Contacts of the helix formed by residues 452 - 470 (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 GLY 452 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D CYS* 3.2 20.9 - - - -
204D THR 3.9 13.0 - - - -
206D ILE* 3.3 16.7 - - - +
209D ILE* 3.9 0.7 - - - -
451D TYR* 1.3 75.8 - - - +
453D ALA* 1.3 65.5 + - - -
454D GLN* 3.1 5.5 + - - -
455D HIS* 3.3 5.3 + - - -
456D LEU 3.2 18.4 + - - -
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Residues in contact with ALA 453 (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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204D THR 4.7 1.0 + - - -
209D ILE* 3.4 23.6 - - + +
452D GLY* 1.3 71.2 - - - -
454D GLN* 1.3 67.6 + - - +
456D LEU* 3.9 6.9 - - + +
457D LEU* 3.2 19.2 + - - +
491D LEU* 5.7 5.3 - - + +
498D PHE* 3.5 32.8 - - + +
499D PHE* 3.4 27.5 - - + -
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Residues in contact with GLN 454 (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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183D GLN* 5.1 0.9 - - - +
184D LEU* 5.1 1.0 - - - +
187D ASP* 3.9 11.8 - - - +
198D VAL* 3.8 20.4 - - + +
202D CYS* 4.2 3.1 - - - -
452D GLY* 3.1 6.4 + - - -
453D ALA* 1.3 87.7 + - - +
455D HIS* 1.3 70.4 + - + +
457D LEU* 3.8 4.3 + - - +
458D ARG* 3.3 21.8 + - - +
498D PHE 4.0 17.2 + - - -
499D PHE* 4.2 18.7 - - + +
500D PRO* 4.4 5.7 + - - +
503D ALA* 3.4 28.9 - - - +
504D TYR* 3.1 34.8 - - + +
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Residues in contact with HIS 455 (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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198D VAL* 3.6 34.4 - - + +
200D LEU* 5.2 0.2 - - + -
265D PHE* 3.7 27.6 - - + -
269D LEU* 4.0 11.2 - - + -
273D LEU* 4.2 3.6 - - + +
274D LEU* 4.5 4.0 - - + +
278D GLU* 3.0 12.1 + - - -
281D GLN* 5.6 1.5 + - - -
451D TYR* 3.3 39.1 - + + +
452D GLY 3.3 6.8 + - - +
454D GLN* 1.3 77.4 - - + +
456D LEU* 1.3 66.0 - - - +
457D LEU 3.1 2.2 - - - -
458D ARG* 3.0 58.2 + - + +
459D LEU 3.4 4.5 + - - -
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Residues in contact with LEU 456 (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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206D ILE* 3.7 27.8 - - + -
209D ILE* 4.1 20.9 - - + -
210D LEU* 4.3 9.0 - - + -
261D LEU* 4.3 18.2 - - + -
265D PHE* 3.8 15.0 - - + -
452D GLY 3.2 17.6 + - - +
453D ALA* 3.9 5.8 - - - +
455D HIS* 1.3 75.6 - - - +
457D LEU* 1.3 61.6 + - - +
459D LEU* 3.3 17.3 - - + +
460D PHE* 3.3 27.7 - - + -
487D PHE* 3.8 26.9 - - + -
491D LEU* 5.0 5.8 - - + -
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Residues in contact with LEU 457 (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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176D ILE* 5.1 2.9 - - + -
180D LEU* 3.8 31.6 - - + +
183D GLN* 4.0 12.6 - - + -
184D LEU* 3.8 35.8 - - + +
453D ALA 3.2 14.1 + - - +
454D GLN 3.9 5.2 - - - +
455D HIS 3.1 0.8 - - - -
456D LEU* 1.3 78.5 - - - +
458D ARG* 1.3 66.4 + - - +
460D PHE* 3.0 24.3 + - + +
461D VAL 3.9 1.6 + - - -
488D LEU* 4.1 26.5 - - + -
491D LEU* 4.4 9.4 - - + +
499D PHE* 3.9 22.2 - - + -
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Residues in contact with ARG 458 (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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184D LEU* 4.1 9.2 - - + -
187D ASP* 2.6 39.4 + - - +
191D ILE* 3.5 14.1 - - - +
273D LEU* 3.1 30.8 + - + -
274D LEU* 4.5 0.2 - - - +
275D TYR* 3.6 12.2 - - - -
278D GLU* 2.5 38.9 + - - -
454D GLN 3.3 18.3 + - - +
455D HIS* 3.0 36.1 + - - +
457D LEU* 1.3 76.4 - - - +
459D LEU* 1.3 56.9 + - - +
461D VAL* 2.9 30.0 + - - +
462D LYS 3.6 0.9 + - - -
589H PHE* 3.3 41.0 - - + -
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Residues in contact with LEU 459 (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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261D LEU* 3.9 25.8 - - + +
264D THR* 4.3 7.4 - - + -
265D PHE* 4.1 27.1 - - + +
268D THR* 3.9 36.1 - - + +
273D LEU* 3.7 19.4 - - + +
455D HIS 3.4 3.2 + - - +
456D LEU* 3.3 15.5 - - + +
457D LEU 3.2 0.4 - - - -
458D ARG* 1.3 77.8 - - - +
460D PHE* 1.3 56.2 + - - +
461D VAL 3.1 0.2 - - - -
462D LYS* 3.0 2.6 + - + -
463D LEU* 2.8 53.1 + - + +
466D ILE* 4.4 6.3 - - + -
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Residues in contact with PHE 460 (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* 4.5 15.8 - - + +
176D ILE* 4.4 13.7 - - + +
261D LEU* 3.6 26.2 - - + -
456D LEU* 3.3 23.8 - - + -
457D LEU* 3.0 17.1 + - + +
459D LEU* 1.3 77.3 - - + +
461D VAL* 1.3 61.0 + - - +
463D LEU* 4.1 15.9 - - + +
464D PRO* 3.6 13.2 - - - +
484D PHE* 3.9 30.7 - + + -
487D PHE* 3.4 39.0 - + - -
488D LEU* 3.9 39.3 - - + -
491D LEU* 4.9 1.3 - - + -
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Residues in contact with VAL 461 (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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176D ILE* 3.8 12.6 - - + -
184D LEU* 3.8 29.4 - - + -
457D LEU 4.7 0.7 - - - +
458D ARG 2.9 14.3 + - - +
460D PHE* 1.3 78.9 - - - +
462D LYS* 1.3 64.6 + - + +
464D PRO* 3.4 15.2 - - - +
465D GLU* 5.6 0.3 - - - +
589H PHE* 3.8 23.8 - - + -
590H GLU 5.4 7.6 - - - -
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Residues in contact with LYS 462 (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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272D VAL* 3.5 37.5 + - + +
273D LEU* 3.8 27.4 - - + -
458D ARG 3.6 0.6 + - - -
459D LEU* 3.0 7.2 + - + +
461D VAL* 1.3 82.3 - - + +
463D LEU* 1.3 65.3 + - - +
464D PRO* 3.4 0.7 - - - -
465D GLU* 3.1 41.2 + - + +
466D ILE* 3.3 20.5 + - + +
587H GLN* 3.5 23.4 + - - +
588H ASN 4.6 4.2 + - - -
589H PHE* 3.8 21.3 - - + +
590H GLU 4.9 3.0 - - - +
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Residues in contact with LEU 463 (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* 3.8 13.2 - - + -
261D LEU* 4.7 6.3 - - + -
264D THR* 4.8 9.6 - - + -
459D LEU* 2.8 54.3 + - + +
460D PHE* 4.2 12.1 - - + +
462D LYS* 1.3 76.3 - - - +
464D PRO* 1.3 64.3 - - + +
466D ILE* 3.0 10.1 + - + +
467D LEU* 2.7 44.1 + - + +
484D PHE* 3.5 45.5 - - + -
577H PHE* 5.2 4.7 - - + -
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Residues in contact with PRO 464 (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* 3.4 48.1 - - + +
173D THR* 5.5 0.2 - - - -
174D ILE* 3.9 16.6 - - + +
460D PHE 3.6 9.6 - - - +
461D VAL 3.4 17.7 - - - +
462D LYS 3.4 1.1 - - - -
463D LEU* 1.3 92.5 - - + +
465D GLU* 1.3 63.8 + - + +
467D LEU* 3.3 4.4 + - + +
468D GLY* 3.0 21.3 + - - -
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Residues in contact with GLU 465 (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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272D VAL* 4.9 3.9 - - - +
461D VAL 5.6 0.2 - - - +
462D LYS* 3.1 39.2 + - + +
464D PRO* 1.3 83.3 - - + +
466D ILE* 1.3 69.7 + - - +
468D GLY* 3.3 8.1 + - - -
469D LYS* 3.5 38.8 + - - +
584H LEU* 4.4 7.4 - - - +
587H GLN* 5.1 5.6 - - - +
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Residues in contact with ILE 466 (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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264D THR* 4.7 6.5 - - + -
268D THR* 4.0 23.8 - - + +
272D VAL* 4.9 0.7 - - + -
459D LEU* 4.4 6.7 - - + -
462D LYS* 3.5 25.1 - - + +
463D LEU* 3.0 10.6 + - + +
465D GLU* 1.3 82.5 - - - +
467D LEU* 1.3 58.4 + - + +
469D LYS* 3.0 27.8 + - - +
470D MET* 3.4 31.3 - - + +
581H LEU* 4.6 7.0 - - + -
582H PRO* 3.9 15.9 - - + +
584H LEU* 3.9 30.1 - - + -
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Residues in contact with LEU 467 (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 15.9 - - + +
174D ILE* 3.8 26.2 - - + -
463D LEU* 2.7 37.0 + - + +
464D PRO* 3.8 5.2 - - + +
466D ILE* 1.3 69.1 - - + +
468D GLY* 1.3 60.1 + - - +
469D LYS 3.3 0.2 - - - -
470D MET* 2.8 38.7 - - + +
472D PHE* 3.5 35.6 + - + -
477D LEU* 5.0 1.8 - - + -
480D LEU* 4.0 12.1 - - + -
481D LEU* 4.4 10.5 - - + -
484D PHE* 4.0 8.3 - - + -
577H PHE* 4.1 14.4 - - + -
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Residues in contact with GLY 468 (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 11.4 - - - +
464D PRO 3.0 13.1 + - - -
465D GLU 3.8 5.4 - - - -
466D ILE 3.1 0.8 - - - -
467D LEU* 1.3 79.7 - - - +
469D LYS* 1.3 61.1 + - - +
470D MET 3.6 4.9 + - - +
471D SER* 4.6 3.3 + - - -
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Residues in contact with LYS 469 (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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465D GLU* 3.5 31.9 + - - +
466D ILE* 3.0 9.9 + - - +
468D GLY* 1.3 77.2 - - - +
470D MET* 1.3 58.0 + - - +
471D SER 3.9 2.1 + - - -
569F THR* 3.8 29.3 + - + +
571F PHE* 4.0 6.9 - - - -
568G ILE* 6.1 3.2 - - - +
570G PRO* 5.2 15.3 - - - +
582H PRO* 3.7 20.4 - - + -
583H LYS 4.5 6.2 + - - +
584H LEU* 3.8 30.5 - - + +
585H ALA 5.8 1.0 - - - +
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Residues in contact with MET 470 (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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264D THR* 5.2 1.1 - - + -
466D ILE* 3.4 41.3 - - + +
467D LEU* 2.8 33.4 - - + +
468D GLY 3.9 2.1 - - - +
469D LYS* 1.3 73.2 - - - +
471D SER* 1.3 60.1 + - - +
472D PHE* 3.1 36.1 + - + -
571F PHE* 4.5 8.5 - - + -
576H ALA 4.5 6.1 - - - +
577H PHE* 4.8 8.1 - - + -
579H ARG* 4.2 13.9 - - + +
580H PRO* 3.5 22.7 - - + +
581H LEU* 3.6 20.0 - - + -
582H PRO* 3.6 10.8 - - + -
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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