Contacts of the helix formed by residues 473 - 494 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A SER 3.9 1.4 + - - -
472A PHE* 1.3 76.8 - - - +
474A GLU* 1.3 64.7 - - - +
475A LYS* 4.1 2.6 + - - +
476A ASN* 3.2 32.5 + - - +
477A LEU* 3.0 23.0 + - - +
579E ARG* 5.6 2.8 - - - +
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Residues in contact with GLU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A PHE 3.9 2.0 + - - +
473A SER* 1.3 74.0 - - - +
475A LYS* 1.3 67.5 + - + +
477A LEU* 3.9 11.0 - - - +
478A LYS* 3.3 35.1 + - - +
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Residues in contact with LYS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A SER* 3.4 2.9 + - - +
474A GLU* 1.3 83.1 - - + +
476A ASN* 1.3 70.4 + - - +
478A LYS* 3.9 4.8 + - - +
479A ALA* 3.6 19.9 + - - +
553H VAL* 4.2 15.9 - - + +
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Residues in contact with ASN 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PHE* 4.9 8.7 - - + -
473A SER* 3.2 24.9 + - - +
474A GLU 3.3 0.2 - - - -
475A LYS* 1.3 79.0 - - - +
477A LEU* 1.3 63.4 + - - +
479A ALA* 3.5 2.6 + - - +
480A LEU* 3.1 18.4 + - - +
553H VAL* 3.3 23.5 - - - +
555H SER 3.0 25.0 + - - +
556H PHE* 3.3 36.3 - - + +
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ILE* 3.8 35.9 - - + -
467A LEU* 5.0 3.8 - - + -
472A PHE* 3.8 32.5 - - + +
473A SER 3.0 18.3 + - - +
474A GLU* 3.9 12.1 - - - +
476A ASN* 1.3 74.3 - - - +
478A LYS* 1.3 56.1 + - + +
480A LEU* 3.0 16.7 + - + +
481A LEU* 2.8 63.1 + - + +
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Residues in contact with LYS 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A GLU* 3.3 22.8 + - - +
475A LYS* 4.3 4.7 - - - +
477A LEU* 1.3 77.1 - - + +
479A ALA* 1.3 63.4 + - - +
481A LEU* 3.3 12.6 + - + +
482A LYS* 3.0 39.4 + - - +
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Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ALA* 4.2 17.0 - - + +
253A LEU* 4.5 2.5 - - + -
475A LYS 3.6 5.6 + - - +
476A ASN 3.5 8.2 + - - +
477A LEU 3.2 0.8 - - - -
478A LYS* 1.3 78.0 - - - +
480A LEU* 1.3 61.6 + - - +
482A LYS* 3.7 9.5 - - - +
483A HIS* 3.1 30.7 + - - -
553H VAL* 3.7 29.6 - - + -
556H PHE* 4.3 7.9 - - + -
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A MET* 4.3 5.8 - - + -
467A LEU* 4.0 9.2 - - + -
472A PHE* 3.8 32.8 - - + -
476A ASN 3.1 13.4 + - - +
477A LEU* 3.0 19.4 + - + +
479A ALA* 1.3 75.6 - - - +
481A LEU* 1.3 59.7 + - - +
483A HIS* 2.9 20.7 + - - +
484A PHE* 3.1 41.0 + - + -
577E PHE* 3.4 33.4 - - + -
556H PHE* 3.6 25.1 - - + -
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ILE* 4.0 19.1 - - + -
173A THR 4.5 7.4 - - - +
174A ILE* 3.8 32.9 - - + +
467A LEU* 4.4 3.4 - - + -
477A LEU* 2.8 53.1 + - + +
478A LYS* 3.3 12.3 + - + +
480A LEU* 1.3 72.4 - - + +
482A LYS* 1.3 60.6 + - - +
484A PHE* 3.2 12.9 + - + +
485A ASP* 3.0 30.1 + - - +
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Residues in contact with LYS 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ALA* 6.4 1.1 - - + -
248A GLU* 3.6 35.2 - - + +
478A LYS* 3.0 30.3 + - + +
479A ALA* 3.7 9.9 - - - +
481A LEU* 1.3 76.8 - - + +
483A HIS* 1.3 56.8 + - - +
485A ASP* 3.1 11.2 + - - +
486A LEU* 3.0 31.3 + - - +
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Residues in contact with HIS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A TYR* 4.0 5.6 + + - -
217A PHE* 3.6 28.6 - + - -
247A ALA 2.9 35.8 + - - -
248A GLU* 4.2 4.2 - - + -
253A LEU* 3.7 22.3 - - + +
254A CYS* 3.8 28.6 + - + -
257A MET* 3.5 25.6 - - + +
479A ALA 3.1 20.4 + - - +
480A LEU* 2.9 11.9 + - - +
482A LYS* 1.3 76.7 - - - +
484A PHE* 1.3 62.1 + - - +
486A LEU* 3.9 9.3 + - + +
487A PHE* 3.2 21.7 + - - +
556H PHE* 4.9 1.5 - + + -
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Residues in contact with PHE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE* 4.2 20.9 - - + -
257A MET* 3.5 31.6 - - + -
261A LEU* 4.4 6.5 - - + -
460A PHE* 3.9 22.7 - + + -
463A LEU* 3.5 31.4 - - + -
467A LEU* 4.0 9.0 - - + -
480A LEU* 3.1 49.1 + - + -
481A LEU* 3.4 14.8 - - + +
482A LYS 3.2 0.2 - - - -
483A HIS* 1.3 76.2 - - - +
485A ASP* 1.3 54.5 + - - +
487A PHE* 3.1 5.4 + - - +
488A LEU* 2.7 40.8 + - - +
577E PHE* 3.9 16.8 - + - -
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Residues in contact with ASP 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE* 4.6 12.0 - - - +
175A GLU* 4.9 15.0 + - - +
248A GLU* 5.9 0.2 - - - +
481A LEU* 3.0 20.4 + - - +
482A LYS* 3.1 13.4 + - - +
484A PHE* 1.3 76.6 - - - +
486A LEU* 1.3 52.5 + - + +
488A LEU* 3.1 8.1 + - - +
489A ARG* 2.8 51.3 + - + +
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A TYR* 3.4 15.2 - - + +
217A PHE* 4.0 14.8 - - + -
248A GLU* 3.5 52.3 - - + +
482A LYS 3.0 17.4 + - - +
483A HIS* 4.0 9.6 - - + +
485A ASP* 1.3 76.7 - - + +
487A PHE* 1.3 58.6 + - - +
489A ARG* 3.3 12.0 + - + +
490A PHE* 2.9 28.1 + - - +
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Residues in contact with PHE 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ILE* 4.5 4.3 - - + -
210A LEU* 3.8 22.4 - - + -
213A TYR* 3.6 49.5 + + + -
257A MET* 4.5 10.3 - - + -
261A LEU* 4.7 4.5 - - + -
456A LEU* 3.8 23.8 - - + -
460A PHE* 3.4 39.9 - + - -
483A HIS 3.2 16.3 + - - +
484A PHE* 3.1 6.8 + - - +
486A LEU* 1.3 78.5 - - - +
488A LEU* 1.3 58.6 + - - +
490A PHE* 3.3 9.8 + + - +
491A LEU* 2.8 51.0 + - + +
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Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE* 3.9 22.2 - - + -
175A GLU 3.7 22.4 - - - +
176A ILE* 4.7 4.3 - - + -
177A PRO* 3.8 18.8 - - + -
180A LEU* 3.4 27.1 - - + +
457A LEU* 4.1 13.0 - - + -
460A PHE* 3.9 37.2 - - + -
484A PHE 2.7 25.2 + - - +
485A ASP* 3.6 7.2 - - - +
487A PHE* 1.3 70.9 - - - +
489A ARG* 1.3 55.5 + - - +
491A LEU* 3.1 8.1 + - + -
492A ALA* 2.8 30.7 + - - +
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Residues in contact with ARG 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO* 3.8 37.5 - - - +
179A VAL* 6.3 0.4 - - - +
485A ASP* 2.8 37.0 + - + +
486A LEU* 3.4 14.4 - - + +
488A LEU* 1.3 77.5 - - - +
490A PHE* 1.3 51.8 + - - +
492A ALA* 3.2 8.6 + - - +
493A GLU* 2.8 38.6 + - - +
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Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ILE* 4.6 2.9 - - + -
212A SER* 4.4 1.6 - - - -
213A TYR* 3.3 54.5 - + + -
216A HIS* 3.8 36.6 - + + -
486A LEU 2.9 13.2 + - - +
487A PHE* 3.4 14.6 - + - +
489A ARG* 1.3 77.8 - - - +
491A LEU* 1.3 68.5 + - + +
493A GLU* 3.4 8.4 + - - -
494A TYR* 3.3 48.4 + + - +
498A PHE* 3.6 33.6 - + - -
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Residues in contact with LEU 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.8 11.0 - - + +
209A ILE* 4.4 9.9 - - + -
453A ALA* 5.7 4.0 - - + +
456A LEU* 5.0 7.2 - - + -
457A LEU* 4.4 17.7 - - + -
460A PHE* 4.9 3.1 - - + -
487A PHE* 2.8 50.9 + - + +
488A LEU* 3.1 19.7 + - + +
490A PHE* 1.3 83.3 - - + +
492A ALA* 1.3 59.9 + - - +
494A TYR 3.7 1.2 - - - -
495A HIS* 3.3 22.7 + - - +
498A PHE* 4.0 26.6 - - + -
499A PHE* 4.3 19.3 - - + -
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Residues in contact with ALA 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO* 3.9 24.2 - - + -
179A VAL* 4.5 18.7 - - + +
180A LEU* 3.9 13.6 - - + +
488A LEU 2.8 15.3 + - - +
489A ARG* 3.6 10.3 - - - +
491A LEU* 1.3 75.4 - - - +
493A GLU* 1.3 66.2 + - - +
495A HIS* 3.2 18.3 + - - +
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Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A ARG* 2.8 19.4 + - - +
490A PHE* 3.8 9.6 - - - +
492A ALA* 1.3 77.1 - - - +
494A TYR* 1.3 90.9 + - + +
495A HIS 3.5 0.6 + - - -
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Residues in contact with TYR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A HIS* 4.6 19.7 + + - -
490A PHE* 3.3 43.2 + + - -
491A LEU 3.7 4.0 - - - -
492A ALA 3.2 0.4 - - - -
493A GLU* 1.3 108.0 + - + +
495A HIS* 1.3 63.2 + - - +
496A ASP* 3.3 3.4 - - - -
497A ASP* 3.1 32.4 + - + +
498A PHE* 3.1 31.1 + + + -
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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