Contacts of the strand formed by residues 707 - 712 (chain A) in PDB entry 2O8C
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 CYS 707 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A MET* 3.9 4.7 - - - -
301A LYS* 3.3 38.8 - - + +
705A VAL* 3.4 6.5 - - - +
706A ASP* 1.3 92.0 - - - +
708A ILE* 1.3 58.7 + - - +
709A LEU* 3.5 25.7 + - + -
738A SER* 4.5 10.3 - - - -
743A SER* 3.4 18.1 - - - +
744A LEU 2.9 24.1 + - - +
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Residues in contact with ILE 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A MET* 3.6 26.2 - - + -
301A LYS 3.4 5.7 + - - -
302A LEU* 3.6 16.2 - - + +
306A ALA* 3.4 19.8 - - + +
310A LEU* 4.6 10.1 - - + -
683A GLY* 3.5 22.7 - - - +
686A VAL* 4.1 13.9 - - + -
687A LEU* 4.0 17.9 - - + -
705A VAL* 4.2 4.7 - - + -
707A CYS* 1.3 71.3 - - - +
709A LEU* 1.3 66.7 + - - +
744A LEU* 3.4 22.0 - - + +
746A ILE* 3.8 28.3 - - + -
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Residues in contact with LEU 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LYS* 5.0 2.5 - - + -
302A LEU 4.5 4.0 - - - +
303A ASP* 3.4 33.9 - - - +
707A CYS* 3.8 31.4 - - + +
708A ILE* 1.3 80.9 - - - +
710A ALA* 1.3 62.4 + - - +
735A ILE* 3.8 40.8 - - + +
738A SER* 4.5 7.4 - - - -
739A ALA* 3.8 24.9 - - + +
743A SER* 5.4 0.4 - - - -
744A LEU 2.8 13.0 + - - +
745A ILE* 3.3 3.2 - - + -
746A ILE* 2.9 23.4 + - - +
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Residues in contact with ALA 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ASP* 3.5 8.5 + - - +
305A ALA* 4.0 7.5 - - - +
306A ALA* 4.0 25.0 - - + +
309A ALA* 4.5 5.2 - - + -
708A ILE 5.5 0.2 - - - -
709A LEU* 1.3 76.7 - - - +
711A ARG* 1.3 59.8 + - - +
712A VAL* 4.0 10.8 - - + -
731A GLU* 2.9 20.8 - - - +
735A ILE* 3.6 9.5 - - - +
745A ILE* 5.4 0.7 - - - -
746A ILE* 3.4 27.6 - - + +
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Residues in contact with ARG 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710A ALA* 1.3 72.1 - - - +
712A VAL* 1.3 64.7 + - - +
713A GLY* 3.4 37.4 - - - +
727A ALA 5.5 1.0 + - - -
728A GLU* 3.5 56.4 + - - +
731A GLU* 4.2 14.9 + - - +
732A THR* 3.8 27.8 - - + -
735A ILE* 4.1 6.7 - - + +
745A ILE* 5.9 0.2 - - - +
746A ILE 3.1 6.5 + - - -
747A ILE* 3.6 20.8 - - + +
748A ASP* 2.9 28.3 + - - +
749A GLU 4.0 15.0 + - - -
750A LEU* 4.1 5.3 - - + +
752A ARG* 4.6 9.7 - - - +
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Residues in contact with VAL 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ALA* 4.8 16.0 - - - +
309A ALA* 3.9 26.7 - - + -
680A ARG* 3.5 30.7 - - + +
710A ALA* 4.0 3.9 + - + -
711A ARG* 1.3 91.5 + - - +
713A GLY* 1.3 70.2 + - - +
746A ILE* 4.2 10.3 - - + +
748A ASP* 3.6 30.1 - - + +
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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