576B ASN* 3.5 25.9 + - - +
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Residues in contact with TYR 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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277B ILE* 3.6 34.1 - - + -
281B ARG* 3.9 21.7 + - - +
443B HIS* 3.4 55.0 + + + -
446B GLY* 2.9 33.4 + - - -
447B GLU 3.9 0.7 - - - -
448B CYS* 4.1 17.9 - - + -
451B CYS* 4.2 7.0 - - - +
568B ALA* 2.9 36.5 + - + +
569B VAL* 2.9 5.9 + - - +
571B LYS* 1.3 96.8 - - + +
573B THR* 1.3 59.0 + - - +
576B ASN* 2.9 12.4 - - - +
577B LYS* 4.4 1.0 - - - -
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Residues in contact with THR 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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451B CYS* 4.7 13.8 - - - +
453B TYR* 3.1 28.2 + - - -
478B MET* 5.6 1.2 - - - +
569B VAL* 2.9 31.1 + - + +
572B TYR* 1.3 76.2 - - - +
574B TYR* 1.3 92.1 + - + +
576B ASN 3.2 8.2 - - - +
577B LYS* 3.5 21.8 - - - +
605B GLN* 5.8 0.8 - - + +
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Residues in contact with TYR 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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453B TYR* 3.5 19.1 - - - -
486B GLU* 4.9 2.2 - - + +
490B LEU* 6.3 0.9 - - + -
548B LEU* 3.3 30.0 - - + +
570B ILE* 3.3 33.9 + - + +
573B THR* 1.3 103.7 - - + +
575B GLN* 1.3 66.5 + - + +
576B ASN 3.2 2.1 + - - -
577B LYS* 3.9 17.0 - - - +
598B GLN 3.5 11.1 - - - +
600B GLN 4.6 0.2 - - - +
601B ARG* 4.5 19.7 - - + -
602B GLY 5.0 1.1 - - - -
605B GLN* 3.6 25.1 + - + +
607B VAL* 3.5 30.0 - - + +
608B THR* 4.2 3.0 - - + +
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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