Contacts of the strand formed by residues 747 - 754 (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 GLU 747 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A ASN* 4.3 7.8 + - - -
742A GLU* 4.1 0.7 - - - +
743A LEU* 2.8 38.4 + - + +
744A GLY 3.1 14.6 + - - +
745A ASN* 4.3 6.5 - - - +
746A GLY* 1.3 81.2 - - - +
748A TYR* 1.3 65.6 + - - +
768A LYS* 4.1 23.4 + - + +
769A PHE 3.4 9.2 - - - +
770A ASN* 4.2 15.4 + - + +
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Residues in contact with TYR 748 (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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686A ILE* 4.0 13.2 - - + -
688A THR* 2.5 36.5 + - - +
689A MET 4.4 2.9 + - - -
690A HIS* 5.3 0.3 + - - -
697A ILE* 3.7 14.1 - - + -
740A LEU* 5.2 0.7 - - + -
741A GLN 3.4 6.1 - - - +
742A GLU* 3.6 29.9 + - + -
743A LEU* 3.6 5.8 - - - -
746A GLY* 3.8 21.9 - - - -
747A GLU* 1.3 78.3 - - - +
749A GLY* 1.3 59.8 + - - +
768A LYS* 3.1 7.4 - - - +
769A PHE* 2.7 75.1 + + + -
770A ASN 4.7 0.9 - - - -
771A TRP* 3.6 15.5 - + - -
774A LEU* 3.6 19.7 - - + -
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Residues in contact with GLY 749 (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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336A LEU* 3.8 6.7 - - - +
740A LEU* 3.5 7.2 - - - +
741A GLN 2.9 34.1 + - - +
743A LEU* 3.4 12.6 - - - +
748A TYR* 1.3 75.0 - - - +
750A ILE* 1.3 60.3 + - - +
766A PHE* 3.8 14.6 - - - -
767A ARG 3.3 8.7 - - - -
769A PHE* 4.9 0.7 - - - -
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Residues in contact with ILE 750 (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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336A LEU* 4.3 0.4 - - - -
699A SER* 3.3 35.0 - - - +
711A VAL* 4.8 1.3 - - + -
730A ILE* 3.8 31.9 - - + -
735A PHE* 4.4 8.3 - - + -
738A ASN* 4.0 13.0 - - + +
739A SER 3.4 10.3 - - - +
740A LEU* 4.1 14.4 - - + -
749A GLY* 1.3 75.7 - - - +
751A LEU* 1.3 68.7 + - - +
752A TYR* 4.1 15.0 - - + -
765A SER 3.7 0.9 - - - +
766A PHE* 3.2 10.0 - - - -
767A ARG* 2.9 45.4 + - + +
769A PHE* 4.1 3.6 - - + -
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Residues in contact with LEU 751 (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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314A ILE* 3.5 37.7 - - + -
315A PHE* 4.8 1.6 - - + -
334A PRO* 3.6 23.2 - - + +
335A ALA 3.6 23.6 - - - +
336A LEU* 4.1 18.6 - - + +
346A ALA* 3.7 18.6 - - + -
347A GLY 4.1 6.5 - - - +
738A ASN* 3.1 3.6 - - - +
739A SER 2.8 31.7 + - - +
750A ILE* 1.3 71.3 - - - +
752A TYR* 1.3 61.7 + - - +
764A LEU* 4.2 9.6 - - + -
765A SER 3.3 18.2 - - - +
766A PHE* 4.2 5.6 - - + -
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Residues in contact with TYR 752 (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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311A LYS* 3.6 10.2 - - - +
334A PRO* 4.2 4.0 - - - -
730A ILE* 5.5 2.2 - - + -
731A GLN* 2.8 35.0 + - + -
735A PHE* 3.6 27.6 - + + -
737A TYR 3.3 11.0 - - - +
738A ASN* 3.7 11.7 - - + +
750A ILE* 4.1 22.0 - - + -
751A LEU* 1.3 79.9 - - - +
753A GLU* 1.3 66.9 + - - +
754A HIS* 3.6 21.1 - + + -
763A THR 3.4 0.9 - - - +
764A LEU* 3.3 7.5 - - - -
765A SER* 3.0 50.5 + - - -
767A ARG* 2.9 35.8 + - + -
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Residues in contact with GLU 753 (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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332A ARG* 2.9 37.5 + - - -
333A ILE 3.0 18.0 + - - -
334A PRO* 3.8 11.4 - - + -
735A PHE* 3.3 8.7 + - - -
736A ALA* 3.0 29.6 + - + +
737A TYR* 2.7 49.9 + - - +
752A TYR* 1.3 75.2 - - - +
754A HIS* 1.3 61.6 + - - +
762A TYR* 3.5 23.2 - - + -
763A THR 3.8 4.3 - - - -
764A LEU* 3.9 12.1 - - + -
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Residues in contact with HIS 754 (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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311A LYS* 4.0 16.4 - - + -
731A GLN* 3.4 21.1 + - + +
732A LYS 3.3 22.9 - - - -
733A GLY* 4.6 1.6 - - - -
734A GLU 2.6 28.5 + - - +
752A TYR* 3.6 19.0 + - + +
753A GLU* 1.3 76.5 - - - +
755A THR* 1.3 82.7 + - - +
756A GLU* 2.7 31.4 + - + -
759A GLN* 5.3 0.9 - - - -
762A TYR* 3.7 5.0 - - - -
763A THR* 2.9 38.9 + - - +
765A SER* 5.2 3.4 - - - +
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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