Contacts of the strand formed by residues 698 - 708 (chain C) in PDB entry 4YOC
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 698 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579C GLN* 3.2 18.8 - - - -
691C MET 3.6 0.9 - - - +
692C TYR* 3.4 10.4 - - - -
693C ASP* 2.9 36.1 + - - +
696C THR* 2.8 27.9 + - - -
697C ARG* 1.3 75.3 - - - +
699C LEU* 1.3 62.1 + - - +
700C ASN* 4.0 10.0 + - - +
786C TYR* 4.9 2.2 - - - -
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Residues in contact with LEU 699 (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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577C GLY* 5.3 3.1 + - - -
578C HIS 4.0 14.4 - - - +
579C GLN* 2.9 47.5 + - - +
580C GLY 3.9 9.4 - - - +
690C LYS* 4.3 18.8 - - + -
691C MET 3.5 4.3 - - - +
692C TYR* 4.1 19.1 - - + -
698C SER* 1.3 76.4 - - - +
700C ASN* 1.3 68.1 + - - +
701C TYR 4.2 0.8 + - - -
767C VAL* 4.1 26.2 - - + -
786C TYR* 3.8 12.6 - - + -
787C PHE* 3.6 30.5 - - + -
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Residues in contact with ASN 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C GLY 6.1 0.4 - - - +
690C LYS* 3.6 3.1 - - - -
691C MET* 2.9 72.5 + - + +
693C ASP* 4.2 7.1 - - - +
698C SER* 4.0 13.2 + - - +
699C LEU* 1.3 81.0 + - - +
701C TYR* 1.3 67.0 + - - +
702C CYS* 3.3 6.8 + - - -
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Residues in contact with TYR 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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572C GLU* 2.8 31.5 + - + -
575C PHE* 3.2 51.8 - + + +
576C CYS* 3.9 31.0 - - + -
577C GLY 4.6 4.5 - - - +
578C HIS 5.8 1.9 + - - +
583C MET* 5.5 4.5 - - - -
688C PHE* 3.2 35.5 - + + -
689C LEU 4.2 6.3 - - - -
690C LYS* 4.8 16.8 - - + +
699C LEU 4.2 1.2 + - - -
700C ASN* 1.3 72.3 - - - +
702C CYS* 1.3 62.0 + - - +
703C GLY* 3.4 31.8 + - - -
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Residues in contact with CYS 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689C LEU* 2.8 27.1 + - + +
691C MET* 3.8 21.3 - - - -
700C ASN* 3.3 18.6 + - - -
701C TYR* 1.3 74.0 - - - +
703C GLY* 1.3 67.3 + - - +
723C ARG* 3.1 52.2 + - + -
724C ALA* 4.1 7.2 - - - -
768C PHE* 4.0 11.0 - - + -
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Residues in contact with GLY 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C GLU* 3.7 4.9 - - - -
688C PHE* 3.8 1.4 - - - -
689C LEU* 3.0 26.4 + - - +
701C TYR* 3.4 35.0 + - - -
702C CYS* 1.3 79.5 - - - +
704C HIS* 1.3 61.1 + - - -
723C ARG* 4.5 4.5 - - - -
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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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572C GLU* 2.6 40.7 + - - -
661C PHE* 4.7 3.1 - + - -
663C GLU* 2.7 37.7 + - + -
664C THR 5.7 1.1 - - - -
686C MET* 3.4 28.9 - - + -
687C LEU 3.1 13.7 - - - +
688C PHE* 3.7 23.7 - + + -
689C LEU* 4.8 0.9 - - - +
701C TYR* 4.4 0.2 + - - -
703C GLY* 1.3 73.5 - - - -
705C ILE* 1.3 65.9 + - - +
706C TYR* 4.3 4.7 - + - -
723C ARG* 2.9 24.3 + - - +
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Residues in contact with ILE 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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685C VAL 3.5 0.3 - - - +
686C MET* 3.2 5.8 - - - -
687C LEU* 2.9 53.5 + - + +
689C LEU* 4.1 23.1 - - + -
704C HIS* 1.3 83.7 - - - +
706C TYR* 1.3 69.9 + - - +
707C THR* 4.4 8.1 - - + -
716C LEU* 3.8 32.5 - - + -
719C VAL* 4.0 14.8 - - + -
723C ARG* 3.6 26.0 - - - +
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Residues in contact with TYR 706 (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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621C ARG* 3.0 36.2 + - - -
623C TRP* 3.4 11.5 - + - -
663C GLU* 2.3 43.9 + - - -
677C PRO* 3.9 24.2 - - + -
678C LYS 3.7 15.9 - - - +
679C PHE* 3.8 22.7 - + + -
684C ASP* 5.2 5.2 - - - +
685C VAL 3.5 2.9 - - - -
686C MET* 3.7 25.4 - - + -
704C HIS* 4.3 2.5 - + - -
705C ILE* 1.3 81.8 - - - +
707C THR* 1.3 60.1 + - - +
708C PRO* 4.7 1.3 - - - +
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Residues in contact with THR 707 (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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684C ASP* 3.8 6.1 - - - +
685C VAL* 2.9 41.0 + - + +
687C LEU* 4.2 13.9 - - + -
705C ILE* 4.4 10.3 - - + -
706C TYR* 1.3 77.0 - - - +
708C PRO* 1.3 83.5 + - - +
711C CYS* 3.5 17.3 - - - +
716C LEU* 4.0 12.7 - - + +
753C LEU* 3.6 23.0 - - + +
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Residues in contact with PRO 708 (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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683C HIS* 3.3 12.1 - - + +
684C ASP* 3.4 13.0 - - - +
706C TYR 4.7 0.9 - - - +
707C THR* 1.3 94.0 + - - +
709C ILE* 1.3 66.3 + - - +
710C SER* 4.1 14.6 - - - +
711C CYS* 3.1 26.6 + - + +
753C LEU* 3.9 4.7 - - - +
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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