Contacts of the helix formed by residues 558 - 575 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A HIS* 3.5 38.3 - + + +
501A VAL* 3.9 20.1 - - + +
530A MET 6.0 0.4 + - - -
557A ASN* 1.3 92.8 + - - +
559A SER* 1.3 64.2 + - - +
560A VAL 3.0 3.1 - - - -
561A ASP* 3.0 20.0 + - - +
562A TRP* 3.3 37.2 - + - -
623A GLY 3.6 14.1 + - - -
624A VAL* 3.9 20.1 + - + +
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Residues in contact with SER 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A GLU* 2.6 26.3 + - - +
556A TYR* 4.7 0.7 - - - +
557A ASN* 3.0 22.0 + - - -
558A HIS* 1.3 79.2 + - - +
560A VAL* 1.3 64.0 + - - +
562A TRP* 3.1 13.4 + - - +
563A TRP 3.2 3.8 + - - -
618A PRO* 3.5 20.9 - - - +
619A GLU* 5.9 0.2 - - - -
621A ARG* 2.9 18.4 + - - -
624A VAL* 3.5 28.0 - - - -
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Residues in contact with VAL 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A VAL* 3.9 16.8 - - + -
503A ARG* 4.2 11.9 - - + -
547A ALA* 3.7 14.3 - - + +
549A GLU* 3.5 20.0 - - + +
550A ILE* 3.6 32.5 - - + -
556A TYR* 3.6 29.6 - - + -
557A ASN 3.5 11.4 - - - +
558A HIS 3.0 1.4 - - - -
559A SER* 1.3 80.6 + - - +
561A ASP* 1.3 61.2 + - - +
563A TRP* 3.4 3.6 + - - +
564A SER* 3.1 31.0 + - - -
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Residues in contact with ASP 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU* 4.1 12.3 - - + +
496A HIS* 2.8 31.4 + - + +
501A VAL* 3.7 8.5 - - - +
502A TYR* 2.9 33.2 + - - +
503A ARG* 2.8 30.1 + - - -
505A LEU* 3.8 7.8 - - - +
558A HIS 3.0 10.8 + - - +
560A VAL* 1.3 78.8 - - - +
562A TRP* 1.3 57.3 + - - +
564A SER* 3.5 7.1 + - - -
565A PHE* 3.0 27.9 + - - +
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Residues in contact with TRP 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ILE* 3.8 31.0 - - + -
492A LEU* 3.9 20.4 - - + -
493A GLN* 3.8 33.9 - - + -
496A HIS* 3.5 18.8 + + - -
558A HIS* 3.3 45.7 - + - -
559A SER* 3.1 7.5 + - - +
561A ASP* 1.3 75.6 - - - +
563A TRP* 1.3 64.3 + - - +
565A PHE* 3.5 21.4 + + + +
566A GLY 3.1 17.2 + - - -
613A LEU* 3.7 12.3 - - + +
621A ARG* 4.1 8.5 - - + -
622A LEU 3.7 14.6 - - - +
623A GLY* 3.4 27.8 + - - -
624A VAL* 4.1 3.6 - - + -
628A ILE* 3.9 19.1 - - + -
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Residues in contact with TRP 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ASP 5.2 0.4 + - - -
545A TYR 3.7 13.9 - - - -
546A ILE 3.6 10.9 + - - -
547A ALA* 3.6 18.4 - - + -
548A PRO* 3.4 33.9 - - + -
559A SER 3.2 6.3 + - - -
560A VAL 3.4 7.6 + - - +
562A TRP* 1.3 74.1 - - - +
564A SER* 1.3 65.0 + - - +
566A GLY* 3.1 11.3 + - - -
567A VAL* 3.1 23.9 + - + +
579A PHE* 3.5 30.2 - + - -
591A ILE* 3.9 8.8 - - + +
613A LEU 3.8 15.3 - - - -
614A PHE* 3.6 41.5 - + + -
615A VAL 3.9 5.2 - - - -
616A ARG* 4.0 20.6 - - + -
621A ARG* 3.6 29.6 - - - +
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Residues in contact with SER 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ARG* 5.2 5.4 + - - -
505A LEU* 3.9 33.2 + - - -
545A TYR* 2.8 31.3 + - - +
546A ILE* 5.0 0.2 - - - -
547A ALA 5.1 0.3 + - - -
560A VAL 3.1 14.6 + - - -
561A ASP* 3.7 9.5 + - - -
563A TRP* 1.3 75.4 - - - +
565A PHE* 1.3 57.4 + - - +
567A VAL* 3.2 6.4 + - - +
568A LEU* 2.9 29.6 + - - +
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Residues in contact with PHE 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ALA* 3.4 45.8 - - + -
488A ILE* 3.6 29.6 - - + -
489A ILE* 3.5 24.7 - - + -
492A LEU* 4.2 5.2 - - + -
505A LEU* 3.6 10.3 - - + +
561A ASP 3.0 17.5 + - - +
562A TRP* 3.5 24.9 - + + +
563A TRP 3.2 0.2 - - - -
564A SER* 1.3 73.1 - - - +
566A GLY* 1.3 59.0 + - - +
568A LEU* 3.4 7.9 + - + +
569A LEU* 2.8 34.3 + - + +
609A LEU* 4.8 7.2 - - + -
613A LEU* 3.6 21.5 - - + -
628A ILE* 4.0 9.2 - - + -
634A PHE* 4.8 0.4 - + - -
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Residues in contact with GLY 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A TRP 3.1 8.2 + - - -
563A TRP 3.1 8.4 + - - -
565A PHE* 1.3 74.1 - - - +
567A VAL* 1.3 59.4 + - - +
569A LEU* 4.4 0.2 - - - -
570A TYR* 2.8 32.2 + - - +
610A LEU* 3.4 8.4 - - - +
613A LEU* 3.7 23.6 - - - -
614A PHE* 3.5 15.7 - - - -
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Residues in contact with VAL 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ASP* 3.6 26.2 - - + +
545A TYR* 3.5 26.7 - - + -
563A TRP* 3.1 34.7 + - + +
564A SER 3.2 6.7 + - - +
566A GLY* 1.3 75.2 - - - +
568A LEU* 1.3 57.9 + - - +
570A TYR* 3.4 2.1 + - - +
571A GLU* 3.0 41.3 + - - +
578A PRO* 3.8 22.9 - - + -
579A PHE* 4.4 1.8 - - + -
614A PHE* 3.8 15.0 - - + -
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Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ILE* 3.7 17.9 - - + -
505A LEU* 3.9 17.7 - - + -
506A LYS* 3.6 35.0 - - - +
507A LEU* 3.6 18.7 - - + +
510A ILE* 4.1 13.0 - - + -
545A TYR* 3.9 11.2 - - + -
564A SER 2.9 16.2 + - - +
565A PHE* 3.7 11.9 - - + +
567A VAL* 1.3 76.7 - - - +
569A LEU* 1.3 62.7 + - - +
571A GLU* 3.3 6.2 + - - +
572A MET* 3.0 48.8 + - + +
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Residues in contact with LEU 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A ALA* 4.3 7.0 - - + +
482A THR 5.4 0.2 - - - +
485A ALA* 4.1 19.3 - - + -
565A PHE* 2.8 24.8 + - + +
566A GLY* 3.7 4.5 - - - +
568A LEU* 1.3 71.7 - - + +
570A TYR* 1.3 67.6 + - - +
572A MET* 3.3 22.0 + - + +
573A LEU* 3.1 44.9 + - + +
606A ALA 5.1 0.4 - - - +
609A LEU* 3.6 33.2 - - + -
610A LEU* 3.9 21.1 - - + -
613A LEU* 4.6 4.5 - - + -
633A LEU* 4.5 9.9 - - + -
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Residues in contact with TYR 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A GLY 2.8 22.2 + - - +
567A VAL* 3.4 6.1 - - - +
569A LEU* 1.3 73.9 - - - +
571A GLU* 1.3 56.2 + - - +
573A LEU* 3.3 1.0 + - - -
574A ILE* 2.9 63.5 + - + +
576A GLN* 3.1 24.8 - - + +
577A SER 3.8 3.5 + - - -
578A PRO* 3.6 32.4 + - + +
596A PRO* 3.9 14.4 - - + -
597A PHE* 2.6 43.4 + - - +
598A TYR* 4.2 4.0 - + - -
610A LEU* 3.7 23.0 - - + +
614A PHE* 4.1 12.8 - + + -
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Residues in contact with GLU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A MET* 4.5 4.5 - - - +
470A ILE* 3.5 8.4 - - + +
507A LEU* 3.6 19.2 - - + +
544A ASP* 4.6 1.2 - - - +
545A TYR* 2.4 43.3 + - - -
567A VAL* 3.0 22.5 + - - +
568A LEU* 3.6 5.6 - - - +
570A TYR* 1.3 72.1 - - - +
572A MET* 1.3 61.5 + - - +
575A GLY* 2.7 30.0 + - - -
576A GLN 3.5 25.6 - - - +
577A SER* 2.6 29.7 + - - -
578A PRO* 4.5 0.4 - - + -
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Residues in contact with MET 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A LEU* 4.1 7.6 - - - -
470A ILE* 3.7 8.7 - - - +
475A LYS* 3.5 1.6 - - - +
476A PHE* 2.8 54.5 + - + +
481A ALA* 3.4 31.2 - - + +
484A TYR* 3.8 21.8 - - + -
485A ALA* 3.9 14.1 - - + +
507A LEU* 3.7 15.3 - - + -
568A LEU* 3.0 38.9 + - + +
569A LEU* 3.6 21.3 - - + +
571A GLU* 1.3 77.1 - - - +
573A LEU* 1.3 60.1 + - - +
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Residues in contact with LEU 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A LYS* 3.4 19.6 - - - +
476A PHE 4.4 5.9 - - - +
478A LEU* 4.0 29.8 - - + -
481A ALA* 3.5 21.8 - - + -
482A THR* 5.5 0.7 - - - +
569A LEU* 3.1 40.4 + - + +
570A TYR 3.9 2.2 - - - +
572A MET* 1.3 77.4 - - - +
574A ILE* 1.3 68.8 + - + +
601A TRP* 3.5 13.1 - - + -
602A LEU* 4.3 11.9 - - + -
606A ALA* 3.8 24.2 - - + -
610A LEU* 4.2 17.9 - - + -
633A LEU* 5.7 1.3 - - + -
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Residues in contact with ILE 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A HIS* 3.7 13.0 + - - -
475A LYS* 3.9 12.9 + - - +
570A TYR* 2.9 65.6 + - + +
573A LEU* 1.3 85.3 - - + +
575A GLY* 1.3 60.4 + - - +
576A GLN* 4.3 19.1 + - + +
597A PHE* 4.3 4.3 - - + +
598A TYR* 4.9 0.2 - - + -
599A PRO* 3.9 36.8 - - + -
601A TRP* 4.5 8.0 - - + -
602A LEU* 4.3 15.9 - - + -
610A LEU* 4.5 5.2 - - + -
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Residues in contact with GLY 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A ILE* 4.8 1.3 - - - -
474A HIS* 3.3 40.3 + - - +
475A LYS* 3.9 1.5 - - - +
571A GLU* 2.7 26.0 + - - -
573A LEU 3.8 0.2 - - - -
574A ILE* 1.3 74.6 - - - +
576A GLN* 1.3 62.4 + - - +
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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