Contacts of the helix formed by residues 602 - 616 (chain A) in PDB entry 2XPH
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 ASP 602 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463A LEU* 4.0 10.6 - - - +
597A GLN* 4.7 0.2 - - - -
599A ASN* 3.2 22.6 + - - +
601A SER* 1.3 73.0 + - - +
603A CYS* 1.3 56.5 + - - +
604A GLY 3.3 1.6 - - - -
605A MET* 3.4 9.6 + - + +
606A PHE* 2.8 51.8 + - + -
624A GLN* 3.0 26.8 + - - +
627A MET* 3.6 14.6 - - + +
628A PRO* 5.6 0.7 - - - +
631A ARG* 2.6 45.4 + - - +
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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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465A TRP* 3.8 21.3 - - - -
533A HIS* 3.4 28.7 - - + +
534A TRP* 3.9 25.1 - - - +
551A SER* 4.2 2.7 + - - -
597A GLN* 3.3 24.8 + - - +
600A GLY 3.3 18.6 + - - +
601A SER 2.9 3.7 + - - -
602A ASP* 1.3 78.6 - - - +
604A GLY* 1.3 67.2 + - - +
606A PHE* 3.3 2.4 + - - +
607A ALA* 3.1 28.1 + - - +
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Residues in contact with GLY 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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466A LEU* 4.0 15.8 - - - +
471A ILE* 3.9 11.2 - - - +
534A TRP* 3.7 24.2 - - - -
601A SER 3.9 3.6 + - - -
603A CYS* 1.3 82.4 - - - +
605A MET* 1.3 57.8 + - - +
607A ALA* 3.7 3.0 + - - +
608A CYS* 3.1 32.4 + - - -
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Residues in contact with MET 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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460A LEU* 3.7 22.9 - - - -
466A LEU* 3.9 16.8 - - + +
602A ASP* 3.4 12.0 + - - +
604A GLY* 1.3 74.3 - - - +
606A PHE* 1.3 57.1 + - - +
608A CYS* 3.2 3.4 + - - +
609A LYS* 2.7 44.6 + - + +
627A MET* 3.4 19.1 - - - -
630A PHE* 3.6 33.7 - - + -
631A ARG* 3.9 26.7 - - + +
634A MET* 3.4 32.1 - - + -
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Residues in contact with PHE 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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551A SER* 3.4 21.8 - - - +
595A PRO* 3.6 20.9 - - + -
596A GLN 3.4 23.3 - - - -
597A GLN* 3.5 21.1 - - + -
602A ASP* 2.8 31.4 + - + +
603A CYS 3.3 1.8 + - - +
605A MET* 1.3 75.1 - - - +
607A ALA* 1.3 60.6 + - - +
609A LYS* 4.5 1.3 - - - +
610A TYR* 2.7 60.3 + + + -
622A PHE* 3.9 20.6 - + - -
624A GLN* 3.8 25.6 - - - -
627A MET* 3.8 27.1 - - + -
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Residues in contact with ALA 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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471A ILE* 5.9 2.9 - - + -
475A MET* 4.3 6.7 - - + -
527A PRO* 6.2 1.8 - - + -
534A TRP* 4.6 5.6 - - + -
535A CYS* 4.3 30.5 - - - +
536A LEU* 3.4 13.0 - - + +
603A CYS 3.1 13.1 + - - +
604A GLY 3.8 5.4 - - - +
605A MET 3.3 0.2 - - - -
606A PHE* 1.3 80.7 - - - +
608A CYS* 1.3 65.2 + - - +
610A TYR* 4.0 9.8 - - - -
611A ALA* 3.2 21.7 + - - +
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Residues in contact with CYS 608 (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* 4.5 2.7 - - - -
471A ILE* 4.2 18.2 - - - -
474A TYR* 3.6 43.8 - - + -
475A MET* 3.9 16.6 - - - -
604A GLY 3.1 17.7 + - - +
605A MET 3.4 7.9 - - - +
607A ALA* 1.3 76.7 - - - +
609A LYS* 1.3 57.1 + - - +
611A ALA* 2.9 20.6 + - - +
612A ASP* 2.9 13.2 + - - +
634A MET* 3.8 19.5 - - + -
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Residues in contact with LYS 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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474A TYR* 3.5 17.5 + - + +
605A MET* 2.7 33.4 + - + +
606A PHE 4.2 0.2 - - - +
608A CYS* 1.3 70.2 - - - +
610A TYR* 1.3 67.2 + - - +
612A ASP* 2.9 32.0 + - - +
613A CYS* 3.1 27.4 + - - -
622A PHE* 3.6 24.9 - - + -
627A MET* 4.6 0.4 - - + -
630A PHE* 3.6 45.9 - - + +
633A ARG* 3.7 29.5 - - - +
634A MET* 4.7 3.1 - - + -
637A GLU* 4.8 3.4 + - - -
1649A GOL 4.0 9.6 - - - -
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Residues in contact with TYR 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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535A CYS* 6.4 0.2 - - - -
536A LEU* 4.2 8.5 - - + -
549A TYR* 3.9 25.1 - + + -
550A ASP 4.4 0.7 - - - -
551A SER* 3.3 34.4 - - - -
594A ILE* 3.4 17.9 - - + +
595A PRO* 2.2 50.5 + - + -
606A PHE* 2.7 37.7 + + + +
607A ALA* 3.7 9.6 - - - +
609A LYS* 1.3 72.9 - - - +
611A ALA* 1.3 52.5 + - - +
613A CYS* 3.4 2.6 + - - +
614A ILE* 2.9 49.1 + - + +
620A ILE* 3.6 28.2 - - + +
622A PHE* 4.0 8.5 - + - -
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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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475A MET* 3.9 13.2 - - + -
478A LEU* 3.6 17.3 - - + -
525A LEU* 4.2 11.0 - - + -
536A LEU* 3.7 15.7 - - + -
607A ALA 3.2 10.9 + - - +
608A CYS 2.9 12.0 + - - +
610A TYR* 1.3 77.3 - - - +
612A ASP* 1.3 52.2 + - - +
614A ILE* 3.7 5.3 - - - -
615A THR* 2.7 44.6 + - - +
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Residues in contact with ASP 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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474A TYR* 3.3 19.4 + - - +
478A LEU* 3.7 6.0 - - + +
481A ARG* 2.5 42.6 + - - +
608A CYS 2.9 8.6 + - - +
609A LYS* 2.9 40.2 + - - +
611A ALA* 1.3 72.2 - - - +
613A CYS* 1.3 67.1 + - - +
615A THR* 3.0 17.3 + - - -
616A LYS* 3.1 16.6 + - - +
633A ARG* 4.3 3.8 + - - -
643A LEU* 5.5 1.5 - - - +
1649A GOL 3.7 10.9 + - - -
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Residues in contact with CYS 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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609A LYS 3.1 12.6 + - - -
610A TYR 3.7 7.2 - - - +
612A ASP* 1.3 80.7 - - - +
614A ILE* 1.3 62.4 + - - +
616A LYS* 3.2 6.4 + - - +
617A ASP 3.0 3.8 + - - -
618A ARG* 2.9 41.9 + - - +
620A ILE* 3.8 26.5 - - + -
621A ASN* 3.9 24.9 - - - -
622A PHE* 4.0 10.8 - - - -
1649A GOL 3.9 16.8 - - - -
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Residues in contact with ILE 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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523A ILE* 4.2 10.4 - - + +
525A LEU* 5.1 1.3 - - + -
536A LEU* 4.8 0.7 - - + -
538A VAL* 4.1 30.5 - - + -
540A ASP* 6.0 1.3 - - - +
543A LYS* 6.2 2.0 - - - +
549A TYR* 3.4 48.0 - - + +
610A TYR* 2.9 33.4 + - + +
611A ALA* 3.7 6.3 - - - +
613A CYS* 1.3 78.2 - - - +
615A THR* 1.3 66.6 + - + +
617A ASP* 3.1 22.4 + - - +
618A ARG 4.8 3.6 - - - +
620A ILE* 4.4 11.0 - - + -
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Residues in contact with THR 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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478A LEU* 4.0 13.1 - - + +
481A ARG* 3.2 15.0 + - - -
482A SER* 5.9 0.8 - - - -
487A LEU* 4.5 5.6 - - - +
488A PRO* 3.2 29.5 - - - +
490A VAL* 3.6 29.4 - - + -
523A ILE* 4.6 8.5 - - + -
525A LEU* 4.0 29.8 - - + -
611A ALA 2.7 29.5 + - - +
612A ASP* 3.0 11.3 + - - -
614A ILE* 1.3 76.1 - - + +
616A LYS* 1.3 54.1 + - - +
617A ASP 3.2 0.4 - - - -
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Residues in contact with LYS 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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481A ARG* 3.2 28.1 - - - +
487A LEU* 4.3 23.0 - - + +
488A PRO* 5.1 0.4 - - - -
612A ASP* 3.1 35.3 + - - +
613A CYS* 3.8 7.4 - - - +
615A THR* 1.3 74.0 - - - +
617A ASP* 1.3 70.3 + - - +
618A ARG* 3.2 29.4 + - + +
633A ARG* 5.1 0.2 - - - +
644A LEU* 4.5 10.1 + - - -
1649A GOL 3.2 29.7 + - - -
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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
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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