Contacts of the strand formed by residues 763 - 770 (chain A) in PDB entry 2YA6
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 THR 763 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS* 5.6 0.9 - - - +
313A ASP* 3.9 22.9 - - + +
315A PHE 3.4 12.8 - - - +
316A GLU* 3.7 10.7 - - + +
317A SER* 3.0 28.1 + - - -
752A TYR 3.4 1.7 - - - +
753A GLU* 3.8 0.7 - - - -
754A HIS 2.9 39.1 + - - +
755A THR* 4.2 0.4 - - - +
759A GLN* 3.6 23.0 - - - +
760A ASN 3.8 0.8 + - - -
762A TYR* 1.3 73.2 - - - +
764A LEU* 1.3 61.8 + - - +
765A SER* 3.7 19.1 + - - +
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Residues in contact with LEU 764 (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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313A ASP* 3.7 0.9 - - - -
314A ILE* 2.7 32.6 + - - +
315A PHE* 2.9 33.4 + - + +
331A TYR* 3.5 31.6 - - + +
332A ARG* 4.1 4.3 - - - +
334A PRO* 3.8 33.2 - - + -
347A GLY 4.4 0.7 - - - +
348A ALA* 3.5 31.4 - - + -
751A LEU* 4.2 8.7 - - + -
752A TYR 3.3 7.9 - - - +
753A GLU* 3.9 18.2 - - + -
762A TYR* 4.1 0.9 - - + +
763A THR* 1.3 77.2 - - - +
765A SER* 1.3 55.2 + - - +
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Residues in contact with SER 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LYS* 3.8 24.7 + - - +
312A THR 3.2 7.0 - - - -
313A ASP* 2.8 27.0 + - - -
751A LEU* 3.3 5.1 - - - +
752A TYR* 3.0 47.7 + - - -
754A HIS* 5.2 3.3 + - - +
763A THR* 3.7 12.0 + - - +
764A LEU* 1.3 75.0 - - - +
766A PHE* 1.3 61.9 + - - +
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Residues in contact with PHE 766 (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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309A THR* 5.9 0.2 - - - -
310A GLU 3.8 1.2 - - - +
311A LYS* 3.4 3.7 - - - -
312A THR* 2.7 42.2 + - - +
314A ILE* 3.7 21.8 - - + -
336A LEU* 4.0 18.6 - - + -
344A LEU* 3.8 25.8 - - + -
371A ASN 4.2 0.2 - - - -
372A GLY* 3.6 31.0 - - - -
375A TRP* 4.2 9.6 - + - -
743A LEU* 4.3 0.4 - - + -
749A GLY* 3.8 20.4 - - - -
750A ILE 3.2 17.5 - - - -
751A LEU* 4.2 3.1 - - + -
765A SER* 1.3 75.1 - - - +
767A ARG* 1.3 64.6 + - - +
768A LYS* 3.7 36.3 - - + -
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Residues in contact with ARG 767 (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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308A LEU* 3.7 35.3 + - + +
309A THR* 2.7 41.7 + - - +
310A GLU* 3.8 14.3 + - - +
311A LYS* 3.7 24.9 - - - +
730A ILE* 3.6 21.2 + - - -
731A GLN* 3.1 23.4 + - - +
749A GLY* 3.3 3.5 - - - -
750A ILE* 2.9 42.9 + - + +
752A TYR* 2.9 22.3 + - + +
765A SER 4.3 0.2 - - - -
766A PHE* 1.3 83.4 - - - +
768A LYS* 1.3 62.7 - - - +
769A PHE* 4.9 0.2 - - - -
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Residues in contact with LYS 768 (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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308A LEU* 3.6 3.2 - - - +
309A THR* 3.0 50.9 + - + +
371A ASN* 2.8 37.0 + - - +
372A GLY* 4.8 2.2 - - - -
373A LYS* 4.0 30.6 - - - +
743A LEU* 3.3 33.7 - - + -
747A GLU* 4.1 16.5 + - - +
748A TYR 3.1 3.8 - - - +
766A PHE* 3.7 19.9 - - + -
767A ARG* 1.3 72.9 - - - +
769A PHE* 1.3 65.2 + - - +
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Residues in contact with PHE 769 (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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307A ALA 3.1 14.8 - - - +
308A LEU* 4.0 5.2 - - + -
697A ILE* 4.6 2.7 - - + -
711A VAL* 3.9 13.9 - - + -
730A ILE* 3.6 29.8 - - + -
740A LEU* 3.9 22.2 - - + -
747A GLU* 3.4 5.6 - - - -
748A TYR* 2.7 73.1 + + + +
750A ILE* 4.1 15.5 - - + -
768A LYS* 1.3 77.1 - - - +
770A ASN* 1.3 65.2 + - - +
773A PHE* 3.5 26.5 - + + -
774A LEU* 3.9 20.6 - - + -
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Residues in contact with ASN 770 (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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307A ALA* 3.3 24.5 + - - +
746A GLY 3.3 16.6 - - - +
747A GLU* 4.2 15.4 + - + +
748A TYR* 4.7 0.7 - - - -
769A PHE* 1.3 81.3 - - - +
771A TRP* 1.3 64.6 + - - +
772A GLU* 3.3 29.1 + - - +
773A PHE* 3.3 21.5 + - - +
774A LEU* 3.5 7.0 + - - +
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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