Contacts of the strand formed by residues 699 - 705 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640C LEU* 4.7 0.2 - - - +
648C LYS* 3.0 38.9 + - - +
649C CYS* 3.1 15.0 - - + +
650C GLY 2.9 26.9 + - - -
698C VAL* 1.3 76.6 - - - +
700C TYR* 1.3 60.0 + - - +
731C GLN* 6.3 0.9 - - + -
758C PHE* 3.5 14.8 - - + -
761C GLN* 5.1 10.4 + - - +
762C CYS* 4.8 9.5 - - - +
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Residues in contact with TYR 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637C SER* 2.8 26.0 + - - -
640C LEU* 3.5 29.2 - - + -
650C GLY 3.7 1.6 - - - -
652C ALA* 3.3 27.0 - - + +
695C PHE* 3.8 33.2 - + + +
698C VAL* 3.8 5.2 + - + +
699C GLU* 1.3 73.4 - - - +
701C LEU* 1.3 63.9 + - - +
702C LEU* 3.4 29.4 - - + +
719C ILE* 4.1 13.1 - - + +
723C LEU* 3.8 25.6 - - + -
728C VAL* 6.5 0.2 - - + -
729C ASP 5.4 1.3 + - - +
730C PHE* 3.6 15.4 - - + +
731C GLN* 2.6 36.8 + - - +
758C PHE* 4.2 3.1 - - - -
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Residues in contact with LEU 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650C GLY 3.0 10.4 + - - +
651C ILE* 3.4 21.6 - - + +
652C ALA* 2.9 28.1 + - - +
700C TYR* 1.3 77.4 - - - +
702C LEU* 1.3 61.8 + - - +
703C ILE* 4.0 24.2 - - + -
731C GLN* 3.4 23.8 - - + -
732C ALA* 4.1 6.3 - - - +
754C HIS* 4.2 26.5 - - + +
755C MET* 4.3 3.6 - - + -
758C PHE* 3.6 45.3 - - + -
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Residues in contact with LEU 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652C ALA 3.6 3.1 - - - +
655C PRO* 3.9 14.4 - - + -
700C TYR* 3.4 31.9 - - + +
701C LEU* 1.3 72.0 - - - +
703C ILE* 1.3 63.9 + - - +
716C SER* 3.4 48.2 - - - +
719C ILE* 4.1 18.2 - - + -
720C SER* 4.3 7.6 - - - +
730C PHE* 4.7 7.6 - - + -
731C GLN 2.9 14.6 + - - +
732C ALA* 3.3 4.1 - - - +
733C MET 3.0 25.8 + - - +
734D TRP* 3.9 17.4 - - + -
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Residues in contact with ILE 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651C ILE* 4.1 5.8 - - + -
652C ALA 2.8 13.0 + - - +
653C VAL* 4.3 8.1 - - + -
654C ALA 2.7 29.5 + - - -
655C PRO* 3.9 3.1 - - - +
701C LEU* 4.0 24.2 - - + -
702C LEU* 1.3 80.8 - - - +
704C HIS* 1.3 63.0 + - - +
716C SER* 4.1 1.0 + - - -
733C MET* 3.3 11.9 - - + +
735C TYR* 3.6 30.1 - - + +
742C ILE* 4.5 0.9 - - + -
751C ILE* 3.7 26.5 - - + +
754C HIS* 5.0 6.5 - - + -
755C MET* 3.8 29.8 - - + -
734D TRP* 5.5 0.4 - - - -
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Residues in contact with HIS 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654C ALA* 3.5 24.4 - - + +
655C PRO 4.2 2.2 - - - -
703C ILE* 1.3 80.8 - - - +
705C GLY* 1.3 90.6 - - - +
708C ASP* 3.2 12.3 + - - +
711C VAL* 2.6 40.6 + - + -
712C HIS 3.5 13.7 - - - -
713C PHE* 3.7 20.6 + + + -
716C SER* 2.6 37.6 + - - +
733C MET 3.3 3.6 + - - -
734C TRP* 3.2 10.0 - - - +
735C TYR* 3.1 20.3 + - - -
742C ILE* 4.8 3.4 - - - -
734D TRP* 5.1 1.5 - - + -
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Residues in contact with GLY 705 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654C ALA* 5.2 0.4 - - - +
704C HIS* 1.3 94.7 - - - +
706C THR* 1.3 65.9 + - - -
707C ALA 3.3 2.5 - - - -
708C ASP* 3.3 9.8 + - - +
713C PHE* 3.6 4.2 - - - +
735C TYR* 3.4 16.6 - - - -
738C GLU* 3.5 15.9 - - - -
739C ASP 4.6 4.8 + - - -
742C ILE* 4.5 8.5 - - - +
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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