Contacts of the helix formed by residues 599 - 620 (chain A) in PDB entry 2PZ5
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 THR 599 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A GLN 4.7 5.2 - - - +
598A MET* 1.3 76.7 - - - +
600A PHE* 1.3 58.3 + - - +
601A LYS* 3.7 11.2 + - - +
602A ASP* 2.7 62.5 + - - +
603A LEU* 3.1 12.0 + - - +
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Residues in contact with PHE 600 (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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598A MET 4.1 0.6 + - - -
599A THR* 1.3 71.7 - - - +
601A LYS* 1.3 60.3 + - - +
603A LEU* 3.3 13.8 + - + +
604A VAL* 3.1 35.6 + - + +
697A PHE* 4.0 13.2 - + - -
727A ASN 4.8 10.3 - - - -
728A CYS* 4.9 0.7 - - - -
729A THR* 3.9 27.4 - - + -
732A LEU* 3.6 33.2 - - + -
760A ILE* 5.3 4.7 - - + -
764A THR* 3.6 34.8 - - + -
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Residues in contact with LYS 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A THR* 3.1 8.2 + - - +
600A PHE* 1.3 77.7 - - - +
602A ASP* 1.3 73.2 + - - +
604A VAL* 3.0 8.8 + - - +
605A SER* 2.8 37.4 + - - -
761A LEU* 4.1 8.7 - - + -
764A THR* 4.2 16.8 - - + +
765A THR* 3.2 39.0 - - + -
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Residues in contact with ASP 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A GLN 4.3 2.4 - - - +
598A MET* 3.7 27.3 - - + +
599A THR* 2.7 55.2 + - - +
601A LYS* 1.3 83.1 + - - +
603A LEU* 1.3 57.6 + - - +
605A SER* 3.1 8.9 + - - -
606A CYS* 2.8 30.1 + - - +
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Residues in contact with LEU 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A LEU* 4.2 1.6 - - + -
598A MET* 3.7 26.7 - - + +
599A THR 3.1 13.4 + - - +
600A PHE* 3.5 14.4 - - + +
601A LYS 3.2 0.2 - - - -
602A ASP* 1.3 75.6 - - - +
604A VAL* 1.3 58.5 + - - +
606A CYS* 3.3 7.2 - - - +
607A THR* 2.9 31.8 + - - -
696A ILE* 3.7 21.6 - - + +
697A PHE* 3.5 36.1 - - + +
699A LEU* 3.7 30.7 - - + -
727A ASN 4.9 6.5 - - - +
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Residues in contact with VAL 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE* 3.1 46.7 - - + +
601A LYS* 3.0 8.6 + - - +
603A LEU* 1.3 73.1 - - - +
605A SER* 1.3 56.5 + - - +
607A THR* 3.2 7.1 + - - -
608A TYR* 2.7 33.1 + - + +
697A PHE* 4.1 12.1 - - + -
732A LEU* 4.2 4.9 - - + -
757A LEU* 4.5 14.5 - - + +
760A ILE* 4.5 9.6 - - + -
761A LEU* 3.9 35.9 - - + +
764A THR* 5.0 2.7 - - - +
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Residues in contact with SER 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A LYS* 2.8 20.8 + - - -
602A ASP* 3.5 11.7 - - - -
604A VAL* 1.3 73.0 - - - +
606A CYS* 1.3 57.5 + - - +
608A TYR* 3.1 6.0 + - - +
609A GLN* 2.8 56.1 + - - +
761A LEU* 4.1 19.8 - - - +
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Residues in contact with CYS 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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572A LEU* 3.8 9.0 - - - -
576A LEU* 5.8 0.2 - - - -
598A MET* 4.9 9.0 - - + -
602A ASP 2.8 13.2 + - - +
603A LEU* 3.3 13.5 - - - +
605A SER* 1.3 77.3 - - - +
607A THR* 1.3 62.4 + - - +
609A GLN* 3.3 5.4 + - - +
610A LEU* 3.2 27.1 + - - +
640A MET* 3.2 47.5 - - + +
696A ILE* 3.7 26.0 - - - -
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Residues in contact with THR 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A LEU 2.9 15.4 + - - -
604A VAL* 3.5 9.4 - - - -
606A CYS* 1.3 77.9 - - - +
608A TYR* 1.3 62.3 + - - +
610A LEU* 3.2 5.3 + - - +
611A ALA* 3.0 22.0 + - - +
689A PHE* 3.7 6.6 - - + -
693A MET* 3.9 29.1 - - + +
696A ILE* 3.9 16.6 - - + +
697A PHE* 3.5 19.4 - - + -
757A LEU* 3.5 28.5 - - + -
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Residues in contact with TYR 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A VAL* 2.7 20.6 + - + +
605A SER* 3.4 5.8 - - - +
607A THR* 1.3 74.8 - - - +
609A GLN* 1.3 71.7 + - + +
611A ALA* 3.1 4.5 + - - +
612A ARG* 3.0 64.4 + - + +
754A VAL* 3.7 21.1 - - + +
757A LEU* 3.9 18.3 - - + +
758A ASP* 3.5 53.0 + - + +
761A LEU* 3.8 24.9 - - + -
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Residues in contact with GLN 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A ASN* 3.2 43.5 + - - +
605A SER* 2.8 47.5 + - - +
606A CYS* 3.6 8.8 - - - +
608A TYR* 1.3 82.9 - - + +
610A LEU* 1.3 61.3 + - - +
612A ARG* 3.5 3.1 + - - +
613A GLY 3.2 10.6 + - - -
638A ASN 4.2 8.7 + - - -
639A VAL* 3.6 10.9 - - - +
640A MET* 3.1 33.5 + - + +
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Residues in contact with LEU 610 (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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546A ASN 5.2 0.4 - - - +
572A LEU* 4.1 12.1 - - + -
606A CYS* 3.2 22.6 + - - +
607A THR 3.2 6.3 + - - +
609A GLN* 1.3 75.0 - - - +
611A ALA* 1.3 67.3 + - - +
613A GLY* 3.2 2.6 + - - +
614A MET* 3.0 26.3 + - + +
632A VAL* 3.9 21.8 - - + -
640A MET* 3.8 20.4 - - + +
642A ILE* 3.9 24.4 - - + +
689A PHE* 3.9 14.8 - - + -
692A LEU* 4.1 15.5 - - + -
696A ILE* 3.8 25.4 - - + -
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Residues in contact with ALA 611 (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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607A THR 3.0 12.9 + - - +
608A TYR 3.1 8.5 + - - +
610A LEU* 1.3 75.8 - - - +
612A ARG* 1.3 52.5 + - - +
614A MET* 3.1 5.4 + - - +
615A GLU* 2.7 35.9 + - - +
689A PHE* 3.7 16.0 - - + -
750A PHE* 4.4 4.8 - - + +
753A LEU* 4.7 4.7 - - + -
754A VAL* 3.6 22.1 - - + +
757A LEU* 3.7 21.1 - - + -
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Residues in contact with ARG 612 (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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544A HIS* 3.8 12.8 + - + +
546A ASN* 3.9 11.6 + - - +
608A TYR* 3.0 57.4 + - + +
609A GLN* 3.6 9.0 - - - +
611A ALA* 1.3 76.5 - - - +
613A GLY* 1.3 61.8 + - - +
615A GLU* 3.3 9.7 + - - +
616A TYR* 3.0 23.7 + - - +
754A VAL* 3.9 20.1 - - + +
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Residues in contact with GLY 613 (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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544A HIS* 3.9 18.5 - - - -
546A ASN* 4.1 9.2 - - - -
547A ILE* 3.9 6.5 - - - +
609A GLN 3.2 4.6 + - - -
610A LEU 3.2 6.9 + - - -
612A ARG* 1.3 79.4 - - - +
614A MET* 1.3 56.6 + - - +
616A TYR* 3.3 3.1 + - - +
617A LEU* 2.8 28.8 + - - +
642A ILE* 3.7 15.7 - - - -
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Residues in contact with MET 614 (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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610A LEU* 3.0 15.9 + - + +
611A ALA 3.7 2.9 - - - +
613A GLY* 1.3 73.2 - - - +
615A GLU* 1.3 61.2 + - - +
617A LEU* 3.6 29.1 - - + +
618A ALA* 2.7 33.6 + - + +
622A CYS 5.4 0.9 - - - +
624A HIS* 4.3 1.8 - - + -
627A LEU* 3.7 28.9 - - + -
642A ILE* 3.6 15.9 - - + +
685A ASP* 3.5 29.8 - - + +
689A PHE* 4.4 3.8 - - + -
692A LEU* 6.2 0.2 - - + -
750A PHE* 3.4 49.7 - - + -
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Residues in contact with GLU 615 (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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611A ALA 2.7 20.2 + - - +
612A ARG* 3.6 11.3 - - - +
614A MET* 1.3 73.5 - - - +
616A TYR* 1.3 62.6 + - - +
618A ALA* 3.6 3.3 - - - +
619A SER* 2.9 23.7 + - - -
750A PHE* 3.6 15.2 - - + +
751A LYS* 3.6 35.1 - - + +
754A VAL* 3.6 31.0 - - + +
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Residues in contact with TYR 616 (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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541A ILE* 2.7 38.6 + - + -
542A GLY* 3.8 8.5 - - - -
543A LYS 3.9 13.2 + - - -
544A HIS* 3.4 47.8 - + + +
547A ILE* 3.8 7.9 - - + -
612A ARG 3.0 9.3 + - - +
613A GLY 3.6 5.6 - - - +
615A GLU* 1.3 78.7 - - - +
617A LEU* 1.3 65.5 + - - +
619A SER* 2.5 28.1 + - - -
620A GLN* 3.0 33.7 + - + +
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Residues in contact with LEU 617 (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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541A ILE* 3.3 28.9 - - + -
547A ILE* 4.5 4.5 - - + -
613A GLY 2.8 17.3 + - - +
614A MET* 3.6 35.2 - - + +
616A TYR* 1.3 80.8 - - - +
618A ALA* 1.3 65.1 + - - +
620A GLN* 3.0 14.5 + - - +
622A CYS* 3.3 52.6 + - + +
624A HIS* 4.0 19.1 - - + +
642A ILE* 5.0 3.4 - - + -
645A PHE* 4.1 20.0 - - + -
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Residues in contact with ALA 618 (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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614A MET* 2.7 22.8 + - + +
615A GLU* 3.6 5.6 - - - +
617A LEU* 1.3 73.6 - - - +
619A SER* 1.3 57.9 + - - +
621A LYS* 2.9 21.5 + - - +
622A CYS 4.0 1.6 - - - -
682A HIS* 3.5 39.6 + - + +
750A PHE* 4.2 16.2 - - + -
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Residues in contact with SER 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A GLU* 2.9 14.5 + - - -
616A TYR* 2.5 29.5 + - - -
618A ALA* 1.3 78.4 - - - +
620A GLN* 1.3 71.8 + - - +
621A LYS* 3.0 11.5 + - - +
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Residues in contact with GLN 620 (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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540A MET* 3.5 22.8 - - + +
541A ILE* 3.4 37.6 - - + +
616A TYR* 3.0 37.3 + - + +
617A LEU 3.0 9.1 + - - +
619A SER* 1.3 93.5 + - - +
621A LYS* 1.3 71.5 + - - +
622A CYS 3.3 1.2 + - - -
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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