Contacts of the strand formed by residues 699 - 705 (chain B) in PDB entry 5Y7K
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 699 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648B LYS* 2.8 41.1 + - + +
649B CYS* 3.1 14.7 - - + +
650B GLY* 2.9 28.4 + - - +
698B VAL* 1.3 75.2 - - - +
700B TYR* 1.3 59.0 + - - +
758B PHE* 3.6 10.9 - - + -
761B GLN* 2.9 32.2 + - - +
762B CYS* 4.6 0.8 - - - -
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Residues in contact with TYR 700 (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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637B SER* 2.8 29.7 + - - -
640B LEU* 3.4 26.5 - - + -
650B GLY 3.7 1.1 - - - -
652B ALA* 3.5 15.6 - - + +
695B PHE* 3.4 39.3 - + + +
698B VAL* 3.7 5.5 + - + +
699B GLU* 1.3 73.4 - - - +
701B LEU* 1.3 59.4 + - - +
702B LEU* 3.4 38.6 - - + +
719B ILE* 4.0 12.4 - - + +
723B LEU* 3.8 24.7 - - + -
729B ASP 5.4 1.9 + - - +
730B PHE* 3.5 16.7 - + + +
731B GLN* 2.8 35.0 + - - +
758B PHE* 4.3 2.0 - - - -
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Residues in contact with LEU 701 (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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650B GLY 3.0 14.1 + - - +
651B ILE* 3.4 22.0 - - + +
652B ALA* 2.9 29.6 + - - +
700B TYR* 1.3 75.8 - - - +
702B LEU* 1.3 64.1 + - - +
703B ILE* 4.0 26.2 - - + -
731B GLN* 3.4 26.0 - - + +
732B ALA* 4.1 7.0 - - - +
754B HIS* 4.3 19.3 - - + +
755B MET* 4.4 3.4 - - + -
758B PHE* 3.8 40.4 - - + -
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Residues in contact with LEU 702 (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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734A TRP* 4.1 15.3 - - + -
652B ALA 3.6 5.4 - - - +
655B PRO* 3.6 27.6 - - + -
700B TYR* 3.4 29.1 - - + +
701B LEU* 1.3 72.7 - - - +
703B ILE* 1.3 60.8 + - - +
716B SER* 3.6 38.6 - - - +
719B ILE* 3.8 20.2 - - + -
720B SER* 4.2 8.5 - - - +
730B PHE* 4.9 7.0 - - + -
731B GLN 3.0 12.3 + - - +
732B ALA* 3.3 4.3 - - - +
733B MET 3.0 25.6 + - - +
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Residues in contact with ILE 703 (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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734A TRP* 5.4 0.2 - - - -
651B ILE* 4.2 5.8 - - + -
652B ALA 2.9 13.7 + - - +
653B VAL* 4.3 7.0 - - + -
654B ALA* 2.8 24.6 + - - -
655B PRO* 3.8 2.6 - - - +
701B LEU* 4.0 21.5 - - + -
702B LEU* 1.3 80.6 - - - +
704B HIS* 1.3 68.0 + - - +
716B SER* 4.9 0.7 - - - -
733B MET* 3.2 20.6 - - + +
735B TYR* 3.6 31.4 - - + -
742B ILE* 4.5 0.9 - - + -
751B ILE* 3.7 21.1 - - + +
754B HIS* 4.7 6.3 - - + -
755B MET* 3.8 29.8 - - + -
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Residues in contact with HIS 704 (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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734A TRP* 5.0 1.5 - - + -
654B ALA* 3.5 25.1 - - - +
655B PRO 4.0 2.0 - - - -
703B ILE* 1.3 79.3 - - - +
705B GLY* 1.3 93.2 + - - +
706B THR 3.8 0.3 + - - -
708B ASP* 3.3 11.7 + - - +
711B VAL* 2.5 42.3 + - + -
712B HIS 3.4 14.8 + - - -
713B PHE* 3.7 17.2 + + + -
716B SER* 2.5 40.7 + - - +
733B MET 3.3 4.4 + - - -
734B TRP* 3.4 8.8 - - - +
735B TYR 3.3 18.9 + - - -
742B ILE* 4.6 5.2 - - - -
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Residues in contact with GLY 705 (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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654B ALA* 5.3 0.8 - - - +
704B HIS* 1.3 94.0 - - - +
706B THR* 1.3 66.1 + - - -
707B ALA 3.2 2.9 - - - -
708B ASP* 3.3 10.4 + - - +
713B PHE* 3.9 3.4 - - - +
735B TYR* 3.5 16.6 - - - -
738B GLU* 3.5 15.7 - - - -
739B ASP 4.5 5.7 + - - -
742B ILE* 4.2 9.1 - - - +
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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