Contacts of the strand formed by residues 763 - 770 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B LYS* 5.8 0.2 - - - +
313B ASP* 3.8 33.7 - - + +
315B PHE 3.3 14.8 - - - +
316B GLU* 3.9 8.2 - - + -
317B SER* 2.9 25.8 + - - +
752B TYR 3.6 0.5 - - - +
753B GLU* 3.7 0.9 - - - -
754B HIS 2.9 40.1 + - - +
755B THR* 4.1 0.4 - - - +
759B GLN* 3.2 25.9 + - - +
760B ASN 3.8 1.0 + - - -
762B TYR* 1.3 72.8 - - - +
764B LEU* 1.3 64.5 + - - +
765B SER* 3.9 6.9 + - - +
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Residues in contact with LEU 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASP* 4.0 0.2 - - - -
314B ILE* 2.9 27.1 + - - +
315B PHE* 2.9 27.8 + - + -
331B TYR* 3.7 31.4 - - + +
332B ARG* 3.9 5.6 - - - +
334B PRO* 3.8 28.7 - - + -
347B GLY 4.4 0.4 - - - +
348B ALA* 3.7 29.4 - - + -
751B LEU* 4.3 9.2 - - + -
752B TYR 3.1 7.6 - - - +
753B GLU* 3.6 29.2 - - + -
762B TYR* 4.1 1.6 - - + -
763B THR* 1.3 77.6 - - - +
765B SER* 1.3 60.3 - - - +
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Residues in contact with SER 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LYS* 3.8 24.3 + - - +
312B THR 3.4 7.6 - - - -
313B ASP* 3.0 26.8 + - - +
751B LEU* 3.3 7.3 - - - -
752B TYR* 2.9 50.3 + - - -
754B HIS* 4.9 3.8 - - - +
763B THR* 4.1 9.9 + - - +
764B LEU* 1.3 74.4 - - - +
766B PHE* 1.3 60.3 - - - +
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Residues in contact with PHE 766 (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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309B THR* 4.7 0.8 + - - -
310B GLU 3.9 1.4 - - - +
311B LYS* 3.7 2.3 - - - -
312B THR* 2.8 37.4 + - - +
314B ILE* 3.7 23.8 - - + +
336B LEU* 4.2 14.1 - - + -
344B LEU* 3.6 29.8 - - + -
371B ASN 4.3 0.2 - - - -
372B GLY* 3.7 28.5 - - - -
375B TRP* 4.2 9.9 - + - -
743B LEU* 4.5 1.3 - - + -
749B GLY* 3.8 24.0 - - - -
750B ILE 3.4 13.7 - - - -
751B LEU* 4.4 4.7 - - + -
765B SER* 1.3 73.2 - - - +
767B ARG* 1.3 65.4 + - - +
768B LYS* 3.6 36.1 - - + -
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Residues in contact with ARG 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 3.7 30.5 - - + +
309B THR* 2.8 41.6 + - - +
310B GLU* 3.8 4.2 - - - +
311B LYS* 3.7 28.4 - - - +
730B ILE* 3.4 24.9 + - - -
731B GLN* 3.3 23.4 + - - +
748B TYR 3.8 0.2 - - - +
749B GLY* 3.5 3.3 - - - -
750B ILE* 3.1 43.5 + - + +
752B TYR* 2.9 20.5 + - + +
766B PHE* 1.3 81.7 - - - +
768B LYS* 1.3 62.1 + - - +
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Residues in contact with LYS 768 (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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307B ALA 3.8 1.5 - - - +
308B LEU* 3.4 4.0 - - - +
309B THR* 3.0 55.5 + - + +
371B ASN* 3.6 29.7 + - - +
372B GLY 5.2 2.6 + - - -
373B LYS* 4.5 23.8 - - - +
743B LEU* 3.6 22.4 - - + -
747B GLU* 4.3 22.4 - - - +
748B TYR 3.3 5.6 - - - +
766B PHE* 3.6 21.1 - - + -
767B ARG* 1.3 72.6 - - - +
769B PHE* 1.3 65.0 + - - +
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Residues in contact with PHE 769 (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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307B ALA 3.2 10.5 - - - +
308B LEU* 3.9 7.2 - - + -
697B ILE* 4.5 3.4 - - + -
711B VAL* 4.0 12.8 - - + -
730B ILE* 3.7 19.5 - - + -
740B LEU* 3.7 28.7 - - + -
747B GLU* 3.4 5.0 - - - -
748B TYR* 2.6 79.8 + + + -
750B ILE* 4.0 15.3 - - + -
768B LYS* 1.3 78.5 - - - +
770B ASN* 1.3 64.6 + - - +
773B PHE* 3.7 30.3 - + + -
774B LEU* 3.9 20.9 - - + -
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Residues in contact with ASN 770 (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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307B ALA* 3.3 20.9 + - - +
746B GLY 3.0 16.4 - - - +
747B GLU* 4.1 16.8 + - + +
748B TYR* 4.7 0.2 - - - -
769B PHE* 1.3 80.5 - - - +
771B TRP* 1.3 64.3 + - - +
772B GLU* 3.0 45.1 + - - +
773B PHE* 3.2 14.6 + - - +
774B LEU* 3.3 12.9 + - - +
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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
------------------------------------------------------------
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