Contacts of the strand formed by residues 708 - 713 (chain C) in PDB entry 6DBV
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 ARG 708 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C TRP* 3.1 5.5 - - - -
539C GLN* 2.9 53.3 + - + +
540C PRO* 5.7 0.7 - - + -
609C SER* 3.2 24.7 + - - -
706C GLU 4.2 3.8 - - - +
707C SER* 1.3 81.3 + - - +
709C LEU* 1.3 62.4 + - - +
710C ILE* 3.7 5.5 + - + +
719C SER* 3.2 28.1 + - - +
720C PHE 3.5 6.3 - - - +
721C ARG* 3.8 29.1 - - + +
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Residues in contact with LEU 709 (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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536C PHE* 4.2 5.4 - - + -
537C GLU 3.2 20.0 - - - +
538C TRP* 3.5 39.7 - - + +
582C LEU* 5.6 1.8 - - + -
583C VAL* 3.8 20.6 - - + +
586C LEU* 4.7 5.2 - - + -
707C SER 4.1 0.2 + - - -
708C ARG* 1.3 70.5 - - - +
710C ILE* 1.3 63.8 + - - +
711C ILE* 3.5 36.5 + - + -
718C ARG 3.4 4.9 - - - +
719C SER* 3.4 0.9 - - - -
720C PHE* 2.8 46.7 + - + +
722C PHE* 3.9 23.8 - - + -
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Residues in contact with ILE 710 (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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536C PHE* 3.4 3.0 - - - +
537C GLU* 2.9 52.7 + - + +
539C GLN* 3.3 45.1 - - + +
708C ARG* 4.3 7.2 - - + +
709C LEU* 1.3 73.7 - - - +
711C ILE* 1.3 70.6 + - - +
717C LEU* 4.3 27.6 - - + -
718C ARG 3.3 15.0 - - - +
719C SER* 3.7 23.1 - - - +
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Residues in contact with ILE 711 (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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535C GLN 5.0 1.6 - - - +
536C PHE* 3.8 13.0 - - + -
583C VAL* 4.1 13.9 - - + +
586C LEU* 4.3 18.6 - - + -
587C LYS* 3.5 33.9 - - + +
709C LEU* 3.5 39.3 - - + +
710C ILE* 1.3 84.8 - - - +
712C SER* 1.3 60.2 + - - +
713C VAL* 3.2 19.1 + - + +
716C LEU 3.0 4.9 - - - +
717C LEU* 3.3 3.2 - - - -
718C ARG* 2.9 32.7 + - - +
720C PHE* 4.6 7.2 - - + -
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Residues in contact with SER 712 (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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534C HIS* 5.8 0.7 - - - +
535C GLN* 4.3 20.0 + - - +
536C PHE* 5.4 1.6 - - - +
587C LYS* 2.7 24.5 + - - +
710C ILE 4.4 0.4 + - - -
711C ILE* 1.3 70.3 - - - +
713C VAL* 1.3 53.7 + - - +
714C GLY 4.3 0.5 + - - -
715C GLY* 4.9 5.5 + - - -
716C LEU 3.5 9.6 - - - +
717C LEU* 4.5 4.3 - - - +
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Residues in contact with VAL 713 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586C LEU 5.4 1.6 - - - +
587C LYS* 3.4 6.5 - - - +
590C GLU* 3.2 37.2 - - + -
593C ILE* 4.2 10.8 - - + -
594C MET* 4.1 7.2 - - + -
711C ILE* 3.6 20.9 - - + +
712C SER* 1.3 72.7 - - - +
714C GLY* 1.3 61.0 + - - +
715C GLY 3.1 1.3 - - - -
716C LEU 2.9 24.3 + - - +
718C ARG* 3.3 43.0 + - + +
720C PHE* 5.0 7.4 - - + -
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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