Contacts of the helix formed by residues 452 - 470 (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 GLY 452 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A CYS* 3.3 21.6 - - - -
204A THR 3.9 13.2 - - - -
206A ILE* 3.3 17.2 - - - +
209A ILE* 3.9 0.7 - - - -
451A TYR* 1.3 75.0 - - - +
453A ALA* 1.3 65.7 + - - -
454A GLN* 3.2 5.4 + - - -
455A HIS* 3.3 5.1 + - - -
456A LEU 3.2 18.0 + - - -
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Residues in contact with ALA 453 (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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204A THR 4.6 1.4 + - - -
209A ILE* 3.4 23.7 - - + +
452A GLY* 1.3 69.0 - - - -
454A GLN* 1.3 69.5 + - - +
456A LEU* 3.9 6.1 - - - +
457A LEU* 3.3 18.4 + - - +
491A LEU* 5.7 4.4 - - + +
498A PHE* 3.5 33.4 - - + +
499A PHE* 3.4 26.7 - - + -
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Residues in contact with GLN 454 (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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183A GLN* 5.7 0.9 - - - +
184A LEU* 5.1 1.0 - - - +
187A ASP* 4.0 10.3 - - - +
198A VAL* 3.8 22.5 - - + +
202A CYS* 4.2 3.1 - - - -
452A GLY* 3.2 6.1 + - - -
453A ALA* 1.3 87.6 + - - +
455A HIS* 1.3 70.7 + - + +
457A LEU* 3.8 4.7 + - - +
458A ARG* 3.2 21.9 + - - +
498A PHE 4.1 16.8 + - - -
499A PHE* 4.1 17.7 - - + +
500A PRO* 4.3 6.7 + - - +
503A ALA* 3.4 28.9 - - - +
504A TYR* 3.1 35.2 - - + +
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Residues in contact with HIS 455 (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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198A VAL* 3.7 34.6 - - + +
265A PHE* 3.7 29.1 - - + -
269A LEU* 4.0 11.2 - - + -
273A LEU* 4.2 3.3 - - + +
274A LEU* 4.5 3.5 - - + +
278A GLU* 3.0 22.8 + - - -
281A GLN* 5.6 2.2 + - - -
451A TYR* 3.3 38.9 - + + +
452A GLY 3.3 7.2 + - - +
454A GLN* 1.3 77.6 - - + +
456A LEU* 1.3 66.0 + - - +
457A LEU 3.1 2.2 - - - -
458A ARG* 3.0 47.4 + - + +
459A LEU 3.4 4.3 + - - -
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Residues in contact with LEU 456 (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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206A ILE* 3.8 30.1 - - + -
209A ILE* 4.1 22.0 - - + -
210A LEU* 4.4 5.4 - - + -
261A LEU* 4.3 17.9 - - + +
265A PHE* 3.9 13.2 - - + -
452A GLY 3.2 17.3 + - - +
453A ALA* 3.9 5.6 - - - +
454A GLN 3.5 0.2 - - - -
455A HIS* 1.3 75.3 - - - +
457A LEU* 1.3 63.4 + - - +
459A LEU* 3.3 24.2 - - + +
460A PHE* 3.3 23.8 - - + -
487A PHE* 3.8 25.8 - - + -
491A LEU* 5.0 6.3 - - + -
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Residues in contact with LEU 457 (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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176A ILE* 5.1 3.4 - - + -
180A LEU* 3.8 39.7 - - + +
183A GLN* 4.0 12.3 - - + -
184A LEU* 3.8 26.3 - - + +
453A ALA 3.3 15.0 + - - +
454A GLN 3.9 5.6 - - - +
455A HIS 3.1 0.6 - - - -
456A LEU* 1.3 77.2 - - - +
458A ARG* 1.3 67.3 + - - +
460A PHE* 3.0 25.1 + - + +
461A VAL 3.9 1.6 + - - -
488A LEU* 4.1 25.4 - - + -
491A LEU* 4.4 8.7 - - + +
499A PHE* 3.9 22.0 - - + -
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Residues in contact with ARG 458 (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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184A LEU* 4.1 9.9 - - + -
187A ASP* 2.5 43.3 + - - +
191A ILE* 3.5 11.9 - - - +
273A LEU* 3.2 30.1 + - + +
274A LEU* 4.6 0.2 - - - +
275A TYR* 3.7 10.6 - - - -
278A GLU* 2.6 39.9 + - - -
454A GLN 3.2 19.0 + - - +
455A HIS* 3.0 35.1 + - - +
457A LEU* 1.3 75.6 - - - +
459A LEU* 1.3 57.7 + - - +
461A VAL* 2.9 29.9 + - - +
462A LYS 3.6 1.2 + - - -
589E PHE* 3.5 42.7 - - + -
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Residues in contact with LEU 459 (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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261A LEU* 3.9 26.9 - - + +
264A THR* 4.3 7.6 - - + -
265A PHE* 4.1 27.6 - - + +
268A THR* 3.9 36.8 - - + +
273A LEU* 3.7 18.0 - - + +
455A HIS 3.4 2.4 + - - +
456A LEU* 3.3 17.2 + - + +
458A ARG* 1.3 78.8 - - - +
460A PHE* 1.3 57.1 + - + +
462A LYS* 3.0 3.2 + - + -
463A LEU* 2.8 53.0 + - + +
466A ILE* 4.4 5.8 - - + -
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Residues in contact with PHE 460 (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* 4.5 15.5 - - + +
176A ILE* 4.4 15.0 - - + +
261A LEU* 3.6 26.7 - - + -
456A LEU* 3.3 22.9 - - + -
457A LEU* 3.0 18.4 + - + +
459A LEU* 1.3 75.8 - - + +
461A VAL* 1.3 60.5 + - - +
463A LEU* 4.1 16.6 - - + +
464A PRO* 3.7 13.2 - - - +
484A PHE* 3.9 31.2 - + + -
487A PHE* 3.4 38.6 - + - -
488A LEU* 3.9 38.4 - - + -
491A LEU* 4.9 0.9 - - + -
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Residues in contact with VAL 461 (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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176A ILE* 3.8 12.1 - - + -
184A LEU* 3.8 29.6 - - + -
457A LEU 4.7 0.2 - - - +
458A ARG 2.9 12.9 + - - +
460A PHE* 1.3 80.2 - - - +
462A LYS* 1.3 66.2 + - + +
464A PRO* 3.5 14.9 - - - +
465A GLU* 4.6 3.6 - - - +
589E PHE* 4.0 23.8 - - + -
590E GLU 4.2 3.6 - - - +
591E LEU* 4.6 2.7 - - + -
592E PRO* 3.5 33.9 - - + +
593E TRP* 4.5 10.5 - - + -
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Residues in contact with LYS 462 (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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272A VAL* 3.5 30.0 + - + +
273A LEU* 3.7 26.9 - - + -
458A ARG 3.6 0.4 + - - -
459A LEU* 3.0 7.3 + - + +
461A VAL* 1.3 79.5 - - + +
463A LEU* 1.3 66.3 + - - +
464A PRO* 3.4 0.9 - - - -
465A GLU* 2.9 49.4 + - - +
466A ILE* 3.4 22.3 + - + +
587E GLN* 3.0 38.6 + - - +
588E ASN 4.9 3.2 + - - -
589E PHE* 4.0 20.6 - - + +
590E GLU 4.8 8.8 + - - +
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Residues in contact with LEU 463 (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* 3.8 14.1 - - + -
261A LEU* 4.8 4.9 - - + -
264A THR* 4.7 11.2 - - + -
459A LEU* 2.8 53.3 + - + +
460A PHE* 4.2 12.8 - - + +
462A LYS* 1.3 75.4 - - - +
464A PRO* 1.3 65.9 - - + +
466A ILE* 3.1 9.1 + - + +
467A LEU* 2.8 42.5 + - + +
484A PHE* 3.5 46.0 - - + -
577E PHE* 5.3 3.6 - - + -
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Residues in contact with PRO 464 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ILE* 3.3 47.6 - - + +
174A ILE* 3.8 17.7 - - + +
460A PHE 3.7 10.3 - - - +
461A VAL 3.5 16.8 - - - +
462A LYS 3.4 1.3 - - - -
463A LEU* 1.3 93.3 - - + +
465A GLU* 1.3 59.8 + - + +
467A LEU* 3.4 3.1 + - + +
468A GLY* 3.0 26.0 + - - -
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Residues in contact with GLU 465 (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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272A VAL* 5.0 2.3 - - - +
461A VAL* 4.6 4.8 - - - +
462A LYS* 2.9 57.2 + - - +
464A PRO* 1.3 76.0 - - + +
466A ILE* 1.3 64.3 + - - +
468A GLY* 3.3 10.7 + - - -
469A LYS* 3.4 23.5 + - - +
584E LEU* 5.2 6.6 - - + +
587E GLN* 4.9 3.2 - - - +
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Residues in contact with ILE 466 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A THR* 4.7 11.0 - - + -
267A TYR* 6.6 0.2 - - + -
268A THR* 4.1 22.7 - - + +
272A VAL* 4.9 0.7 - - + -
459A LEU* 4.4 8.5 - - + -
462A LYS* 3.4 26.7 - - + +
463A LEU* 3.1 7.8 + - + +
465A GLU* 1.3 77.7 - - - +
467A LEU* 1.3 58.8 + - + +
469A LYS* 3.0 24.4 + - - +
470A MET* 3.3 32.9 - - + +
581E LEU* 5.2 1.1 - - + -
582E PRO* 3.7 20.8 - - + +
584E LEU* 3.9 34.3 - - + -
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Residues in contact with LEU 467 (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 16.4 - - + +
174A ILE* 3.8 25.8 - - + -
463A LEU* 2.8 37.5 + - + +
464A PRO* 3.8 5.2 - - + +
466A ILE* 1.3 70.1 - - + +
468A GLY* 1.3 59.5 + - - +
470A MET* 2.8 39.2 - - + +
472A PHE* 3.5 36.1 - - + -
477A LEU* 5.0 1.8 - - + -
480A LEU* 4.0 13.2 - - + -
481A LEU* 4.4 10.5 - - + -
484A PHE* 4.0 9.6 - - + -
577E PHE* 4.5 11.7 - - + -
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Residues in contact with GLY 468 (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 11.4 - - - +
464A PRO 3.0 15.4 + - - -
465A GLU 3.3 5.8 + - - -
466A ILE 3.2 0.4 - - - -
467A LEU* 1.3 76.8 - - - +
469A LYS* 1.3 62.5 + - - +
470A MET 3.5 4.9 + - - +
471A SER* 4.6 3.3 + - - -
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Residues in contact with LYS 469 (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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465A GLU* 3.4 18.1 + - - +
466A ILE* 3.0 9.4 + - - +
468A GLY* 1.3 78.5 - - - +
470A MET* 1.3 58.1 + - - +
471A SER* 3.9 2.1 + - - -
582E PRO* 3.8 16.8 - - + -
583E LYS* 3.3 27.8 + - - +
584E LEU* 4.1 18.5 - - + +
585E ALA 5.7 0.6 - - - +
569G THR* 3.2 31.1 + - + +
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Residues in contact with MET 470 (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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264A THR* 5.2 2.2 - - + -
466A ILE* 3.3 43.3 - - + +
467A LEU* 2.8 35.0 - - + +
468A GLY 3.9 1.9 - - - +
469A LYS* 1.3 74.6 - - - +
471A SER* 1.3 59.9 + - - +
472A PHE* 3.1 33.8 + - + -
576E ALA 4.5 6.7 - - - +
577E PHE* 5.0 6.7 - - + -
579E ARG* 3.7 23.3 - - + +
580E PRO* 3.7 21.1 - - + +
581E LEU* 4.0 12.8 - - + -
582E PRO* 3.9 12.1 - - + -
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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
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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