Contacts of the helix formed by residues 558 - 576 (chain B) in PDB entry 4JWE
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 PRO 558 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B LYS 3.9 6.3 - - - +
557B LEU* 1.4 95.4 - - + +
559B ALA* 1.3 60.3 + - - +
560B ASP* 3.3 17.7 - - - +
561B ASP* 3.1 37.9 + - - +
562B LYS 3.2 9.0 + - - -
597B LYS* 4.6 21.3 - - + +
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Residues in contact with ALA 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B LEU 3.5 3.7 + - - -
558B PRO* 1.3 71.4 - - - +
560B ASP* 1.4 58.2 + - - +
562B LYS* 3.4 14.5 + - + +
563B THR* 3.1 25.2 + - - -
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Residues in contact with ASP 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B PRO* 3.4 19.4 - - - +
559B ALA* 1.4 72.7 + - - +
561B ASP* 1.4 74.2 - - - +
563B THR* 3.3 10.9 + - - -
564B ALA* 3.2 25.1 + - - +
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Residues in contact with ASP 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B LEU* 4.1 14.4 - - + -
558B PRO* 3.1 27.6 + - + +
560B ASP* 1.4 92.3 - - - +
562B LYS* 1.4 59.9 + - - +
564B ALA* 3.5 8.3 + - - +
565B ILE* 2.9 39.9 + - + +
594B VAL 4.4 9.4 - - - +
596B GLN 5.7 0.2 + - - -
597B LYS* 4.3 17.2 + - - +
598B LEU 6.2 0.2 - - - +
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Residues in contact with LYS 562 (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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550B VAL* 4.7 13.9 - - + -
551B GLU* 5.9 2.6 + - - -
557B LEU* 3.8 26.8 - - + +
558B PRO 3.2 7.6 + - - +
559B ALA* 3.4 16.4 - - + +
560B ASP 3.3 0.4 - - - -
561B ASP* 1.4 73.5 - - - +
563B THR* 1.4 54.9 + - - +
565B ILE* 4.4 4.5 - - - -
566B GLU* 2.8 58.8 + - + +
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Residues in contact with THR 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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559B ALA 3.1 14.4 + - - -
560B ASP* 3.3 12.1 + - - -
562B LYS* 1.4 76.3 - - - +
564B ALA* 1.4 53.2 - - - +
566B GLU* 4.0 3.9 - - - +
567B SER* 2.9 41.9 + - - +
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Residues in contact with ALA 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B ASP 3.2 12.4 + - - +
561B ASP* 3.7 11.2 - - - +
562B LYS 3.4 0.2 - - - -
563B THR* 1.4 76.8 - - - +
565B ILE* 1.4 58.9 + - - +
567B SER* 3.8 5.6 + - - -
568B ALA* 3.3 16.1 + - - +
594B VAL* 3.4 35.5 - - + +
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Residues in contact with ILE 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B THR* 4.1 16.6 - - + -
550B VAL* 4.1 15.5 - - + -
557B LEU* 4.3 6.7 - - + -
561B ASP* 2.9 24.9 + - + +
562B LYS* 3.9 4.3 - - - +
564B ALA* 1.4 73.7 - - - +
566B GLU* 1.3 54.1 + - - +
568B ALA* 3.1 4.8 + - - +
569B LEU* 2.8 51.7 + - + +
591B LEU* 5.1 1.6 - - + +
594B VAL* 3.3 31.6 - - + +
595B SER* 3.4 19.1 - - - +
598B LEU* 3.8 30.5 - - + +
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Residues in contact with GLU 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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547B ARG* 4.6 5.2 + - - +
550B VAL* 3.9 21.7 - - - +
562B LYS* 2.8 42.8 + - + +
563B THR* 4.2 3.4 - - - +
565B ILE* 1.3 69.9 - - + +
567B SER* 1.4 57.0 + - - +
569B LEU* 3.5 25.0 - - - +
570B THR* 2.6 35.3 + - - -
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Residues in contact with SER 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B THR* 2.9 28.4 + - - +
564B ALA* 3.9 7.4 - - - -
565B ILE 3.3 0.2 - - - -
566B GLU* 1.4 76.0 - - - +
568B ALA* 1.4 56.6 + - - +
570B THR* 3.7 5.9 + - - -
571B ALA* 3.3 24.6 + - - +
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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
----------------------------------------------------------
564B ALA 3.3 15.6 + - - +
565B ILE 3.1 5.7 + - - +
567B SER* 1.4 76.8 - - - +
569B LEU* 1.4 59.7 + - - +
570B THR 3.5 0.2 - - - -
571B ALA* 3.7 8.5 + - - +
572B LEU* 3.4 21.5 + - - +
587B LYS 4.4 5.0 - - - +
590B GLU* 4.1 9.2 - - + +
591B LEU* 3.8 36.2 - - + +
594B VAL* 4.1 6.5 - - + -
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Residues in contact with LEU 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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543B LEU* 3.3 56.2 - - + +
546B THR* 4.4 8.3 - - + -
547B ARG* 3.9 29.6 - - + +
550B VAL* 5.5 0.2 - - + -
565B ILE* 2.8 36.6 + - + +
566B GLU* 3.5 33.9 - - - +
567B SER 3.4 0.4 - - - -
568B ALA* 1.4 72.2 - - - +
570B THR* 1.4 63.8 + - - +
572B LEU 3.5 1.6 + - - -
573B GLU* 3.4 13.8 + - - +
591B LEU* 3.8 22.9 - - + -
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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
----------------------------------------------------------
566B GLU 2.6 22.8 + - - -
567B SER* 3.7 7.1 + - - -
569B LEU* 1.4 76.8 - - - +
571B ALA* 1.4 54.2 + - - +
573B GLU* 3.5 17.1 + - + +
574B THR* 2.8 32.4 + - - +
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Residues in contact with ALA 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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567B SER 3.3 14.6 + - - +
568B ALA* 3.8 11.0 - - - +
569B LEU 3.3 0.4 - - - -
570B THR* 1.4 76.6 - - - +
572B LEU* 1.3 64.4 + - - +
574B THR* 3.4 10.3 + - - -
575B ALA* 3.3 15.8 + - - +
587B LYS* 3.8 30.1 - - + +
590B GLU* 4.6 6.3 - - + +
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Residues in contact with LEU 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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539B GLY* 3.4 24.9 - - - +
542B LEU* 3.9 25.1 - - + -
543B LEU* 4.0 15.3 - - + -
568B ALA 3.4 13.4 + - - +
569B LEU 3.5 5.1 + - - +
570B THR 3.4 0.4 - - - -
571B ALA* 1.3 75.6 - - - +
573B GLU* 1.4 66.1 + - - +
575B ALA* 3.2 2.3 + - - +
576B LEU* 3.1 43.1 + - + +
584B ILE* 3.7 30.7 - - + +
587B LYS* 3.8 16.3 - - + +
588B MET* 3.7 12.6 - - + -
591B LEU* 4.4 5.4 - - + -
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Residues in contact with GLU 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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543B LEU* 3.7 20.1 - - + +
547B ARG* 3.6 33.2 + - - -
569B LEU 3.4 13.7 + - - +
570B THR* 3.6 19.9 - - + +
572B LEU* 1.4 76.3 - - - +
574B THR* 1.3 59.2 + - - +
576B LEU* 3.9 15.3 + - - +
577B LYS* 3.9 16.3 - - - +
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Residues in contact with THR 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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570B THR* 2.8 19.4 + - - +
571B ALA* 3.6 8.2 + - - -
572B LEU 3.2 0.4 - - - -
573B GLU* 1.3 74.8 - - - +
575B ALA* 1.4 63.5 + - - +
577B LYS* 3.4 30.2 + - - +
578B GLY 4.2 1.6 + - - -
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Residues in contact with ALA 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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571B ALA 3.3 2.1 + - - +
572B LEU 3.2 7.0 + - - +
574B THR* 1.4 75.8 - - - +
576B LEU* 1.4 63.2 + - - +
578B GLY* 3.2 15.9 + - - +
580B ASP 5.1 0.5 + - - +
583B ALA* 3.9 18.7 - - + +
584B ILE* 3.4 21.4 - - - +
587B LYS* 3.6 31.4 - - + -
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Residues in contact with LEU 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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536B ARG* 2.8 68.5 + - + +
539B GLY* 3.8 20.6 - - - -
540B ASP* 4.3 11.7 - - - +
543B LEU* 4.2 17.7 - - + -
572B LEU* 3.1 31.2 + - + +
573B GLU* 4.0 9.6 - - - +
574B THR 3.3 0.4 - - - -
575B ALA* 1.4 76.2 - - - +
577B LYS* 1.4 54.4 - - + +
578B GLY 3.5 0.9 - - - +
584B ILE* 3.8 26.9 - - + -
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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
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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