Contacts of the helix formed by residues 473 - 494 (chain D) in PDB entry 2Y0N
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 SER 473 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D SER 3.9 1.6 + - - -
472D PHE* 1.3 76.2 - - - +
474D GLU* 1.3 66.7 + - - +
475D LYS* 4.1 2.7 + - - +
476D ASN* 3.1 33.4 + - - +
477D LEU* 3.0 22.7 + - - +
579H ARG* 5.0 1.4 - - - +
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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
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472D PHE 3.9 1.3 + - - +
473D SER* 1.3 74.6 - - - +
475D LYS* 1.3 66.6 + - + +
477D LEU* 3.4 11.4 + - - +
478D LYS* 3.3 33.5 + - - +
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Residues in contact with LYS 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D SER* 3.4 3.0 + - - +
474D GLU* 1.3 83.3 - - + +
476D ASN* 1.3 69.7 + - - +
478D LYS* 3.9 4.2 + - - +
479D ALA* 3.6 20.3 + - - +
551E PRO* 2.9 49.6 - - - +
552E GLU 4.7 9.2 - - - +
553E VAL* 4.3 8.6 - - + +
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Residues in contact with ASN 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D PHE* 4.9 9.6 - - + -
473D SER* 3.1 24.7 + - - +
474D GLU 3.3 0.6 - - - -
475D LYS* 1.3 82.9 - - - +
477D LEU* 1.3 64.0 + - - +
479D ALA* 3.6 3.3 + - - +
480D LEU* 3.2 23.0 + - - +
553E VAL* 3.9 14.4 - - - +
555E SER 3.6 6.6 + - - +
556E PHE* 3.3 47.8 - - + +
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Residues in contact with LEU 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D ILE* 3.8 36.8 - - + -
467D LEU* 5.0 3.6 - - + -
472D PHE* 3.8 35.1 - - + +
473D SER 3.0 17.9 + - - +
474D GLU* 3.4 12.5 + - - +
476D ASN* 1.3 75.4 - - - +
478D LYS* 1.3 57.0 + - + +
480D LEU* 3.1 14.6 + - + +
481D LEU* 2.8 65.0 + - + +
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Residues in contact with LYS 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D GLU* 3.3 23.1 + - - +
475D LYS* 4.3 4.9 - - - +
477D LEU* 1.3 78.4 - - + +
479D ALA* 1.3 62.6 + - - +
481D LEU* 3.3 12.2 + - + +
482D LYS* 3.0 40.0 + - - +
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Residues in contact with ALA 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D GLU* 3.3 24.9 - - - +
253D LEU* 4.4 3.4 - - + -
475D LYS 3.6 15.6 + - - +
476D ASN 3.8 5.2 - - - +
477D LEU 3.3 0.6 - - - -
478D LYS* 1.3 78.3 - - - +
480D LEU* 1.3 60.7 - - - +
482D LYS* 3.7 1.1 - - - +
483D HIS* 3.0 31.4 + - - -
553E VAL* 3.9 20.9 - - + -
556E PHE* 4.3 10.3 - - + -
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Residues in contact with LEU 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D MET* 4.4 6.5 - - + -
467D LEU* 4.0 9.2 - - + -
472D PHE* 3.8 33.7 - - + -
476D ASN 3.2 11.1 + - - +
477D LEU* 3.1 17.8 + - + +
479D ALA* 1.3 78.4 - - - +
481D LEU* 1.3 64.6 + - - +
483D HIS* 3.0 15.4 + - - +
484D PHE* 3.1 51.1 + - + -
556E PHE* 3.9 26.9 - - + -
577H PHE* 3.8 24.0 - - + -
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Residues in contact with LEU 481 (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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172D ILE* 4.0 19.7 - - + -
173D THR 4.5 7.4 - - - +
174D ILE* 3.8 32.7 - - + +
467D LEU* 4.4 3.8 - - + -
477D LEU* 2.8 54.3 + - + +
478D LYS* 3.8 11.0 - - + +
480D LEU* 1.3 72.6 - - - +
482D LYS* 1.3 58.5 + - + +
484D PHE* 3.2 14.3 + - + +
485D ASP* 3.0 33.1 + - - +
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Residues in contact with LYS 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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247D ALA* 6.2 0.4 - - - +
248D GLU* 3.1 29.8 + - + +
478D LYS* 3.0 29.2 + - - +
479D ALA* 3.7 6.3 - - - +
481D LEU* 1.3 77.0 - - + +
483D HIS* 1.3 56.6 + - - +
485D ASP* 3.2 11.3 + - - +
486D LEU* 3.0 33.8 + - + +
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Residues in contact with HIS 483 (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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213D TYR* 4.1 4.1 + - - -
217D PHE* 3.9 28.9 - + - -
248D GLU* 3.2 32.9 - - + +
250D ASN 4.1 1.2 + - - -
253D LEU* 3.7 29.0 - - + +
254D CYS* 3.8 30.6 + - + -
257D MET* 3.4 31.2 - - + +
479D ALA 3.0 20.5 + - - +
480D LEU* 3.0 12.5 + - - +
482D LYS* 1.3 75.1 - - - +
484D PHE* 1.3 62.8 + - - +
486D LEU* 4.0 6.8 - - + +
487D PHE* 3.2 16.5 + - - +
556E PHE* 4.9 1.9 - + + -
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Residues in contact with PHE 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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174D ILE* 4.2 20.4 - - + -
257D MET* 3.5 30.3 - - + -
261D LEU* 4.4 6.5 - - + -
460D PHE* 3.9 23.6 - + + -
463D LEU* 3.5 29.2 - - + -
467D LEU* 4.0 8.1 - - + -
480D LEU* 3.1 49.6 + - + -
481D LEU* 3.2 16.8 + - + +
483D HIS* 1.3 77.1 - - - +
485D ASP* 1.3 54.2 + - - +
487D PHE* 3.2 4.7 + - - +
488D LEU* 2.7 40.4 + - - +
577H PHE* 4.1 17.3 - + - -
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Residues in contact with ASP 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ILE* 4.6 11.3 - - - +
175D GLU* 4.9 13.7 + - - +
177D PRO* 5.6 0.2 - - - +
481D LEU* 3.0 16.0 + - - +
482D LYS* 3.2 13.4 + - - +
484D PHE* 1.3 76.5 - - - +
486D LEU* 1.3 58.8 + - + +
488D LEU* 3.1 8.0 + - - +
489D ARG* 2.8 42.0 + - + +
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Residues in contact with LEU 486 (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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213D TYR* 3.4 14.8 - - + +
217D PHE* 4.2 15.7 - - + -
248D GLU* 3.9 36.3 - - + +
482D LYS* 3.0 19.0 + - + +
483D HIS* 4.0 6.5 - - + +
484D PHE 3.3 0.2 - - - -
485D ASP* 1.3 78.2 - - + +
487D PHE* 1.3 57.6 + - - +
489D ARG* 3.4 26.3 + - + +
490D PHE* 2.9 28.1 + - - +
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Residues in contact with PHE 487 (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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209D ILE* 4.5 4.9 - - + -
210D LEU* 3.8 20.4 - - + -
213D TYR* 3.6 49.8 + + + -
257D MET* 4.5 9.4 - - + -
261D LEU* 4.6 4.9 - - + -
456D LEU* 3.8 24.5 - - + -
460D PHE* 3.4 37.2 - + - -
483D HIS 3.2 15.4 + - - +
484D PHE* 3.2 6.3 + - - +
486D LEU* 1.3 78.4 - - - +
488D LEU* 1.3 58.7 + - - +
490D PHE* 3.3 11.2 + + - +
491D LEU* 2.8 52.4 + - + +
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Residues in contact with LEU 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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174D ILE* 3.9 15.7 - - + -
175D GLU 3.7 22.4 - - - +
176D ILE* 4.7 5.2 - - + -
177D PRO* 3.8 16.4 - - + -
180D LEU* 3.3 27.4 - - + +
457D LEU* 4.1 12.8 - - + -
460D PHE* 3.9 43.1 - - + -
484D PHE 2.7 24.6 + - - +
485D ASP* 3.6 6.7 - - - +
487D PHE* 1.3 71.4 - - - +
489D ARG* 1.3 59.5 + - - +
491D LEU* 3.2 8.3 + - + -
492D ALA* 2.8 25.8 + - - +
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Residues in contact with ARG 489 (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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177D PRO* 4.4 7.6 - - + +
485D ASP* 2.8 25.1 + - + +
486D LEU* 3.6 26.1 - - + +
488D LEU* 1.3 72.5 - - - +
490D PHE* 1.3 56.6 + - - +
492D ALA* 3.0 7.1 + - - +
493D GLU* 2.7 40.9 + - - +
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Residues in contact with PHE 490 (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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209D ILE* 4.6 3.8 - - + -
212D SER* 4.4 6.7 - - - -
213D TYR* 3.3 54.7 - + + -
216D HIS* 4.4 25.8 - + + -
486D LEU 2.9 14.5 + - - +
487D PHE* 3.3 15.9 - + - +
488D LEU 3.3 0.2 - - - -
489D ARG* 1.3 75.1 - - - +
491D LEU* 1.3 70.2 + - + +
493D GLU* 4.4 8.3 - - - -
494D TYR* 3.3 50.8 + + - +
498D PHE* 3.6 34.3 - + - -
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Residues in contact with LEU 491 (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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180D LEU* 3.8 10.8 - - + +
209D ILE* 4.4 10.1 - - + -
453D ALA* 5.7 3.6 - - + +
456D LEU* 5.0 6.5 - - + -
457D LEU* 4.4 17.3 - - + +
460D PHE* 4.9 3.4 - - + -
487D PHE* 2.8 49.1 + - + +
488D LEU* 3.2 23.3 + - + +
490D PHE* 1.3 81.2 - - + +
492D ALA* 1.3 59.8 + - - +
494D TYR 3.7 1.6 - - - -
495D HIS* 3.3 22.2 + - - +
498D PHE* 4.0 27.1 - - + -
499D PHE* 4.3 19.3 - - + -
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Residues in contact with ALA 492 (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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177D PRO* 3.9 24.2 - - + -
179D VAL* 4.5 18.5 - - + +
180D LEU* 3.9 13.2 - - + +
488D LEU 2.8 17.2 + - - +
489D ARG* 3.5 5.8 - - - +
491D LEU* 1.3 75.3 - - - +
493D GLU* 1.3 64.8 + - - +
494D TYR 3.2 0.2 - - - -
495D HIS* 3.2 17.6 + - - +
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Residues in contact with GLU 493 (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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489D ARG* 2.7 22.8 + - - +
490D PHE* 3.4 10.6 + - - +
492D ALA* 1.3 74.0 - - - +
494D TYR* 1.3 91.6 + - + +
495D HIS 3.5 0.7 + - - -
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Residues in contact with TYR 494 (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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216D HIS* 5.5 6.4 + + + +
490D PHE* 3.3 42.3 + + - +
491D LEU 3.7 3.1 - - - -
492D ALA 3.2 0.4 - - - -
493D GLU* 1.3 112.0 + - + +
495D HIS* 1.3 63.7 + - - +
496D ASP* 3.2 3.4 - - - -
497D ASP* 3.1 33.1 + - + +
498D PHE* 3.1 31.3 + + + -
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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
------------------------------------------------------------
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