Contacts of the helix formed by residues 488 - 496 (chain B) in PDB entry 1Y1V
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 TYR 488 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 5.9 0.7 - - - +
197B PHE* 2.9 28.6 + - + -
198B ASP* 4.9 1.6 - - - -
199B MET* 3.2 35.3 - - + +
485B ARG* 6.0 0.2 - - - -
487B THR* 1.3 77.3 - - + +
489B SER* 1.3 70.5 + - - +
491B THR* 2.7 23.1 + - - -
492B LEU* 3.2 18.4 + - + +
780B VAL 4.0 5.3 + - - +
781B PHE* 3.8 16.9 - - - +
782B LEU* 5.2 2.5 - - + -
812B LEU 3.1 29.2 - - - -
813B LYS* 3.3 34.9 - - + +
814B PHE* 6.1 1.6 - + + -
817B LEU* 3.6 33.9 - - + +
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Residues in contact with SER 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B THR* 3.7 16.6 - - - +
488B TYR* 1.3 80.8 - - - +
490B SER* 1.3 64.1 + - - -
491B THR 2.6 13.5 + - - -
492B LEU* 2.8 25.4 + - - +
493B SER* 3.0 12.4 + - - -
751B VAL* 4.1 6.0 - - - +
755B ILE* 3.9 28.6 - - - +
774B GLY 4.1 8.7 + - - -
812B LEU* 5.5 5.8 - - - -
814B PHE* 4.6 13.5 - - - -
819B ALA* 5.7 0.2 - - - +
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Residues in contact with SER 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ASN* 3.6 20.3 + - - +
486B TYR* 3.8 20.2 - - - -
487B THR* 3.8 20.1 + - - -
488B TYR 3.3 0.6 - - - -
489B SER* 1.3 83.3 + - - +
491B THR* 1.3 59.7 + - - +
493B SER* 3.9 12.8 - - - -
494B HIS* 3.5 11.8 + - - +
497B ARG* 5.5 0.7 + - - -
774B GLY 4.3 0.7 - - - -
775B LYS* 4.1 30.4 - - - +
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Residues in contact with THR 491 (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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199B MET* 3.9 21.3 - - + -
483B LEU* 3.4 27.0 - - + +
484B ASN 2.8 15.4 + - - +
485B ARG* 3.5 30.0 + - - +
487B THR 2.8 18.8 + - - -
488B TYR* 2.7 14.5 + - - -
489B SER 2.6 6.1 + - - -
490B SER* 1.3 72.1 - - - +
492B LEU* 1.3 68.8 + - - +
494B HIS* 3.1 11.8 + - - +
495B LEU* 3.3 11.6 + - + +
781B PHE 4.6 1.2 + - - -
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.4 43.7 - - + +
44B VAL* 5.7 0.9 - - + -
199B MET* 3.3 36.8 - - + -
488B TYR* 3.9 17.7 - - + +
489B SER* 2.8 12.4 + - - +
491B THR* 1.3 77.4 - - - +
493B SER* 1.3 55.5 + - - +
495B LEU* 2.4 42.4 + - + +
496B ARG* 3.2 11.2 + - - +
751B VAL* 3.8 10.8 - - + -
812B LEU* 3.9 32.1 - - + +
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Residues in contact with SER 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B SER 3.0 12.6 + - - -
490B SER* 3.9 12.8 - - - -
492B LEU* 1.3 79.6 - - - +
494B HIS* 1.3 61.3 + - - -
495B LEU 3.2 1.0 + - - -
496B ARG 3.4 6.6 + - - -
497B ARG* 3.4 5.1 + - - +
526B GLU* 3.6 8.1 + - - -
538B ASN* 3.1 23.4 + - - +
751B VAL* 3.4 29.4 - - - +
752B ALA* 5.0 1.6 - - - -
775B LYS* 3.4 27.3 - - - -
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Residues in contact with HIS 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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211B VAL* 4.2 10.0 - - + +
213B ILE* 3.8 20.1 - - + +
481B GLN* 2.9 40.0 + - + +
482B VAL 3.7 17.9 - - - -
483B LEU* 3.7 11.2 - - + +
484B ASN* 3.3 39.2 + - + +
490B SER 3.5 11.7 + - - +
491B THR 3.1 10.3 + - - +
492B LEU 2.9 2.6 + - - -
493B SER* 1.3 77.1 - - - +
495B LEU* 1.3 60.6 + - - +
497B ARG* 4.0 30.2 + - - +
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Residues in contact with LEU 495 (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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44B VAL* 3.8 18.4 - - + -
46B GLN* 3.5 6.5 + - - +
47B GLN* 3.1 32.5 + - + +
199B MET* 3.6 22.4 - - + -
200B GLY 3.6 20.0 - - - +
201B GLY* 4.1 24.5 - - - +
202B TYR* 4.5 3.1 - - + +
211B VAL* 4.0 29.6 - - + -
213B ILE* 5.2 0.9 - - - -
483B LEU* 4.3 8.1 - - + -
491B THR* 3.3 17.5 + - + +
492B LEU* 2.4 30.0 + - - +
494B HIS* 1.3 69.7 - - - +
496B ARG* 1.3 57.3 + - + +
497B ARG 3.4 4.1 + - - -
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Residues in contact with ARG 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.2 36.4 + - - +
45B SER* 4.4 9.5 + - - -
46B GLN* 3.3 31.1 - - - +
214B ALA* 6.0 0.2 - - - -
492B LEU* 3.2 14.4 + - - +
493B SER 3.4 4.4 + - - +
495B LEU* 1.3 80.5 - - + +
497B ARG* 1.3 59.3 + - - +
538B ASN* 3.3 6.1 - - - +
539B LEU* 3.1 56.8 + - + +
540B SER 3.0 23.0 + - - -
541B LEU* 3.3 28.6 + - - +
543B SER* 3.6 13.9 + - - -
544B CYS* 5.5 0.2 - - - +
751B VAL* 4.3 22.9 - - + -
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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