Contacts of the helix formed by residues 452 - 470 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C CYS* 3.3 20.5 - - - -
204C THR 3.9 13.2 - - - -
206C ILE* 3.4 16.5 - - - +
209C ILE* 4.3 0.4 - - - -
451C TYR* 1.3 76.5 - - - +
453C ALA* 1.3 66.2 + - - -
454C GLN* 3.1 5.8 + - - -
455C HIS* 3.3 5.4 + - - -
456C LEU 3.2 17.3 + - - -
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Residues in contact with ALA 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C THR 4.7 1.4 + - - -
209C ILE* 3.4 22.9 - - + +
452C GLY* 1.3 71.2 - - - -
454C GLN* 1.3 67.9 + - - +
456C LEU* 3.9 6.6 - - - +
457C LEU* 3.2 19.2 + - - +
491C LEU* 5.7 5.4 - - + +
498C PHE* 3.5 33.0 - - + +
499C PHE* 3.5 27.7 - - + -
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Residues in contact with GLN 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C GLN* 5.0 0.9 - - - +
184C LEU* 5.1 1.0 - - - +
187C ASP* 3.9 12.5 - - - +
198C VAL* 3.8 21.0 - - + +
202C CYS* 4.2 3.1 - - - -
452C GLY* 3.1 6.3 - - - -
453C ALA* 1.3 87.9 + - - +
455C HIS* 1.3 70.6 + - + +
457C LEU* 3.8 4.5 + - - +
458C ARG* 3.3 21.2 + - - +
498C PHE 4.0 17.4 + - - -
499C PHE* 4.1 18.5 - - + +
500C PRO* 4.4 5.9 + - - +
503C ALA* 3.4 28.7 - - - +
504C TYR* 3.0 33.9 - - + +
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Residues in contact with HIS 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C VAL* 3.6 35.1 - - + +
200C LEU* 5.2 0.2 - - + -
265C PHE* 3.7 27.8 - - + -
269C LEU* 4.0 11.2 - - + -
273C LEU* 4.2 3.3 - - + +
274C LEU* 4.5 4.0 - - + +
278C GLU* 3.0 23.2 + - - -
281C GLN* 5.7 1.5 + - - -
451C TYR* 3.3 39.3 - + + +
452C GLY 3.3 6.8 + - - +
454C GLN* 1.3 77.8 - - + +
456C LEU* 1.3 66.3 - - - +
457C LEU 3.1 2.2 - - - -
458C ARG* 3.0 46.9 + - - +
459C LEU 3.4 4.3 + - - -
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Residues in contact with LEU 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ILE* 3.7 27.6 - - + -
209C ILE* 4.1 21.1 - - + -
210C LEU* 4.4 9.2 - - + -
261C LEU* 4.3 17.5 - - + -
265C PHE* 3.8 14.8 - - + -
452C GLY 3.2 16.9 + - - +
453C ALA* 3.9 6.3 - - - +
455C HIS* 1.3 75.0 - - - +
457C LEU* 1.3 62.1 + - - +
459C LEU* 3.3 25.3 - - + +
460C PHE* 3.3 22.7 - - + -
487C PHE* 3.8 26.9 - - + -
491C LEU* 5.0 6.3 - - + -
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Residues in contact with LEU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ILE* 5.1 3.1 - - + -
180C LEU* 3.8 31.0 - - + +
183C GLN* 4.0 12.8 - - + -
184C LEU* 3.8 35.2 - - + +
453C ALA 3.2 14.5 + - - +
454C GLN 3.9 5.2 - - - +
455C HIS 3.1 0.8 - - - -
456C LEU* 1.3 77.9 - - - +
458C ARG* 1.3 66.6 + - - +
460C PHE* 3.0 24.8 + - + +
461C VAL 3.9 1.7 + - - -
488C LEU* 4.1 26.2 - - + -
491C LEU* 4.4 9.4 - - + +
499C PHE* 3.9 22.7 - - + -
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Residues in contact with ARG 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU* 4.1 9.0 - - + -
187C ASP* 2.6 39.6 + - - +
191C ILE* 3.5 14.1 - - - +
273C LEU* 3.1 30.0 + - + -
274C LEU* 4.5 0.4 - - - +
275C TYR* 3.6 12.0 - - - -
278C GLU* 2.5 39.1 + - - -
454C GLN 3.3 18.3 + - - +
455C HIS* 3.0 36.3 + - - +
457C LEU* 1.3 76.3 - - - +
459C LEU* 1.3 57.7 + - - +
461C VAL* 2.9 29.3 + - - +
462C LYS 3.6 0.9 + - - -
589G PHE* 3.3 41.2 - - + -
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Residues in contact with LEU 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C LEU* 3.9 25.4 - - + +
264C THR* 4.4 7.4 - - + -
265C PHE* 4.1 26.2 - - + +
268C THR* 3.9 36.1 - - + +
273C LEU* 3.7 18.5 - - + +
455C HIS 3.4 2.4 + - - +
456C LEU* 3.3 17.2 + - + +
457C LEU 3.1 0.4 - - - -
458C ARG* 1.3 78.2 - - - +
460C PHE* 1.3 56.7 + - - +
461C VAL 3.1 0.2 - - - -
462C LYS* 3.0 2.6 + - + -
463C LEU* 2.8 53.4 + - + +
466C ILE* 4.4 6.1 - - + -
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Residues in contact with PHE 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 4.5 15.3 - - + +
176C ILE* 4.5 13.3 - - + +
261C LEU* 3.6 25.8 - - + -
456C LEU* 3.3 23.8 - - + -
457C LEU* 3.0 16.9 + - + +
459C LEU* 1.3 77.1 - - + +
461C VAL* 1.3 60.8 + - - +
463C LEU* 4.1 15.7 - - + +
464C PRO* 3.6 13.7 - - - +
484C PHE* 3.9 31.0 - + + -
487C PHE* 3.4 39.5 - + - -
488C LEU* 3.9 39.0 - - + -
491C LEU* 4.9 1.3 - - + -
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Residues in contact with VAL 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ILE* 3.8 12.6 - - + -
184C LEU* 3.8 29.8 - - + -
457C LEU 4.7 0.4 - - - +
458C ARG 2.9 14.3 + - - +
460C PHE* 1.3 78.9 - - - +
462C LYS* 1.3 64.8 + - + +
464C PRO* 3.4 15.2 - - - +
465C GLU* 5.4 0.7 - - - +
589G PHE* 3.7 24.2 - - + -
590G GLU 5.4 7.9 - - - -
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Residues in contact with LYS 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C VAL* 3.4 34.2 + - + +
273C LEU* 3.8 27.4 - - + -
458C ARG 3.6 0.6 + - - -
459C LEU* 3.0 7.6 + - + +
461C VAL* 1.3 81.9 - - + +
463C LEU* 1.3 66.2 + - - +
464C PRO* 3.2 0.8 - - - -
465C GLU* 3.0 43.3 + - - +
466C ILE* 3.4 18.8 + - + +
587G GLN* 3.4 29.7 + - - +
588G ASN 4.6 3.8 + - - -
589G PHE* 3.9 21.3 - - + +
590G GLU* 4.9 3.0 - - - +
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Residues in contact with LEU 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 3.8 13.7 - - + -
261C LEU* 4.7 5.8 - - + -
264C THR* 4.8 10.1 - - + -
459C LEU* 2.8 53.7 + - + +
460C PHE* 4.2 13.5 - - + +
462C LYS* 1.3 76.5 - - - +
464C PRO* 1.4 63.0 - - + +
466C ILE* 3.0 10.4 + - + +
467C LEU* 2.8 43.9 + - + +
484C PHE* 3.6 45.1 - - + -
577G PHE* 5.2 4.3 - - + -
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Residues in contact with PRO 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ILE* 3.4 47.6 - - + +
173C THR* 5.5 0.2 - - - -
174C ILE* 3.8 16.8 - - + +
460C PHE 3.6 9.6 - - - +
461C VAL 3.4 17.9 - - - +
462C LYS 3.4 1.3 - - - -
463C LEU* 1.4 92.3 - - + +
465C GLU* 1.3 58.4 + - + +
467C LEU* 3.3 4.8 + - + +
468C GLY* 2.9 26.3 + - - -
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Residues in contact with GLU 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C VAL* 4.9 5.5 - - - +
461C VAL 5.4 0.7 - - - +
462C LYS* 3.0 47.3 + - + +
464C PRO* 1.3 79.2 - - + +
466C ILE* 1.3 74.1 + - - +
468C GLY* 3.3 9.8 + - - +
469C LYS* 3.4 28.0 + - - +
584G LEU* 4.6 11.1 - - - +
587G GLN* 5.0 4.6 - - - +
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Residues in contact with ILE 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C THR* 4.7 7.2 - - + -
268C THR* 4.0 23.8 - - + +
272C VAL* 4.9 0.7 - - + -
459C LEU* 4.4 6.7 - - + -
462C LYS* 3.5 26.0 - - + +
463C LEU* 3.0 10.7 + - + +
465C GLU* 1.3 85.5 - - - +
467C LEU* 1.3 58.3 + - + +
469C LYS* 3.0 27.4 + - - +
470C MET* 3.3 33.4 - - + +
581G LEU* 4.6 7.0 - - + -
582G PRO* 3.8 16.3 - - + +
584G LEU* 3.9 27.1 - - + -
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Residues in contact with LEU 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ILE* 4.0 15.3 - - + +
174C ILE* 3.8 26.2 - - + -
463C LEU* 2.8 37.0 + - + +
464C PRO* 3.7 5.6 - - + +
466C ILE* 1.3 70.0 - - + +
468C GLY* 1.3 60.5 + - - +
470C MET* 2.8 38.2 - - + +
472C PHE* 3.5 35.9 + - + -
477C LEU* 4.9 1.8 - - + -
480C LEU* 4.0 12.3 - - + -
481C LEU* 4.4 10.5 - - + -
484C PHE* 4.0 8.1 - - + -
577G PHE* 4.2 14.1 - - + -
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Residues in contact with GLY 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ILE* 4.1 11.2 - - - -
464C PRO 2.9 13.7 + - - -
465C GLU* 3.7 5.2 - - - -
466C ILE 3.1 0.8 - - - -
467C LEU* 1.3 80.3 - - - +
469C LYS* 1.3 61.1 + - - +
470C MET 3.5 4.9 + - - +
471C SER* 4.6 3.3 + - - -
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Residues in contact with LYS 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465C GLU* 3.4 24.4 + - - +
466C ILE* 3.0 9.5 + - - +
468C GLY* 1.3 78.1 - - - +
470C MET* 1.3 56.8 + - - +
471C SER 3.9 1.8 + - - -
569E THR* 3.8 25.2 + - + +
571E PHE* 4.0 11.6 - - - -
582G PRO* 3.8 20.4 - - + -
583G LYS 4.5 6.6 + - - +
584G LEU* 3.9 30.1 - - + +
585G ALA 5.9 0.8 - - - +
568H ILE 6.2 2.4 - - - -
570H PRO* 5.2 15.5 - - - +
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Residues in contact with MET 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C THR* 5.2 1.1 - - + -
466C ILE* 3.3 42.6 - - + +
467C LEU* 2.8 32.8 - - + +
468C GLY 3.8 2.1 - - - +
469C LYS* 1.3 72.8 - - - +
471C SER* 1.3 60.4 + - - +
472C PHE* 3.1 35.3 + - + -
571E PHE* 4.4 8.3 - - + -
576G ALA 4.5 6.1 - - - +
577G PHE* 4.8 8.3 - - + -
579G ARG* 4.2 13.0 - - + +
580G PRO* 3.4 23.1 - - + +
581G LEU* 3.7 20.0 - - + -
582G PRO* 3.5 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