Contacts of the helix formed by residues 558 - 575 (chain B) in PDB entry 2JED
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 558 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B HIS* 3.7 38.4 + + + +
501B VAL* 3.9 19.1 - - + +
530B MET 5.5 6.7 - - - +
557B ASN* 1.3 97.9 + - + +
559B SER* 1.3 63.3 + - - +
560B VAL 3.1 0.9 - - - -
561B ASP* 2.9 21.4 + - - +
562B TRP* 3.5 22.1 + - - -
623B GLY 4.1 4.9 - - - -
624B VAL* 4.1 34.6 - - + +
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Residues in contact with SER 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B GLU* 2.5 26.0 + - - +
556B TYR* 4.6 0.5 - - - +
557B ASN* 3.1 22.4 + - - -
558B HIS* 1.3 79.4 - - - +
560B VAL* 1.3 60.4 + - - +
562B TRP* 3.1 4.5 + - - -
563B TRP 3.1 12.8 + - - -
618B PRO* 3.6 16.7 - - - +
619B GLU* 5.6 0.2 - - - -
621B ARG* 2.7 24.3 + - - -
624B VAL* 3.6 27.8 - - - -
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Residues in contact with VAL 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B VAL* 3.8 17.5 - - + -
503B ARG* 4.4 9.2 - - + -
547B ALA* 3.8 12.2 - - + +
549B GLU* 3.6 16.6 - - + +
550B ILE* 3.7 29.6 - - + -
556B TYR* 3.5 36.1 - - + -
557B ASN 3.5 11.7 - - - +
558B HIS 3.1 0.2 + - - -
559B SER* 1.3 76.9 + - - +
561B ASP* 1.3 64.0 + - - +
563B TRP* 3.5 2.9 + - - +
564B SER* 3.1 30.5 + - - -
621B ARG* 4.1 0.2 - - - +
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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
----------------------------------------------------------
492B LEU* 4.1 12.2 - - + +
496B HIS* 2.8 31.4 + - + +
501B VAL* 3.7 8.7 - - - +
502B TYR* 2.9 31.3 + - - +
503B ARG* 2.8 29.5 + - - -
505B LEU* 4.0 7.0 + - - +
558B HIS 2.9 10.4 + - - +
560B VAL* 1.3 80.0 - - - +
562B TRP* 1.3 57.5 - - - +
564B SER* 3.5 6.8 + - - -
565B PHE* 2.9 28.5 + - - +
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Residues in contact with TRP 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ILE* 3.8 32.3 - - + -
492B LEU* 3.9 22.9 - - + -
493B GLN* 3.9 28.7 - - + -
496B HIS* 3.6 28.1 + + - -
558B HIS* 3.5 26.1 + - - -
559B SER* 3.1 8.3 + - - +
561B ASP* 1.3 75.4 - - - +
563B TRP* 1.3 62.3 + - - +
565B PHE* 3.5 22.4 + + + +
566B GLY* 3.1 17.3 + - - -
613B LEU* 3.8 13.6 - - + +
621B ARG* 4.4 8.1 - - + -
622B LEU 3.7 14.1 - - - +
623B GLY* 3.5 38.1 + - - -
624B VAL* 3.9 6.1 - - + -
628B ILE* 3.9 17.0 - - + -
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Residues in contact with TRP 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ASP 5.1 0.6 + - - -
545B TYR 3.4 21.5 + - - -
546B ILE 3.5 10.9 + - - -
547B ALA* 3.6 21.3 - - + -
548B PRO* 3.4 34.5 - - + -
559B SER 3.1 6.5 + - - -
560B VAL 3.7 7.9 - - - +
561B ASP 3.4 0.2 - - - -
562B TRP* 1.3 76.6 - - - +
564B SER* 1.3 60.1 + - - +
566B GLY* 3.1 5.0 + - - -
567B VAL* 3.1 30.3 + - + +
579B PHE* 3.3 38.0 - + - -
591B ILE* 4.0 11.1 - - + +
613B LEU 3.7 14.6 - - - -
614B PHE* 3.4 32.0 - + - -
615B VAL 3.9 4.3 - - - -
616B ARG* 3.8 18.6 - - + -
621B ARG* 3.7 20.9 - - - +
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Residues in contact with SER 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B ARG* 5.3 5.4 + - - -
505B LEU* 3.8 24.7 + - - +
545B TYR* 3.0 38.1 + - - +
547B ALA 5.4 0.2 + - - -
560B VAL 3.1 16.7 + - - -
561B ASP* 3.7 8.0 + - - -
563B TRP* 1.3 77.8 - - - +
565B PHE* 1.3 57.7 + - - +
567B VAL* 3.3 3.8 + - - +
568B LEU* 3.0 29.1 + - - +
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Residues in contact with PHE 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B ALA* 3.5 44.0 - - + -
488B ILE* 3.7 29.4 - - + -
489B ILE* 3.5 24.5 - - + -
492B LEU* 4.2 6.1 - - + -
505B LEU* 3.7 10.0 - - + +
561B ASP 2.9 19.4 + - - +
562B TRP* 3.5 24.9 - + + +
564B SER* 1.3 73.0 - - - +
566B GLY* 1.3 58.9 + - - +
568B LEU* 3.4 9.4 + - + +
569B LEU* 2.8 40.4 + - + +
572B MET* 5.8 0.4 - - + -
609B LEU* 5.0 3.1 - - + -
613B LEU* 3.7 24.5 - - + -
628B ILE* 4.1 4.3 - - + -
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Residues in contact with GLY 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B TRP 3.1 9.7 + - - -
563B TRP 3.1 8.4 + - - -
565B PHE* 1.3 76.5 - - - +
567B VAL* 1.3 56.2 + - - +
569B LEU* 4.4 0.2 - - - -
570B TYR* 2.9 30.3 + - - +
610B LEU* 3.4 6.1 - - - +
613B LEU* 3.8 23.3 - - - -
614B PHE* 3.3 17.6 - - - -
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Residues in contact with VAL 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ASP* 3.8 21.1 - - + +
545B TYR* 3.6 29.4 - - + -
563B TRP* 3.1 39.9 + - + +
564B SER* 3.3 6.7 + - - +
566B GLY* 1.3 75.5 - - - +
568B LEU* 1.3 58.0 + - - +
570B TYR* 3.3 3.1 + - - +
571B GLU* 2.9 39.8 + - - +
578B PRO* 3.9 25.1 - - + -
579B PHE* 4.3 1.8 - - + -
614B PHE* 3.6 13.4 - - + -
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Residues in contact with LEU 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ILE* 3.6 33.7 - - + -
505B LEU* 4.5 17.9 - - + -
506B LYS* 3.4 19.1 - - - +
507B LEU* 3.4 46.4 - - + +
510B ILE* 4.5 4.0 - - + -
545B TYR* 3.8 7.8 - - + +
564B SER 3.0 16.2 + - - +
565B PHE* 3.6 8.3 - - + +
567B VAL* 1.3 77.9 - - - +
569B LEU* 1.3 57.6 + - - +
571B GLU* 3.3 7.7 + - - +
572B MET* 2.8 40.3 + - + +
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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
----------------------------------------------------------
481B ALA* 4.4 6.3 - - + +
485B ALA* 4.0 26.5 - - + -
565B PHE* 2.8 26.9 + - + +
566B GLY* 3.8 4.3 - - - +
568B LEU* 1.3 69.6 - - - +
570B TYR* 1.3 67.1 + - - +
572B MET* 3.1 15.6 + - + +
573B LEU* 3.0 48.4 + - + +
606B ALA 5.1 0.4 - - - +
609B LEU* 3.6 33.4 - - + -
610B LEU* 3.8 19.5 - - + -
613B LEU* 4.5 5.2 - - + -
633B LEU* 4.5 8.7 - - + -
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Residues in contact with TYR 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B GLY 2.9 21.1 + - - +
567B VAL 3.4 4.7 - - - +
569B LEU* 1.3 72.9 - - - +
571B GLU* 1.3 57.4 + - - +
573B LEU* 3.8 0.6 - - - -
574B ILE* 2.9 62.1 + - + +
576B GLN* 3.1 28.4 - - + +
577B SER 3.8 4.4 + - - -
578B PRO* 3.6 36.9 + - + +
596B PRO* 3.8 13.7 - - + -
597B PHE* 2.4 41.4 + - - +
598B TYR* 4.2 5.8 - + - -
610B LEU* 3.6 22.8 - - + +
614B PHE* 4.2 9.4 - + + -
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Residues in contact with GLU 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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470B ILE* 3.3 13.4 - - - +
507B LEU* 3.9 14.9 - - + +
544B ASP* 4.5 4.2 - - - +
545B TYR* 2.5 40.0 + - - -
567B VAL* 2.9 28.4 + - - +
568B LEU* 3.6 4.6 - - - +
570B TYR* 1.3 70.6 - - - +
572B MET* 1.3 61.7 + - - +
575B GLY* 2.9 22.1 + - - +
576B GLN 3.4 21.5 - - - +
577B SER* 2.9 23.0 + - - -
578B PRO* 4.2 6.1 - - + -
1713B MPD 3.7 20.1 + - + +
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Residues in contact with MET 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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466B LEU* 4.1 11.0 - - - -
470B ILE* 3.9 6.7 - - - -
475B LYS* 3.7 1.6 - - - -
476B PHE* 2.8 45.9 + - + +
481B ALA* 3.5 29.6 - - + +
484B TYR* 3.8 29.6 - - + -
485B ALA* 4.0 15.3 - - + +
488B ILE* 4.7 1.1 - - + -
507B LEU* 3.8 17.3 - - + -
565B PHE* 5.8 0.7 - - + -
568B LEU* 2.8 30.7 + - + +
569B LEU* 3.1 27.3 + - + +
571B GLU* 1.3 74.9 - - - +
573B LEU* 1.3 59.5 + - - +
574B ILE 3.7 0.2 + - - -
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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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652A ARG* 4.3 7.5 + - - +
475B LYS* 3.3 15.9 - - - +
476B PHE 4.3 4.0 - - - +
478B LEU* 3.8 30.1 - - + -
481B ALA* 3.8 19.7 - - + -
482B THR* 5.4 1.3 - - - +
569B LEU* 3.0 42.8 + - + +
570B TYR 3.9 2.0 - - - +
572B MET* 1.3 77.2 - - - +
574B ILE* 1.3 68.5 + - + +
601B TRP* 3.4 15.6 - - - -
602B LEU* 4.3 10.5 - - + -
606B ALA* 3.9 23.3 - - + -
610B LEU* 4.0 19.7 - - + -
633B LEU* 5.5 2.0 - - + -
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Residues in contact with ILE 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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475B LYS* 3.5 18.3 - - - +
570B TYR* 2.9 64.0 + - + +
573B LEU* 1.3 86.8 - - + +
575B GLY* 1.3 59.1 + - - +
576B GLN* 4.0 19.5 + - + +
597B PHE* 6.2 0.4 - - + -
599B PRO* 3.8 37.7 - - + -
601B TRP* 4.1 11.4 - - + -
602B LEU* 4.0 20.9 - - + -
610B LEU* 4.5 4.3 - - + -
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Residues in contact with GLY 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ILE* 4.7 0.7 - - - -
474B HIS 3.3 25.0 - - - +
475B LYS* 3.8 1.6 - - - +
571B GLU 2.9 19.3 + - - -
573B LEU 3.8 0.6 - - - -
574B ILE* 1.3 77.8 - - - +
576B GLN* 1.3 69.3 + - - +
1713B MPD 3.1 27.1 + - - +
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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