Contacts of the helix formed by residues 598 - 614 (chain A) in PDB entry 1QXP
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 598 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A MET* 5.9 9.6 - - + +
594A LEU* 2.0 39.8 - - + +
595A GLY* 3.5 8.7 - - - -
597A VAL* 1.3 86.4 + - - +
599A PHE* 1.3 61.9 + - - +
600A ASN 2.9 7.3 + - - +
601A ILE* 3.5 26.9 + - + +
602A LEU* 3.6 10.9 + - - +
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Residues in contact with PHE 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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541A SER* 6.5 0.9 - - - -
555A LEU* 3.4 34.8 - - + -
558A ILE* 4.0 27.1 - - + -
559A LEU* 4.1 15.5 - - + -
594A LEU* 5.1 6.9 - - + +
595A GLY 3.2 24.5 + - - +
596A LEU* 4.5 7.4 - - - -
597A VAL 3.6 0.4 - - - -
598A GLU* 1.3 82.0 - - - +
600A ASN* 1.3 56.4 + - - +
602A LEU* 4.1 17.5 - - + -
603A TRP* 3.2 33.8 + + + +
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Residues in contact with ASN 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A LEU 5.0 3.2 + - - +
597A VAL* 3.8 21.0 - - - +
598A GLU* 2.9 2.4 - - - +
599A PHE* 1.3 77.5 - - - +
601A ILE* 1.3 55.3 + - + +
602A LEU 2.7 14.7 + - - -
603A TRP* 2.9 20.3 + - - +
604A ASN* 3.5 11.3 + - - +
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Residues in contact with ILE 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A VAL 4.8 4.3 - - - +
598A GLU* 3.5 23.5 + - + +
600A ASN* 1.3 75.7 - - + +
602A LEU* 1.4 57.9 - - + +
604A ASN* 4.7 3.1 - - - +
605A ARG* 4.1 29.9 + - - +
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Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 4.3 22.4 - - + -
559A LEU* 4.6 8.3 - - + -
582A MET* 3.3 52.7 - - + +
585A LEU* 5.4 2.5 - - + -
586A MET* 5.4 2.7 - - + +
598A GLU 3.6 14.3 + - - +
599A PHE* 4.1 21.1 - - + -
600A ASN 2.7 0.6 - - - -
601A ILE* 1.4 79.9 - - + +
603A TRP* 1.2 71.7 + - - +
604A ASN 3.1 1.8 - - - -
605A ARG* 2.8 45.1 + - + +
606A ILE* 3.0 7.8 + - + +
669A VAL* 6.1 0.2 - - + -
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Residues in contact with TRP 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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559A LEU* 3.9 28.9 - - + -
599A PHE* 3.2 27.4 + + + +
600A ASN* 2.9 12.9 + - - +
602A LEU* 1.2 86.1 - - - +
604A ASN* 1.3 80.6 - - - +
606A ILE* 3.0 23.6 + - + +
607A ARG* 3.3 39.0 + - + +
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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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600A ASN* 3.5 10.2 + - - +
601A ILE 5.0 3.1 - - - +
602A LEU 3.1 0.6 - - - -
603A TRP* 1.3 103.9 - - - +
605A ARG* 1.4 68.0 + - - +
606A ILE 2.9 1.8 - - - -
607A ARG* 2.7 31.8 + - + +
608A ASN* 2.8 23.0 + - - +
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Residues in contact with ARG 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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585A LEU* 3.0 49.7 - - - +
601A ILE* 4.1 24.9 + - - +
602A LEU* 2.8 39.6 + - + +
604A ASN* 1.4 72.4 - - - +
606A ILE* 1.4 71.4 - - + +
608A ASN* 3.1 8.2 - - - +
609A TYR* 3.0 47.4 + - + +
669A VAL* 6.0 3.1 - - - +
672A GLU* 3.0 34.2 + - - +
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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
----------------------------------------------------------
559A LEU* 3.6 38.8 - - + -
574A PHE* 6.1 2.5 - - + -
582A MET* 3.9 20.9 - - - -
602A LEU* 3.0 13.1 + - + +
603A TRP* 3.3 20.0 - - + +
604A ASN 2.9 1.4 + - - -
605A ARG* 1.4 80.0 - - + +
607A ARG* 1.3 54.1 + - - +
608A ASN 2.7 1.0 + - - -
609A TYR* 2.5 38.1 + - + +
610A LEU* 2.9 9.7 + - + -
661A PHE* 3.7 31.0 - - + -
665A VAL* 4.8 7.4 - - + -
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Residues in contact with ARG 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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603A TRP* 3.3 40.7 + - + +
604A ASN* 2.7 24.8 + - + +
606A ILE* 1.3 73.7 - - - +
608A ASN* 1.3 50.4 + - - +
610A LEU* 3.1 22.5 - - + +
611A THR* 2.6 36.3 + - - +
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Residues in contact with ASN 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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604A ASN* 2.8 18.5 + - + +
605A ARG* 3.1 14.9 - - - +
606A ILE 2.7 2.4 + - - -
607A ARG* 1.3 69.5 - - - +
609A TYR* 1.2 75.3 + - + +
610A LEU 3.0 0.4 - - - -
611A THR* 2.8 18.3 + - - -
612A ILE* 3.3 20.5 - - - +
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Residues in contact with TYR 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 ARG* 3.2 40.9 + - + +
606A ILE* 2.5 17.9 + - + +
608A ASN* 1.2 82.9 - - + +
610A LEU* 1.3 54.0 + - - +
612A ILE* 2.7 41.5 + - + +
613A PHE 3.2 5.4 + - - -
636A ALA* 4.9 16.4 - - + -
638A PHE* 5.3 2.4 - - - -
661A PHE* 4.0 4.7 - - + -
664A PHE* 4.1 8.1 - - + -
665A VAL* 4.0 31.4 - - + -
668A LEU* 3.9 34.7 + - + -
669A VAL* 4.3 13.7 - - + -
672A GLU* 3.4 28.1 - - - +
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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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606A ILE* 2.9 7.6 + - + +
607A ARG* 3.1 31.4 - - + +
609A TYR* 1.3 78.4 - - - +
611A THR* 1.3 59.8 + - - +
612A ILE 3.2 0.5 + - - -
613A PHE* 5.0 4.7 - - + -
614A ARG* 3.2 48.1 + - + +
661A PHE* 3.5 38.2 - - + -
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Residues in contact with THR 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 ARG* 2.6 17.4 + - - +
608A ASN* 2.8 18.3 + - - -
610A LEU* 1.3 75.6 - - - +
612A ILE* 1.3 60.8 - - + +
614A ARG* 4.4 6.0 - - - +
615A LYS* 3.1 45.5 + - - +
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Residues in contact with ILE 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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608A ASN* 3.3 26.7 - - - +
609A TYR* 2.7 16.5 + - + +
611A THR* 1.3 80.5 - - + +
613A PHE* 1.3 66.8 + - - +
614A ARG 2.9 2.5 - - - -
615A LYS* 2.9 26.4 + - + +
616A PHE* 3.4 20.5 - - + -
632A ALA* 4.5 7.6 - - + +
635A ALA* 3.5 49.8 - - + +
636A ALA* 3.8 11.2 - - + +
664A PHE* 4.6 10.8 - - + -
668A LEU* 6.3 0.4 - - + -
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Residues in contact with PHE 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 TYR 3.2 4.8 + - - +
610A LEU* 4.4 6.7 - - + +
612A ILE* 1.3 75.3 - - - +
614A ARG* 1.3 68.8 + - - +
616A PHE* 3.0 15.5 + - - +
617A ASP* 3.0 23.5 + - + +
622A GLY* 2.6 33.9 - - - -
623A SER 3.4 14.6 - - - -
624A MET* 3.7 19.2 - - + +
659A ILE 3.5 8.5 - - - -
660A ASP* 3.3 20.9 - - - -
661A PHE* 3.2 38.4 - + + -
664A PHE* 3.5 32.3 - + + -
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Residues in contact with ARG 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* 3.2 40.2 + - + +
611A THR* 4.4 7.0 - - - +
612A ILE 2.9 1.6 - - - -
613A PHE* 1.3 83.0 - - - +
615A LYS* 1.4 54.3 + - - +
617A ASP* 2.7 45.4 + - - +
618A LEU* 3.2 8.4 + - - +
620A LYS* 3.2 56.3 - - - +
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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