Contacts of the strand formed by residues 694 - 701 (chain C) in PDB entry 3FBY
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 TYR 694 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687C GLN* 4.1 13.9 - - + -
688C HIS* 3.3 7.3 + - - -
689C ARG* 2.8 46.8 + - + +
692C VAL* 4.2 9.6 - - + -
693C GLY* 1.3 76.2 - - - +
695C ILE* 1.3 65.1 + - - +
696C ARG* 3.2 40.5 + - + +
711C VAL* 3.4 33.7 - - + +
712C VAL 4.0 1.6 - - - -
713C LEU* 4.3 2.7 - - + -
745C ILE* 5.1 0.2 - - + -
746C PRO* 3.7 28.6 - - + +
748C ASP* 2.6 24.6 + - - -
749C TYR* 3.7 35.4 - + + -
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Residues in contact with ILE 695 (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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601C PHE* 3.6 26.7 - - + -
610C TYR* 3.5 37.9 - - + +
637C LEU* 3.7 27.8 - - + -
667C LEU* 4.8 4.3 - - + -
686C LEU* 4.7 3.4 - - + -
687C GLN 3.3 3.1 - - - -
688C HIS* 3.5 15.5 - - + +
693C GLY 4.9 1.6 - - - +
694C TYR* 1.3 80.6 - - - +
696C ARG* 1.3 67.1 + - - +
697C VAL* 5.0 1.1 - - + +
709C SER* 5.6 0.2 - - - +
711C VAL* 4.0 0.3 - - - -
712C VAL* 2.8 48.2 + - + +
714C ASP* 4.5 14.1 - - + +
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Residues in contact with ARG 696 (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 PHE 3.8 1.2 - - - +
686C LEU* 3.4 4.0 - - - +
687C GLN* 2.8 48.8 + - - +
694C TYR* 3.2 31.9 + - + +
695C ILE* 1.3 74.5 - - - +
697C VAL* 1.3 67.4 + - - +
698C ARG* 2.8 39.5 + - - +
708C ASP* 2.9 36.7 + - - -
709C SER* 3.5 1.8 - - - -
710C ASN* 3.3 33.0 - - - +
711C VAL 3.9 0.7 - - - +
748C ASP* 3.2 28.5 + - - -
1003C SO4 4.6 3.8 + - - -
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Residues in contact with VAL 697 (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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599C PHE* 3.8 20.4 - - + -
612C VAL* 4.2 10.8 - - + -
637C LEU* 4.1 21.1 - - + -
668C TRP* 4.2 11.6 - - + -
684C TRP* 5.4 0.4 - - + -
685C PHE 3.5 7.4 - - - +
686C LEU* 4.4 11.2 - - + -
695C ILE* 5.0 0.9 - - + -
696C ARG* 1.3 76.7 - - - +
698C ARG* 1.3 67.6 + - - +
699C PHE* 3.4 28.9 - - + -
708C ASP* 3.7 1.4 - - - +
709C SER* 2.8 50.0 + - - -
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Residues in contact with ARG 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683C ARG 3.9 0.7 - - - +
684C TRP* 3.6 2.4 - - - +
685C PHE* 2.9 70.8 + - + +
687C GLN* 3.9 9.7 + - - -
696C ARG* 2.8 47.2 + - - +
697C VAL* 1.3 79.4 - - - +
699C PHE* 1.3 67.3 + - - +
700C TYR* 3.9 21.3 + - + -
705C LEU* 3.8 19.4 - - + +
707C ALA 3.3 14.6 - - - +
708C ASP* 3.9 13.3 + - + +
1002C SO4 4.5 5.5 + - - -
1003C SO4 4.6 12.3 + - - -
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Residues in contact with PHE 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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586C PHE* 5.3 5.2 - + + -
599C PHE* 3.8 12.6 - + - -
612C VAL* 3.7 19.1 - - + -
614C TRP* 4.7 17.9 - + + -
635C ILE* 3.5 34.3 - - + -
668C TRP* 4.9 2.9 - + - -
682C TYR* 4.6 17.5 - - + -
683C ARG 3.3 5.4 - - - -
684C TRP* 3.6 22.2 - + + -
697C VAL* 3.4 25.6 - - + -
698C ARG* 1.3 79.4 - - - +
700C TYR* 1.3 59.6 + - - +
705C LEU* 3.5 3.2 - - - +
706C VAL* 2.7 41.1 + - + +
707C ALA* 2.9 25.7 + - + -
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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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257C VAL* 3.5 37.0 - - + -
272C LEU* 4.3 0.2 - - - +
682C TYR* 3.2 7.0 - - - +
683C ARG* 2.5 48.2 + - + +
685C PHE* 5.2 8.5 - - + -
698C ARG* 3.9 23.3 + - + -
699C PHE* 1.3 77.8 - - - +
701C GLU* 1.3 60.3 + - - +
702C GLY 3.6 11.5 + - - +
703C PRO 4.1 6.1 - - - -
704C GLU 3.2 5.6 - - - -
705C LEU* 3.4 51.4 - - + +
706C VAL* 4.4 1.8 - - - -
1002C SO4 4.5 15.9 + - - -
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Residues in contact with GLU 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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672C ARG* 5.1 4.2 + - - -
677C LYS* 4.5 6.6 - - - +
680C LYS* 3.3 34.0 + - + -
681C SER 4.4 1.6 - - - +
682C TYR* 3.8 32.8 + - + -
700C TYR* 1.3 71.6 - - - +
702C GLY* 1.3 68.3 + - - +
703C PRO* 3.1 2.6 - - - +
704C GLU* 2.8 24.6 + - + +
706C VAL* 3.7 27.6 - - + +
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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