Contacts of the strand formed by residues 6864 - 6868 (chain A) in PDB entry 6W75
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 ARG6864 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6862A ASN 3.8 9.0 + - - +
6863A MET* 1.3 74.3 - - - +
6865A VAL* 1.3 62.6 + - - +
6892A LEU* 3.7 10.9 - - + +
6920A ASN* 3.5 5.9 - - - +
6921A LYS 3.0 24.9 + - - -
6922A TRP* 3.6 19.4 - - + -
6923A ASP* 2.8 44.7 + - - +
6924A LEU 3.2 6.2 + - - +
7081A ARG* 3.3 25.2 - - - +
7083A ASN* 3.5 21.4 + - - +
7084A ASN 2.8 27.9 + - - -
7086A VAL* 3.2 28.2 - - + +
7106A FMT 2.8 29.7 + - - -
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Residues in contact with VAL6865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6863A MET* 4.0 6.3 - - + -
6864A ARG* 1.3 78.4 - - - +
6866A ILE* 1.3 68.2 - - - +
6883A LEU* 5.0 2.0 - - + -
6887A LEU* 3.8 21.5 - - + -
6891A THR* 3.6 23.1 - - + -
6892A LEU 2.9 11.5 + - - +
6893A LEU* 3.4 22.8 - - + +
6894A VAL 3.0 24.3 + - - -
6922A TRP* 3.5 7.6 - - - -
6924A LEU* 3.3 35.2 - - + +
6926A ILE* 4.5 9.0 - - + -
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Residues in contact with ILE6866 (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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6865A VAL* 1.3 76.7 - - - +
6867A HIS* 1.3 58.9 + - - +
6868A PHE* 3.6 34.5 - - + -
6894A VAL* 3.2 14.6 - - + +
6895A ASP* 5.3 1.6 - - - -
6896A SER* 5.8 1.8 - - - -
6909A LEU* 5.6 0.7 - - + -
6916A VAL* 4.7 0.7 - - + -
6922A TRP* 3.7 20.6 - - + -
6924A LEU 3.0 4.6 + - - +
6925A ILE* 3.5 25.8 - - + +
6926A ILE* 2.9 30.8 + - - +
6954A PHE* 3.9 21.8 - - + -
7088A ILE* 3.7 31.4 - - + -
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Residues in contact with HIS6867 (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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6845A TYR* 2.6 34.9 + + - -
6866A ILE* 1.3 74.1 - - - +
6868A PHE* 1.3 72.3 + - - +
6870A ALA* 3.3 18.9 - - + +
6879A GLY* 3.9 1.8 - - - -
6880A THR* 2.8 41.7 + - - -
6883A LEU* 3.6 19.3 - - + +
6893A LEU* 4.4 5.8 - - + -
6894A VAL 2.8 14.6 + - - +
6895A ASP* 3.0 8.2 - - + +
6896A SER 2.8 30.8 + - - +
6926A ILE* 3.3 22.7 - - + -
6928A ASP 4.9 0.2 - - - -
7102A SAM 4.6 0.2 - - - -
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Residues in contact with PHE6868 (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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6866A ILE* 3.6 42.6 - - + -
6867A HIS* 1.3 77.9 - - - +
6869A GLY* 1.3 63.7 + - - +
6896A SER* 3.8 15.9 - - - -
6913A CYS* 4.0 18.8 - - + -
6916A VAL* 4.4 11.7 - - + -
6925A ILE* 4.0 18.2 - - + -
6926A ILE 2.8 9.7 + - - +
6927A SER* 3.4 4.7 - - - +
6928A ASP 2.9 23.0 + - - -
6929A MET* 3.7 23.6 - - + -
6950A TYR* 3.8 29.2 - + - -
6951A ILE* 3.9 17.5 - - + -
6954A PHE* 4.1 14.6 - + - -
7102A SAM 6.1 0.2 - + - -
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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