Contacts of the strand formed by residues 747 - 754 (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 GLU 747 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ALA 5.4 1.2 - - - +
371B ASN* 4.8 5.2 + - - +
743B LEU* 2.9 42.3 + - + +
744B GLY 3.8 2.3 + - - -
745B ASN* 3.7 22.2 - - + +
746B GLY 1.3 81.5 + - - +
748B TYR* 1.3 72.9 + - - +
768B LYS* 4.3 23.9 - - + +
769B PHE 3.4 8.0 - - - +
770B ASN* 4.1 19.3 + - + +
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Residues in contact with TYR 748 (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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686B ILE* 4.3 3.8 - - + -
688B THR* 2.6 30.3 + - - -
689B MET 5.0 1.6 + - - -
690B HIS* 4.9 3.8 + - - +
697B ILE* 3.6 18.6 - - + -
740B LEU* 5.3 0.4 - - + -
741B GLN 3.4 11.0 - - - +
742B GLU* 3.3 26.4 + - + -
743B LEU* 3.5 5.8 - - - -
746B GLY* 3.6 24.3 - - - -
747B GLU* 1.3 81.8 - - - +
749B GLY* 1.3 59.6 + - - +
768B LYS* 3.3 4.3 - - - -
769B PHE* 2.6 66.4 + + + -
770B ASN 4.7 0.4 - - - -
771B TRP* 3.5 19.1 - + - -
774B LEU* 3.4 32.5 - - + -
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Residues in contact with GLY 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU* 3.8 9.6 - - - -
740B LEU* 3.4 5.4 - - - +
741B GLN 2.9 32.2 + - - +
743B LEU* 3.4 15.0 - - - +
748B TYR* 1.3 74.4 - - - +
750B ILE* 1.3 62.5 + - - +
766B PHE* 3.8 15.5 - - - -
767B ARG 3.5 6.7 - - - -
769B PHE* 4.6 0.4 - - - -
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Residues in contact with ILE 750 (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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699B SER* 3.3 35.2 - - - +
711B VAL* 4.9 0.4 - - + -
730B ILE* 3.8 31.6 - - + -
735B PHE* 4.4 8.7 - - + -
738B ASN* 4.2 11.7 - - + +
739B SER 3.5 9.0 - - - +
740B LEU* 3.8 15.7 - - + -
749B GLY* 1.3 75.9 - - - +
751B LEU* 1.3 68.6 + - - +
752B TYR* 3.5 10.7 - - + -
765B SER 3.4 6.4 - - - +
766B PHE* 3.4 8.3 - - - -
767B ARG* 3.1 36.6 + - + +
769B PHE* 4.0 4.7 - - + -
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Residues in contact with LEU 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE* 3.8 32.1 - - + -
315B PHE* 4.7 3.6 - - + -
334B PRO* 3.6 24.8 - - + +
335B ALA 3.6 18.4 - - - +
336B LEU* 3.8 18.9 - - + +
346B ALA* 3.5 28.3 - - + -
347B GLY 3.9 7.9 - - - +
738B ASN* 3.1 3.1 - - - -
739B SER* 2.8 36.2 + - - -
750B ILE* 1.3 69.8 - - - +
752B TYR* 1.3 61.2 + - - +
764B LEU* 4.3 11.0 - - + +
765B SER 3.3 15.0 - - - +
766B PHE* 4.4 5.2 - - + -
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Residues in contact with TYR 752 (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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311B LYS* 3.4 12.5 - - - +
334B PRO* 4.2 3.4 - - - -
730B ILE* 5.2 2.5 - - + -
731B GLN* 2.8 38.2 + - + -
735B PHE* 3.4 35.4 - + + -
737B TYR 3.3 10.1 - - - +
738B ASN* 3.7 6.3 - - + -
750B ILE* 3.5 22.9 - - + -
751B LEU* 1.3 75.2 - - - +
753B GLU* 1.3 61.6 + - - +
754B HIS* 3.7 20.2 - - + -
763B THR 3.6 0.5 - - - +
764B LEU* 3.1 6.6 - - - -
765B SER* 2.9 54.9 + - - -
767B ARG* 2.9 34.5 + - + -
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Residues in contact with GLU 753 (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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332B ARG* 2.8 51.5 + - - +
333B ILE 3.0 16.6 + - - -
334B PRO* 3.7 6.1 - - + -
735B PHE* 3.3 8.0 - - - -
736B ALA* 3.0 25.9 + - + +
737B TYR* 2.8 46.1 + - - +
752B TYR* 1.3 74.0 - - - +
754B HIS* 1.3 61.5 + - - +
762B TYR* 3.5 18.8 - - + -
763B THR 3.7 4.9 - - - -
764B LEU* 3.6 15.0 - - + -
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Residues in contact with HIS 754 (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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311B LYS* 3.9 14.6 - - + -
731B GLN* 3.3 35.0 + - - +
732B LYS 3.3 10.5 - - - -
733B GLY* 4.3 1.8 - - - -
734B GLU 2.6 29.5 + - - +
752B TYR* 3.7 19.0 + - + -
753B GLU* 1.3 75.4 - - - +
755B THR* 1.3 83.7 + - - +
756B GLU* 3.0 30.5 + - + +
759B GLN* 4.0 1.8 - - - +
762B TYR* 3.7 5.0 - - - -
763B THR* 2.9 37.3 + - - +
765B SER* 4.9 3.7 + - - +
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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