Contacts of the strand formed by residues 684 - 690 (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 SER 684 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B GLY* 6.1 1.1 - - - -
557B THR 6.1 2.2 - - - -
634B THR* 3.6 10.1 - - - -
682B GLN* 4.8 1.6 - - - -
683B MET* 1.3 75.0 - - - +
685B ALA* 1.3 62.9 + - - +
686B ILE* 6.1 0.7 - - - -
698B LEU* 3.3 4.9 - - - +
699B SER 2.9 31.1 + - - +
738B ASN* 2.8 33.3 + - - -
739B SER* 3.8 4.5 - - - -
740B LEU* 3.0 32.5 + - - +
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Residues in contact with ALA 685 (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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559B ILE* 5.7 0.9 - - - +
634B THR* 3.1 27.6 + - + -
635B VAL 4.2 3.8 - - - +
636B VAL* 3.4 25.2 - - + +
646B PHE* 4.0 13.0 - - + -
684B SER* 1.3 78.2 - - - +
686B ILE* 1.3 69.3 + - - +
696B ILE* 4.2 3.4 - - + -
697B ILE 3.1 12.8 - - - +
698B LEU* 4.1 12.1 - - + -
740B LEU* 4.5 0.7 - - - -
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Residues in contact with ILE 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B ILE* 6.2 3.8 - - + -
636B VAL* 4.2 7.2 - - - -
684B SER* 6.1 0.7 - - - -
685B ALA* 1.3 79.2 - - - +
687B HIS* 1.3 65.1 + - - +
688B THR 3.9 0.2 + - - -
696B ILE* 3.3 6.4 - - - +
697B ILE* 2.9 43.6 + - + +
740B LEU* 3.5 35.4 - - + +
741B GLN* 3.5 44.4 - - - +
742B GLU* 3.7 10.5 - - + +
748B TYR* 4.3 15.5 - - + -
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Residues in contact with HIS 687 (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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562B ARG* 2.9 39.3 + - - +
636B VAL* 3.6 21.7 - - + +
637B GLN 3.6 8.1 - - - +
638B LEU* 4.5 4.9 - - + -
639B ASN* 3.3 7.7 + - - -
686B ILE* 1.3 79.4 - - - +
688B THR* 1.3 65.1 + - - +
689B MET* 3.7 28.2 + - + +
694B GLU* 2.7 37.6 + - + +
695B TYR 3.7 8.3 - - - -
696B ILE* 5.1 0.7 - - + -
742B GLU* 3.7 11.8 - - - +
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Residues in contact with THR 688 (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* 5.4 0.4 - - - -
687B HIS* 1.3 78.8 - - - +
689B MET* 1.3 64.6 + - - +
694B GLU* 4.0 0.7 - - - -
695B TYR* 2.8 64.4 + - + +
697B ILE* 3.8 27.6 - - + +
742B GLU* 2.4 25.1 + - - -
748B TYR* 2.6 29.2 + - - +
771B TRP* 4.3 7.0 - - + -
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Residues in contact with MET 689 (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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639B ASN* 3.7 26.7 - - - +
687B HIS* 3.7 15.4 + - + -
688B THR* 1.3 76.3 + - - +
690B HIS* 1.3 60.2 + - - +
691B GLU 4.0 1.7 + - - -
692B GLY* 3.7 36.6 - - - +
693B LYS 3.5 9.6 - - - +
694B GLU* 3.6 19.7 - - + +
742B GLU* 3.7 5.8 + - - +
748B TYR* 5.0 1.2 + - - -
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Residues in contact with HIS 690 (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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688B THR 3.9 1.8 + - - -
689B MET* 1.3 72.1 - - - +
691B GLU* 1.3 102.9 + - + +
692B GLY 3.3 0.4 - - - -
693B LYS* 3.1 26.7 + - - +
695B TYR* 3.6 17.9 + + + -
745B ASN 5.9 0.4 + - - -
746B GLY* 5.5 7.8 - - - -
748B TYR* 4.9 2.6 + - - +
771B TRP* 3.2 68.3 - + + +
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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