Contacts of the helix formed by residues 469 - 488 (chain D) in PDB entry 2OYQ
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 GLY 469 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424D ASN* 2.9 14.7 + - - +
426D SER* 3.3 12.1 - - - -
428D GLU* 3.2 12.1 - - - -
429D THR* 3.7 4.5 - - - -
468D ASP* 1.3 76.3 + - - +
470D VAL* 1.3 56.4 + - - -
472D PRO* 3.4 9.9 - - - +
473D THR* 2.5 36.8 + - - -
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Residues in contact with VAL 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ILE* 3.7 17.0 - - + -
369D ILE* 5.6 4.0 - - + +
373D LEU* 3.7 36.3 - - + -
426D SER* 3.7 0.4 + - - -
427D PRO* 5.1 0.9 - - + -
428D GLU* 3.1 27.6 + - - +
469D GLY* 1.3 69.0 - - - -
471D VAL* 1.3 73.7 + - + +
473D THR* 3.0 6.2 + - - -
474D GLU* 2.7 54.1 + - + +
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Residues in contact with VAL 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D ILE* 3.8 17.0 - - + -
425D ILE 3.7 6.1 - - - +
426D SER* 3.7 14.8 - - - -
427D PRO* 4.0 13.9 - - + -
470D VAL* 1.3 82.0 - - + +
472D PRO* 1.4 67.8 - - + +
474D GLU* 3.3 7.1 + - + +
475D ILE* 3.2 26.0 + - - +
566D LEU* 4.4 16.4 - - + +
570D LEU* 4.1 30.1 - - + -
577D TYR* 4.7 10.8 - - + -
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Residues in contact with PRO 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D ILE* 3.7 25.5 - - + +
421D ARG* 4.5 7.5 - - - +
424D ASN* 3.4 26.0 - - - +
425D ILE 3.4 17.0 - - - +
426D SER* 3.6 4.0 - - - -
468D ASP* 5.1 2.2 - - - +
469D GLY* 3.4 16.6 - - - +
471D VAL* 1.4 95.0 - - + +
473D THR* 1.3 52.8 + - - +
475D ILE* 3.4 9.2 - - + +
476D THR* 2.8 37.5 + - - +
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Residues in contact with THR 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ASP* 2.8 17.7 + - - +
469D GLY 2.5 23.9 + - - -
470D VAL* 3.0 8.7 + - - -
472D PRO* 1.3 75.5 - - - +
474D GLU* 1.3 69.1 + - - +
475D ILE 3.2 0.4 - - - -
476D THR* 3.8 5.4 - - - -
477D LYS* 3.0 34.1 + - + +
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Residues in contact with GLU 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D TRP* 3.1 21.9 - - + -
368D ILE* 4.3 12.4 - - + +
369D ILE* 4.6 16.4 - - + -
372D SER* 2.9 38.6 + - - -
373D LEU* 4.9 1.6 - - - +
376D GLN* 5.7 0.7 + - - -
470D VAL* 2.7 38.7 + - + +
471D VAL* 3.3 6.7 + - + +
473D THR* 1.3 87.2 - - - +
475D ILE* 1.3 57.3 + - - +
477D LYS* 4.4 7.6 - - - +
478D VAL* 3.1 24.2 - - - +
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Residues in contact with ILE 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D TRP* 3.7 20.6 - - + -
417D PRO* 4.4 9.9 - - + +
420D ILE* 4.6 3.4 - - + -
421D ARG* 3.9 17.3 - - + -
471D VAL 3.2 18.0 + - - +
472D PRO* 3.4 10.8 - - + +
474D GLU* 1.3 78.1 - - - +
476D THR* 1.3 56.9 + - - +
477D LYS 3.3 1.3 - - - -
478D VAL* 3.0 5.8 + - + -
479D PHE* 2.6 56.9 + - + +
563D ILE* 3.8 28.3 - - + +
566D LEU* 3.7 27.1 - - + -
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Residues in contact with THR 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D ARG* 3.3 35.6 + - - +
472D PRO* 2.8 24.3 + - - +
473D THR* 3.8 7.0 - - - -
475D ILE* 1.3 76.6 - - - +
477D LYS* 1.3 52.6 + - - +
478D VAL 2.9 0.3 + - - -
479D PHE* 2.9 8.6 + - + +
480D ASN* 2.6 57.8 + - - +
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Residues in contact with LYS 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D THR* 3.0 24.0 + - + +
474D GLU* 5.0 9.2 - - - +
476D THR* 1.3 74.2 - - - +
478D VAL* 1.3 60.2 + - + +
480D ASN* 4.1 11.4 - - - +
481D GLN* 3.0 35.9 - - - +
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Residues in contact with VAL 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D TYR* 4.2 22.9 - - + +
365D TRP* 4.0 14.6 - - + -
368D ILE* 4.9 11.7 - - + -
474D GLU* 3.1 20.9 - - - +
475D ILE* 3.0 19.4 + - + +
476D THR 2.9 0.6 - - - -
477D LYS* 1.3 80.3 - - + +
479D PHE* 1.3 63.3 + - - +
480D ASN 3.2 0.9 - - - -
481D GLN* 3.6 7.5 - - - +
482D ARG* 3.1 25.3 + - - +
559D ARG* 3.4 26.3 - - - +
562D LEU* 5.1 4.5 - - + -
563D ILE* 4.6 4.7 - - + +
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Residues in contact with PHE 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D SER* 3.6 34.3 - - - -
417D PRO* 4.4 12.6 - - + -
418D SER* 4.5 8.3 - - - -
421D ARG* 3.3 42.4 - - - +
475D ILE* 2.6 35.3 + - + +
476D THR* 3.4 8.3 - - + +
478D VAL* 1.3 74.5 - - - +
480D ASN* 1.3 63.2 + - - +
482D ARG* 3.4 22.2 + - + +
483D LYS* 3.6 10.0 + - - +
563D ILE* 3.8 26.7 - - + -
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Residues in contact with ASN 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476D THR* 2.6 43.3 + - - +
477D LYS* 4.1 9.6 - - - +
479D PHE* 1.3 75.6 - - - +
481D GLN* 1.3 58.5 + - + +
483D LYS* 3.5 12.6 - - - +
484D GLU* 3.1 30.1 + - - +
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Residues in contact with GLN 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D TYR* 2.9 48.8 + - + +
477D LYS* 3.0 24.4 + - - +
478D VAL* 3.4 6.2 + - - +
479D PHE 3.4 0.6 - - - -
480D ASN* 1.3 77.1 - - + +
482D ARG* 1.3 64.9 + - - +
484D GLU* 4.0 19.5 - - - +
485D HIS* 3.4 32.6 + - + +
559D ARG* 4.1 5.2 - - - +
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Residues in contact with ARG 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414D SER* 5.4 5.9 + - - -
478D VAL 3.1 12.6 + - - +
479D PHE* 3.5 17.0 - - + +
480D ASN 3.2 0.4 - - - -
481D GLN* 1.3 76.4 - - - +
483D LYS* 1.3 52.2 + - - +
484D GLU 3.1 0.4 - - - -
485D HIS* 3.0 6.5 + - - +
486D LYS* 2.6 44.8 + - + +
556D GLN* 3.9 19.1 + - - +
559D ARG* 3.9 12.8 - - + +
560D LYS* 3.9 26.1 - - + +
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Residues in contact with LYS 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D PHE 3.6 9.8 + - - +
480D ASN* 3.5 16.6 - - - +
482D ARG* 1.3 78.7 - - - +
484D GLU* 1.3 56.2 + - - +
486D LYS* 4.1 8.3 - - - -
487D GLY* 2.8 28.7 + - - +
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Residues in contact with GLU 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D ASN 3.1 18.5 + - - +
481D GLN* 4.1 21.7 + - - +
482D ARG 3.1 1.2 + - - -
483D LYS* 1.3 79.2 - - + +
485D HIS* 1.3 62.7 + - + +
488D TYR* 3.1 26.3 + - - +
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Residues in contact with HIS 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D TYR* 5.5 6.2 - + - -
481D GLN* 3.4 31.7 + - - +
482D ARG 3.0 3.1 + - - +
484D GLU* 1.3 85.8 - - + +
486D LYS* 1.3 61.2 + - - +
488D TYR* 3.6 2.2 - - - -
489D MET* 2.8 30.8 + - - +
551D ALA 4.8 4.3 - - - -
552D GLY* 4.4 10.5 - - - +
555D ALA* 3.8 33.8 - - + +
556D GLN* 4.4 9.9 - - - +
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Residues in contact with LYS 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ARG* 2.6 35.1 + - + +
483D LYS* 4.1 3.8 - - - -
485D HIS* 1.3 71.8 - - - +
487D GLY* 1.3 61.7 + - - +
489D MET* 3.4 8.5 - - - +
490D LEU* 3.4 22.5 - - - +
556D GLN* 3.8 28.9 + - + +
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Residues in contact with GLY 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D LYS* 2.8 24.2 + - - +
486D LYS* 1.3 73.9 - - - +
488D TYR* 1.3 59.3 + - - +
489D MET 3.7 0.2 + - - -
490D LEU* 3.8 25.0 + - - +
491D ALA* 4.1 4.7 + - - +
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Residues in contact with TYR 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484D GLU 3.1 22.4 + - - +
485D HIS* 3.6 2.7 - - - +
486D LYS 3.3 0.4 - - - -
487D GLY* 1.3 73.9 - - - +
489D MET* 1.3 63.2 + - - +
490D LEU 3.4 1.1 - - - -
491D ALA* 3.7 11.4 + - + +
492D ALA* 3.6 17.0 + - - +
519D ARG* 4.1 19.6 - - + +
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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