Contacts of the helix formed by residues 489 - 503 (chain A) in PDB entry 2P6U
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 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A THR* 4.7 10.4 - - - +
416A ARG* 3.4 22.2 + - - -
417A PHE* 3.9 17.2 - - + +
488A ILE* 1.3 70.7 - - - +
490A PRO* 1.3 85.8 - - - +
491A LEU* 3.0 17.6 + - - +
492A THR* 2.7 30.8 + - - +
493A GLY 3.0 3.8 + - - -
518A PRO* 3.6 15.9 - - + +
519A ASP* 2.6 30.3 + - - +
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Residues in contact with PRO 490 (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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416A ARG* 3.9 31.2 - - + +
417A PHE* 3.9 17.9 - - + +
420A LEU* 3.3 30.1 - - + -
462A LEU* 4.7 3.1 - - + -
465A TRP* 3.7 7.1 - - + -
467A MET* 3.1 21.3 - - - +
483A VAL* 3.6 12.3 - - + -
488A ILE 3.2 6.0 - - - +
489A ASP* 1.3 92.3 - - - +
491A LEU* 1.3 56.5 + - - +
493A GLY 3.7 0.2 - - - -
494A PHE* 2.9 23.2 + - - +
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Residues in contact with LEU 491 (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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416A ARG* 3.9 16.8 - - - +
465A TRP* 3.4 36.3 - - + -
489A ASP* 3.0 14.6 + - - +
490A PRO* 1.3 78.9 - - - +
492A THR* 1.3 64.2 + - - +
494A PHE* 3.0 9.1 + - + -
495A ILE* 2.9 55.8 + - + +
516A ARG 5.8 0.2 - - - +
518A PRO* 3.8 20.2 - - + -
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Residues in contact with THR 492 (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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488A ILE* 3.4 22.0 - - + -
489A ASP 2.7 12.7 + - - -
491A LEU* 1.3 77.6 - - - +
493A GLY* 1.3 63.7 + - - +
494A PHE 2.9 1.4 + - - -
495A ILE* 3.0 6.4 + - - +
496A PHE* 3.0 37.7 + - + -
517A THR* 2.8 29.0 + - + +
518A PRO* 2.9 24.1 - - - +
519A ASP* 3.2 22.9 + - - +
600A LEU* 4.6 2.2 - - + -
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Residues in contact with GLY 493 (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* 4.0 6.0 - - - +
479A LEU* 4.9 0.9 - - - +
483A VAL* 4.3 10.5 - - - -
488A ILE* 3.7 8.3 - - - +
489A ASP 3.0 7.6 + - - -
490A PRO 3.3 4.0 + - - -
491A LEU 3.3 0.2 - - - -
492A THR* 1.3 80.7 - - - +
494A PHE* 1.3 57.0 + - - +
497A HIS* 3.0 30.0 + - - +
607A ILE* 3.6 25.5 - - - +
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Residues in contact with PHE 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ASN 4.9 1.6 - - - -
465A TRP* 3.5 73.1 - + + -
467A MET* 3.7 6.0 - - + +
490A PRO 2.9 14.0 + - - +
491A LEU* 3.0 14.3 + - + +
493A GLY* 1.3 74.7 - - - +
495A ILE* 1.3 72.2 + - + +
496A PHE 2.8 2.0 + - - -
497A HIS* 3.0 10.6 + + + -
498A ASP* 2.6 57.8 + - + +
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Residues in contact with ILE 495 (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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491A LEU* 2.9 48.3 + - + +
492A THR* 3.5 4.5 - - - +
494A PHE* 1.3 77.1 - - + +
496A PHE* 1.3 64.8 + - + +
498A ASP* 4.7 2.7 - - - -
499A VAL* 3.1 29.5 + - + +
513A LEU* 3.7 23.7 - - + +
516A ARG* 4.0 37.2 - - + +
517A THR* 3.8 10.8 - - - +
518A PRO* 3.7 17.7 - - + -
711A PO4 5.0 8.1 - - - +
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Residues in contact with PHE 496 (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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492A THR* 3.0 29.5 + - + -
493A GLY 3.7 4.9 - - - +
494A PHE 2.8 1.4 + - - -
495A ILE* 1.3 76.0 - - + +
497A HIS* 1.3 68.6 + - - +
498A ASP 2.8 1.9 + - - -
500A LEU* 2.9 33.5 + - + +
513A LEU* 3.7 34.3 - - + -
514A ILE* 4.0 24.2 - - + -
517A THR* 3.9 16.8 - - - -
600A LEU* 3.8 14.1 - - + -
603A ALA* 4.3 4.7 - - + -
604A MET* 3.5 43.7 - - + -
607A ILE* 3.8 25.8 - - + -
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Residues in contact with HIS 497 (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 5.2 4.3 - - - -
479A LEU* 4.1 29.0 - - + +
493A GLY 3.0 18.6 + - - +
494A PHE* 3.0 10.3 + + - +
496A PHE* 1.3 77.3 - - - +
498A ASP* 1.3 53.7 + - - +
500A LEU* 4.7 2.2 - - - -
501A SER* 2.7 42.6 + - - +
607A ILE* 3.5 18.6 - - + +
610A GLU* 4.0 20.7 + - - -
611A VAL* 4.2 22.4 - - + +
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Residues in contact with ASP 498 (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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494A PHE* 2.6 51.2 + - + +
495A ILE* 4.1 3.6 - - - +
496A PHE 2.8 1.6 + - - -
497A HIS* 1.3 72.5 - - - +
499A VAL* 1.3 73.3 + - + +
501A SER* 2.9 19.7 + - - -
502A ARG* 3.2 51.6 + - - +
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Residues in contact with VAL 499 (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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495A ILE* 3.1 22.3 + - + +
496A PHE 4.0 0.2 - - - +
498A ASP* 1.3 84.9 - - + +
500A LEU* 1.3 58.7 + - - +
502A ARG* 3.2 4.8 + - - +
503A MET* 2.8 43.3 + - - +
505A LEU* 3.5 22.2 - - + -
513A LEU* 3.8 22.7 - - + -
516A ARG* 4.0 18.8 - - - +
544A SER* 3.4 25.1 - - - +
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Residues in contact with LEU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A PHE* 2.9 30.0 + - + +
497A HIS* 4.5 1.6 - - - +
499A VAL* 1.3 67.6 - - - +
501A SER* 1.3 55.3 + - - +
502A ARG 2.6 16.9 + - - -
503A MET* 2.7 19.6 - - - +
505A LEU* 4.9 13.0 - - + -
513A LEU* 4.4 17.3 - - + -
604A MET* 3.4 21.5 - - + +
607A ILE* 4.4 3.4 - - + -
608A ALA* 3.2 38.4 - - + +
611A VAL* 4.5 5.6 - - + -
613A ASN* 3.2 34.1 + - + +
615A SER* 5.4 0.7 - - - +
616A VAL* 4.8 11.9 - - + -
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Residues in contact with SER 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A HIS* 2.7 32.9 + - - -
498A ASP* 2.9 11.4 + - - -
500A LEU* 1.3 77.6 - - - +
502A ARG* 1.3 63.2 + - - +
611A VAL* 3.2 34.6 - - - +
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Residues in contact with ARG 502 (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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498A ASP* 3.2 47.8 + - - +
499A VAL* 3.2 5.0 + - - +
500A LEU 2.6 6.9 + - - -
501A SER* 1.3 83.3 - - - +
503A MET* 1.3 62.1 + - + +
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Residues in contact with MET 503 (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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499A VAL* 2.8 33.4 + - - +
500A LEU* 2.7 21.4 - - - +
502A ARG* 1.3 78.0 - - + +
504A GLU* 1.3 65.2 + - - +
505A LEU* 3.5 23.8 - - + +
542A GLU 4.6 4.9 - - - +
543A LEU 4.0 8.3 - - - +
544A SER* 3.4 35.0 - - - +
613A ASN* 2.7 8.2 + - - -
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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
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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