Contacts of the helix formed by residues 473 - 494 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B SER 3.9 1.4 + - - -
472B PHE* 1.3 76.4 - - - +
474B GLU* 1.3 65.4 + - - +
475B LYS* 4.1 2.9 + - - +
476B ASN* 3.2 31.8 + - - +
477B LEU* 3.0 22.8 + - - +
579F ARG* 5.5 4.1 - - - +
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Residues in contact with GLU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B PHE 3.9 1.9 + - - +
473B SER* 1.3 73.4 - - - +
475B LYS* 1.3 66.9 + - + +
477B LEU* 3.9 11.2 - - - +
478B LYS* 3.3 34.6 + - - +
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Residues in contact with LYS 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B SER* 3.4 2.9 + - - +
474B GLU* 1.3 83.3 - - + +
476B ASN* 1.3 71.1 + - - +
478B LYS* 3.9 4.8 + - - +
479B ALA* 3.6 19.8 + - - +
553G VAL* 4.2 16.3 - - + +
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Residues in contact with ASN 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B PHE* 4.9 8.5 - - + -
473B SER* 3.2 25.3 + - - +
474B GLU 3.3 0.2 - - - -
475B LYS* 1.3 79.1 - - - +
477B LEU* 1.3 63.5 + - - +
479B ALA* 3.6 2.0 + - - +
480B LEU* 3.1 17.8 + - - +
553G VAL* 3.4 23.1 - - - +
555G SER 3.0 24.8 + - - +
556G PHE* 3.2 38.0 - - + +
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE* 3.8 35.9 - - + -
467B LEU* 5.0 3.4 - - + -
472B PHE* 3.8 32.9 - - + +
473B SER 3.0 18.1 + - - +
474B GLU* 3.9 12.1 - - - +
476B ASN* 1.3 74.8 - - - +
478B LYS* 1.3 62.0 + - + +
480B LEU* 3.0 16.1 + - + +
481B LEU* 2.8 57.6 + - + +
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Residues in contact with LYS 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B GLU* 3.3 22.8 + - - +
475B LYS* 4.3 4.7 - - - +
477B LEU* 1.3 77.6 - - + +
479B ALA* 1.3 63.5 + - - +
481B LEU* 3.3 12.3 + - + +
482B LYS* 3.0 39.8 + - + +
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Residues in contact with ALA 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA* 3.9 18.6 - - + +
253B LEU* 4.5 2.0 - - + -
475B LYS 3.6 15.4 + - - +
476B ASN 3.8 5.2 - - - +
477B LEU 3.2 0.8 - - - -
478B LYS* 1.3 78.6 - - - +
480B LEU* 1.3 61.4 + - - +
482B LYS* 3.7 9.5 - - - +
483B HIS* 3.0 31.4 + - - -
553G VAL* 3.7 22.4 - - + -
556G PHE* 4.3 8.3 - - + -
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B MET* 4.4 5.6 - - + -
467B LEU* 4.0 9.9 - - + -
472B PHE* 3.8 33.0 - - + -
476B ASN 3.1 13.6 + - - +
477B LEU* 3.0 19.6 + - + +
479B ALA* 1.3 75.4 - - - +
481B LEU* 1.3 64.5 + - - +
483B HIS* 2.9 15.5 + - - +
484B PHE* 3.1 39.2 + - + -
577F PHE* 3.4 34.1 - - + -
556G PHE* 3.6 24.7 - - + -
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Residues in contact with LEU 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE* 4.0 18.6 - - + -
173B THR 4.5 7.4 - - - +
174B ILE* 3.8 33.1 - - + +
467B LEU* 4.4 3.6 - - + -
477B LEU* 2.8 54.4 + - + +
478B LYS* 3.3 11.6 + - + +
480B LEU* 1.3 71.5 - - - +
482B LYS* 1.3 60.6 + - - +
484B PHE* 3.2 13.1 + - + +
485B ASP* 2.9 30.2 + - - +
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Residues in contact with LYS 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA* 6.3 2.7 - - + -
248B GLU* 4.5 31.7 + - + +
478B LYS* 3.0 31.6 + - + +
479B ALA* 3.7 10.5 - - - +
481B LEU* 1.3 77.0 - - + +
483B HIS* 1.3 56.8 + - - +
485B ASP* 3.2 11.0 + - - +
486B LEU* 3.0 34.9 + - + +
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Residues in contact with HIS 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 4.0 6.2 + - - -
217B PHE* 3.6 30.0 - + - -
247B ALA 2.6 33.9 + - - -
248B GLU* 4.2 2.4 + - - -
250B ASN 4.0 1.0 + - - -
253B LEU* 3.7 23.4 - - + +
254B CYS* 3.8 28.1 + - + -
257B MET* 3.4 31.5 - - + +
479B ALA 3.0 20.1 + - - +
480B LEU* 2.9 11.9 + - - +
482B LYS* 1.3 77.4 - - - +
484B PHE* 1.3 61.9 + - - +
486B LEU* 4.0 9.7 - - + +
487B PHE* 3.3 15.4 + - - +
556G PHE* 4.8 1.7 - + + -
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Residues in contact with PHE 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 4.1 21.1 - - + -
257B MET* 3.5 32.1 - - + -
261B LEU* 4.4 6.5 - - + -
460B PHE* 3.9 22.2 - + + -
463B LEU* 3.5 31.6 - - + -
467B LEU* 3.9 8.7 - - + -
480B LEU* 3.1 48.0 + - + -
481B LEU* 3.2 15.2 + - + +
483B HIS* 1.3 75.8 - - - +
485B ASP* 1.3 54.7 + - - +
487B PHE* 3.2 5.4 + - - +
488B LEU* 2.7 40.8 + - - +
577F PHE* 3.9 17.3 - + - -
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Residues in contact with ASP 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 4.6 12.1 - - - +
175B GLU* 4.9 14.5 + - - +
481B LEU* 2.9 16.4 + - - +
482B LYS* 3.2 13.2 + - - +
484B PHE* 1.3 76.6 - - - +
486B LEU* 1.3 54.0 + - + +
488B LEU* 3.1 7.9 + - - +
489B ARG* 2.7 45.3 + - + +
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Residues in contact with LEU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 3.4 15.3 - - + +
217B PHE* 4.0 14.6 - - + -
248B GLU* 3.9 29.4 - - + +
482B LYS* 3.0 21.7 + - + +
483B HIS* 4.0 10.3 - - + +
485B ASP* 1.3 76.5 - - + +
487B PHE* 1.3 58.4 + - - +
489B ARG* 3.2 13.1 + - + +
490B PHE* 2.9 28.2 + - - +
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Residues in contact with PHE 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ILE* 4.5 4.3 - - + -
210B LEU* 3.8 22.2 - - + -
213B TYR* 3.6 47.9 + + + -
257B MET* 4.5 11.2 - - + -
261B LEU* 4.6 4.7 - - + -
456B LEU* 3.8 24.0 - - + -
460B PHE* 3.4 41.1 - + - -
483B HIS 3.3 16.5 + - - +
484B PHE* 3.2 6.6 + - - +
486B LEU* 1.3 75.1 - - - +
488B LEU* 1.3 62.0 + - - +
490B PHE* 3.2 10.5 + + - +
491B LEU* 2.8 49.7 + - + +
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Residues in contact with LEU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 3.9 22.2 - - + -
175B GLU 3.7 22.2 - - - +
176B ILE* 4.8 4.0 - - + -
177B PRO* 3.8 18.2 - - + -
180B LEU* 3.4 24.3 - - + +
457B LEU* 4.1 13.0 - - + -
460B PHE* 3.9 36.6 - - + -
484B PHE 2.7 25.2 + - - +
485B ASP* 3.6 7.2 - - - +
487B PHE* 1.3 70.5 - - - +
489B ARG* 1.3 54.9 + - - +
491B LEU* 3.1 10.3 + - + +
492B ALA* 2.8 30.8 + - - +
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Residues in contact with ARG 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B PRO* 3.4 36.2 - - - +
485B ASP* 2.7 31.2 + - + +
486B LEU* 3.3 17.5 - - + +
488B LEU* 1.3 76.5 - - - +
490B PHE* 1.3 52.0 + - - +
492B ALA* 3.2 8.0 + - - +
493B GLU* 2.8 38.3 + - - +
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Residues in contact with PHE 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ILE* 4.6 2.9 - - + -
212B SER* 4.3 7.2 - - - -
213B TYR* 3.3 54.5 - + + -
216B HIS* 3.9 30.1 - + + -
486B LEU 2.9 13.5 + - - +
487B PHE* 3.4 16.2 - + - +
489B ARG* 1.3 76.2 - - - +
491B LEU* 1.3 67.1 + - + +
493B GLU* 3.4 8.4 + - - -
494B TYR* 3.3 48.6 + + - +
498B PHE* 3.7 33.6 - + - -
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Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 3.8 11.0 - - + +
209B ILE* 4.4 10.1 - - + -
453B ALA* 5.7 4.0 - - + +
456B LEU* 5.0 7.0 - - + -
457B LEU* 4.4 17.9 - - + -
460B PHE* 4.9 3.4 - - + -
487B PHE* 2.8 50.9 + - + +
488B LEU* 3.1 19.7 + - + +
490B PHE* 1.3 82.7 - - + +
492B ALA* 1.3 60.3 + - - +
494B TYR 3.8 1.2 - - - -
495B HIS* 3.3 22.7 + - - +
498B PHE* 3.9 26.6 - - + -
499B PHE* 4.3 18.5 - - + -
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PRO* 3.9 24.9 - - + -
179B VAL* 4.4 18.5 - - + +
180B LEU* 3.9 13.6 - - + +
488B LEU 2.8 14.8 + - - +
489B ARG* 3.6 10.3 - - - +
491B LEU* 1.3 76.1 - - - +
493B GLU* 1.3 64.8 + - - +
494B TYR 3.2 0.2 - - - -
495B HIS* 3.2 18.2 + - - +
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Residues in contact with GLU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ARG* 2.8 22.8 + - - +
490B PHE* 3.4 10.3 + - - +
492B ALA* 1.3 73.4 - - - +
494B TYR* 1.3 91.7 + - + +
495B HIS 3.5 0.6 + - - -
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Residues in contact with TYR 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B HIS* 4.5 18.9 + + - -
490B PHE* 3.3 43.0 + + - -
491B LEU 3.8 4.0 - - - -
492B ALA 3.2 0.4 - - - -
493B GLU* 1.3 108.9 + - + +
495B HIS* 1.3 63.2 + - - +
496B ASP* 3.3 3.6 - - - -
497B ASP* 3.1 32.2 + - + +
498B PHE* 3.1 31.6 + + + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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