Contacts of the strand formed by residues 346 - 351 (chain B) in PDB entry 1YA8
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 346 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B VAL* 4.4 1.6 - - + -
228B SER* 3.5 22.3 + - - -
231B VAL* 4.4 21.1 - - + -
243B ALA* 3.2 32.3 - - + -
245B SER* 2.9 32.0 + - - -
249B VAL* 4.6 1.4 - - - +
344B VAL* 3.7 2.0 - - + +
345B PRO* 1.3 75.5 - - - +
347B MET* 1.3 70.7 + - - +
348B VAL* 3.8 19.7 - - + +
433B VAL* 4.0 17.6 - - + +
437B HIS* 3.2 42.6 - + + +
443B PRO 2.9 9.1 + - - -
444B THR* 3.5 8.4 - - + +
445B TYR 3.1 21.5 + - - +
503B PHE* 3.7 4.5 - - - -
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Residues in contact with MET 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ALA 2.8 12.6 + - - +
244B ILE* 3.3 25.7 - - + +
245B SER 2.9 27.0 + - - +
346B TYR* 1.3 73.9 - - - +
348B VAL* 1.3 63.1 + - - +
445B TYR* 3.3 18.2 - - + +
447B TYR* 4.1 12.3 - - + -
499B PHE 4.9 0.2 - - - +
500B TRP* 4.0 23.3 - - + -
503B PHE* 3.6 47.7 - - + -
509B PRO* 4.2 7.9 - - + -
517B TRP* 3.8 31.6 - - + -
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B SER* 3.7 7.2 - - - +
249B VAL* 4.0 14.6 - - + -
346B TYR* 3.8 37.7 - - + +
347B MET* 1.3 78.8 - - - +
349B GLY* 1.3 61.8 + - - +
430B SER* 3.8 37.7 - - - +
433B VAL* 4.6 5.6 - - + -
434B ALA* 4.5 12.3 - - + -
444B THR* 5.4 0.7 - - + -
445B TYR 2.8 10.3 + - - +
446B MET* 2.9 38.4 - - + +
447B TYR* 4.6 2.7 - - - -
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Residues in contact with GLY 349 (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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245B SER 3.2 9.6 + - - +
246B GLU* 3.9 1.2 - - - -
247B SER 2.9 26.0 + - - -
348B VAL* 1.3 77.9 - - - +
350B ILE* 1.3 67.5 + - - +
430B SER* 4.6 1.4 + - - -
446B MET* 5.1 2.7 - - - -
447B TYR* 3.3 34.9 + - - -
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Residues in contact with ILE 350 (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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247B SER* 4.1 3.4 - - - -
349B GLY* 1.3 77.9 - - - +
351B ASN* 1.3 76.8 + - - +
354B GLU* 3.7 13.5 - - + +
422B ALA 5.6 0.7 - - - +
426B PHE* 3.9 11.4 - - + +
427B GLY* 3.9 22.7 - - - +
430B SER* 3.3 35.7 - - - +
431B VAL* 6.1 0.9 - - + -
446B MET* 5.4 2.2 - - + -
447B TYR* 3.0 9.2 + - - +
448B GLU* 3.1 21.6 - - + +
449B PHE 2.8 22.7 + - - -
539B LEU* 5.0 8.5 - - + +
540B LYS* 4.1 24.7 - - + -
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Residues in contact with ASN 351 (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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247B SER* 3.7 7.9 + - - -
350B ILE* 1.3 91.1 - - - +
352B LYS* 1.3 63.5 + - - +
354B GLU* 2.7 34.6 + - - +
447B TYR* 4.4 3.8 - - - -
448B GLU* 4.3 3.1 - - - +
449B PHE* 3.2 30.8 - - - +
466B GLY 3.1 19.5 - - - +
467B ASP 3.0 19.2 - - - +
468B HIS* 4.0 0.2 - - - -
469B GLY 3.4 6.9 + - - -
470B ASP 3.9 0.7 + - - -
471B GLU* 3.0 27.7 + - - +
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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