Contacts of the strand formed by residues 346 - 351 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A VAL* 4.4 1.6 - - + -
228A SER* 3.6 23.1 + - - -
231A VAL* 4.5 19.1 - - + -
243A ALA* 3.2 23.1 - - + -
245A SER* 2.8 32.6 + - - -
249A VAL* 3.9 6.1 - - - +
336A GLN* 5.9 0.2 - - - -
344A VAL* 3.2 1.7 + - + +
345A PRO* 1.3 75.6 - - - +
347A MET* 1.3 74.1 + - - +
348A VAL* 3.5 24.2 + - + -
433A VAL* 3.9 14.8 - - + -
434A ALA* 6.2 0.2 - - - -
437A HIS* 3.4 43.7 - + + +
443A PRO 3.3 6.7 + - - -
444A THR* 3.4 7.6 - - + +
445A TYR* 3.0 24.4 + - - +
503A PHE* 3.9 3.7 - - - -
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Residues in contact with MET 347 (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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243A ALA 2.8 9.1 + - - +
244A ILE* 3.1 33.7 - - + +
245A SER 2.7 32.4 + - - -
346A TYR* 1.3 73.8 - - - +
348A VAL* 1.3 59.9 + - - +
445A TYR* 3.3 17.7 - - + +
447A TYR* 4.1 10.8 - - + -
499A PHE 4.7 0.2 - - - +
500A TRP* 4.0 22.4 - - + -
503A PHE* 3.8 40.1 - - + -
509A PRO* 4.4 7.4 - - + -
517A TRP* 3.7 34.8 - - + -
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Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER* 3.7 5.2 - - - +
248A GLY 6.3 0.7 - - - +
249A VAL* 4.1 13.2 - - + -
346A TYR* 3.5 44.0 - - + +
347A MET* 1.3 73.1 - - - +
349A GLY* 1.3 62.7 + - - +
430A SER* 3.8 38.6 - - - +
433A VAL* 4.4 8.5 - - + -
434A ALA* 4.8 6.5 - - + +
444A THR* 6.0 1.3 - - + -
445A TYR 2.9 9.3 + - - +
446A MET* 3.1 38.9 - - + +
447A TYR* 3.4 3.5 + - - -
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Residues in contact with GLY 349 (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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245A SER 3.0 9.6 + - - +
247A SER* 2.7 32.3 + - - -
248A GLY 4.5 0.5 + - - -
348A VAL* 1.3 79.2 - - - +
350A ILE* 1.3 65.1 + - - +
430A SER* 4.8 0.3 + - - -
446A MET* 4.9 1.1 - - - -
447A TYR* 3.4 34.2 - - - -
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Residues in contact with ILE 350 (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 SER* 3.9 2.2 - - - -
349A GLY* 1.3 79.3 - - - +
351A ASN* 1.3 77.7 + - - +
354A GLU* 3.5 14.8 - - + +
426A PHE* 4.1 12.8 - - + +
427A GLY* 4.1 10.5 - - - +
430A SER* 3.4 32.8 - - - +
446A MET* 5.5 2.7 - - + -
447A TYR* 3.3 6.9 + - - +
448A GLU* 3.2 15.5 - - + +
449A PHE 3.0 20.3 + - - -
539A LEU* 4.2 20.0 - - + -
540A LYS* 3.8 29.6 - - + -
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Residues in contact with ASN 351 (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 SER* 3.9 6.2 + - - -
350A ILE* 1.3 94.0 + - - +
352A LYS* 1.3 63.3 + - - +
353A GLN 3.5 0.2 - - - -
354A GLU* 2.6 31.4 + - - +
447A TYR* 4.4 2.4 - - - -
448A GLU* 4.3 3.2 - - - +
449A PHE* 3.2 33.9 - - - +
466A GLY 3.0 20.6 - - - +
467A ASP 2.7 19.7 - - - +
468A HIS* 4.3 0.5 - - - -
469A GLY 3.9 3.1 + - - -
470A ASP 3.7 2.4 + - - -
471A GLU* 2.8 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
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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