Contacts of the helix formed by residues 588 - 609 (chain A) in PDB entry 4PO2
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 588 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A ARG* 4.1 8.7 - - + -
586A LEU 4.4 6.5 - - - +
587A ALA* 1.3 76.3 - - - +
589A LYS* 1.3 67.5 + - - +
590A ASP* 3.3 17.1 - - - +
591A GLU* 2.9 27.2 + - - +
592A PHE* 3.1 18.2 + - - -
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Residues in contact with LYS 589 (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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531A VAL 5.7 0.7 - - - +
534A GLU* 3.5 45.3 + - + +
535A ARG* 4.0 18.5 - - + +
537A SER* 6.3 0.2 - - - -
538A ALA* 4.0 14.0 - - + +
588A GLU* 1.3 72.8 - - - +
590A ASP* 1.3 58.5 + - - +
592A PHE* 3.3 10.8 + - - +
593A GLU* 2.7 68.1 + - - +
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Residues in contact with ASP 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A GLU* 3.8 18.8 - - - +
589A LYS* 1.3 77.7 - - - +
591A GLU* 1.3 73.2 + - - +
593A GLU* 4.0 10.6 - - - +
594A HIS* 2.9 30.0 + - - +
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Residues in contact with GLU 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A TRP* 4.1 21.4 - - + -
587A ALA* 3.3 11.7 - - - +
588A GLU* 2.9 38.3 + - - +
590A ASP* 1.3 90.2 + - - +
592A PHE* 1.3 59.3 + - - +
594A HIS* 3.3 6.4 + - - +
595A LYS* 2.9 31.4 + - - +
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Residues in contact with PHE 592 (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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535A ARG* 3.9 15.5 - - + -
538A ALA* 3.9 17.3 - - + +
539A LYS* 3.6 46.4 - - + -
542A LEU* 3.7 16.3 - - + +
580A TRP* 3.5 31.0 - + - -
581A LEU* 3.8 13.5 - - + -
584A ASN 4.2 7.6 - - - -
585A THR 4.7 3.4 - - - -
587A ALA* 3.1 34.1 - - + -
588A GLU 3.1 22.4 + - - -
589A LYS* 3.6 6.5 - - - +
591A GLU* 1.3 74.3 - - - +
593A GLU* 1.3 59.6 + - - +
595A LYS* 3.3 3.5 + - - +
596A ARG* 2.9 28.6 + - - +
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Residues in contact with GLU 593 (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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538A ALA* 4.4 10.0 - - + +
589A LYS* 2.7 60.3 + - + +
590A ASP* 4.0 9.3 - - - +
592A PHE* 1.3 74.9 - - - +
594A HIS* 1.3 59.8 + - - +
596A ARG* 3.3 27.7 + - - +
597A LYS* 2.9 37.4 + - + +
550B LYS* 5.3 3.0 + - - -
554B GLU* 5.0 9.2 - - - +
701B SO4 4.9 6.5 + - - -
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Residues in contact with HIS 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A ASP 2.9 19.0 + - - +
591A GLU* 3.6 7.1 + - - +
593A GLU* 1.3 75.1 - - - +
595A LYS* 1.3 62.6 + - - +
597A LYS* 3.3 7.5 + - + +
598A GLU* 2.9 56.0 + - - +
556B GLU* 3.0 36.6 + - - -
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Residues in contact with LYS 595 (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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542A LEU* 3.8 20.2 - - + -
576A GLU* 4.7 9.4 + - - +
577A VAL* 3.9 24.9 - - + +
580A TRP* 3.6 49.8 - - + +
591A GLU 2.9 17.2 + - - +
592A PHE* 3.5 5.4 - - - +
593A GLU 3.2 0.2 - - - -
594A HIS* 1.3 79.5 + - - +
596A ARG* 1.3 57.2 + - - +
598A GLU* 3.1 37.7 + - - +
599A LEU* 2.9 27.0 + - - +
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Residues in contact with ARG 596 (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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538A ALA* 5.3 2.6 + - - +
541A ALA* 4.3 21.7 - - - +
542A LEU* 3.6 32.1 - - + +
545A TYR* 4.1 19.1 - - + -
592A PHE 2.9 16.2 + - - +
593A GLU* 3.3 28.1 + - - +
595A LYS* 1.3 75.4 - - - +
597A LYS* 1.3 65.8 + - - +
599A LEU* 3.2 4.9 + - - +
600A GLU* 2.9 55.6 + - - +
433B ASP* 6.3 0.8 - - - +
434B ASN* 5.1 7.4 - - - +
701B SO4 3.2 37.0 + - - -
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Residues in contact with LYS 597 (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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593A GLU* 2.9 23.4 + - + +
594A HIS* 3.6 7.0 - - - +
595A LYS 3.3 0.2 - - - -
596A ARG* 1.3 97.9 - - - +
598A GLU* 1.3 59.3 + - - +
600A GLU* 3.1 29.4 + - + +
601A GLN* 2.9 28.9 + - - +
551B SER* 4.8 6.3 - - - +
554B GLU* 3.3 56.5 - - + +
555B ASP* 4.8 3.4 - - - +
556B GLU* 4.1 16.4 + - + +
701B SO4 3.0 23.7 + - - -
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Residues in contact with GLU 598 (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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573A LYS* 4.2 24.7 + - - +
576A GLU* 4.3 2.9 - - - +
594A HIS* 2.9 45.2 + - - +
595A LYS* 3.2 38.4 + - + +
597A LYS* 1.3 77.0 - - - +
599A LEU* 1.3 61.7 + - - +
601A GLN* 3.3 20.7 + - - +
602A VAL* 3.6 10.6 + - - +
556B GLU* 4.0 23.9 - - + +
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Residues in contact with LEU 599 (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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542A LEU* 4.9 2.2 - - + -
545A TYR* 3.5 30.5 - - + +
546A ALA* 3.9 28.3 - - + +
549A MET* 4.9 0.7 - - + -
573A LYS* 3.6 33.6 - - + +
574A CYS* 4.0 16.8 - - - +
577A VAL* 4.1 15.7 - - + -
595A LYS 2.9 12.4 + - - +
596A ARG* 3.6 9.0 - - - +
598A GLU* 1.3 75.2 - - - +
600A GLU* 1.3 59.5 + - - +
602A VAL* 3.1 5.9 + - - +
603A CYS* 2.9 46.8 + - - -
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Residues in contact with GLU 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A TYR* 3.5 28.9 - - + +
596A ARG* 2.9 47.1 + - - +
597A LYS* 3.1 34.9 + - + +
599A LEU* 1.3 75.1 - - - +
601A GLN* 1.3 64.2 + - - +
604A ASN* 2.9 50.0 + - - +
434B ASN* 4.6 9.4 + - - -
551B SER* 6.2 0.2 - - - -
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Residues in contact with GLN 601 (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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597A LYS 2.9 14.5 + - - +
598A GLU* 3.5 11.7 - - - +
599A LEU 3.2 0.4 - - - -
600A GLU* 1.3 75.0 - - - +
602A VAL* 1.3 62.6 + - + +
605A PRO* 3.4 19.4 - - - +
555B ASP* 4.9 6.7 - - - +
556B GLU* 3.2 32.9 + - + +
557B GLY* 3.8 23.3 - - - +
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Residues in contact with VAL 602 (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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569A LYS* 4.2 39.0 - - + +
570A VAL* 4.4 5.2 - - - +
573A LYS* 3.8 32.5 - - + +
598A GLU 3.6 6.7 + - - +
599A LEU 3.1 8.8 + - - +
601A GLN* 1.3 80.5 - - + +
603A CYS* 1.3 65.9 + - - +
605A PRO* 3.6 11.0 - - - +
606A ILE* 3.6 17.7 - - + +
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Residues in contact with CYS 603 (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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545A TYR* 3.4 18.4 - - - +
549A MET* 3.6 37.0 - - + -
570A VAL* 4.1 18.2 - - - -
599A LEU* 2.9 38.7 + - - +
600A GLU 3.2 0.2 + - - -
602A VAL* 1.3 82.9 - - - +
604A ASN* 1.3 66.6 + - - +
606A ILE* 3.1 8.5 + - - +
607A ILE* 3.0 25.7 + - - +
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Residues in contact with ASN 604 (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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545A TYR* 3.7 12.3 + - - -
600A GLU* 2.9 51.1 + - - +
603A CYS* 1.3 72.2 - - - +
605A PRO* 1.4 60.3 - - + +
607A ILE* 3.9 3.7 - - - +
608A SER* 2.8 33.3 + - - -
434B ASN* 5.2 1.7 - - - +
466B PRO 4.7 1.9 - - - +
467B ALA* 4.5 4.7 - - - -
468B PRO* 3.5 40.2 - - + +
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Residues in contact with PRO 605 (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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600A GLU 3.9 0.2 - - - +
601A GLN* 3.4 25.4 - - - +
602A VAL* 3.6 7.9 - - - +
603A CYS 3.6 0.9 - - - -
604A ASN* 1.4 95.7 - - + +
606A ILE* 1.3 58.8 + - + +
608A SER* 3.8 5.6 - - - -
609A GLY* 3.0 24.9 + - - -
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Residues in contact with ILE 606 (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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562A ILE* 3.7 29.2 - - + -
566A ASP* 3.7 39.0 - - + +
569A LYS* 4.5 11.7 - - + -
570A VAL* 3.7 24.7 - - + -
602A VAL* 3.6 19.5 - - + +
603A CYS* 3.1 8.1 + - - +
605A PRO* 1.3 78.0 - - + +
607A ILE* 1.3 72.4 + - + +
609A GLY* 3.3 9.7 + - - -
610A LEU* 3.7 13.6 + - + +
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Residues in contact with ILE 607 (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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549A MET* 4.0 25.6 - - + -
552A ALA* 5.3 1.1 - - + -
553A VAL* 5.0 9.2 - - + -
558A LEU* 5.0 4.0 - - + -
562A ILE* 5.8 0.9 - - + -
603A CYS 3.0 14.8 + - - +
604A ASN* 4.1 3.8 - - - +
606A ILE* 1.3 81.1 - - + +
608A SER* 1.3 66.6 + - - +
610A LEU* 3.1 29.8 + - + +
611A TYR* 3.5 8.8 - - + -
465B PRO* 3.8 34.5 - - + -
466B PRO* 3.4 28.3 - - + +
467B ALA* 3.7 17.3 - - + -
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Residues in contact with SER 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ASN 2.8 21.3 + - - -
605A PRO* 3.8 6.7 - - - -
607A ILE* 1.3 75.8 - - - +
609A GLY* 1.3 57.4 + - - +
611A TYR* 3.0 21.0 + - - +
612A GLN* 3.6 8.3 + - - +
468B PRO* 6.0 2.0 - - - +
471B VAL* 3.9 30.0 - - - +
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Residues in contact with GLY 609 (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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605A PRO 3.0 17.4 + - - -
606A ILE* 3.3 4.7 + - - -
607A ILE 3.2 1.0 - - - -
608A SER* 1.3 76.4 - - - +
610A LEU* 1.3 61.3 + - - +
611A TYR 3.1 1.1 + - - -
612A GLN* 3.6 34.0 + - - +
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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
------------------------------------------------------------
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