Contacts of the strand formed by residues 841 - 845 (chain A) in PDB entry 6P0D
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 VAL 841 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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758A ASP* 3.8 29.6 - - + +
759A LEU 3.3 12.1 - - - +
760A VAL* 4.3 16.2 - - + -
839A SER 3.5 11.1 + - - +
840A ALA* 1.3 77.7 - - - +
842A TRP* 1.3 70.8 + - - +
843A GLU 4.5 0.2 + - - -
877A ARG 4.8 1.7 - - - +
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Residues in contact with TRP 842 (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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757A LEU 3.5 0.5 - - - +
758A ASP* 3.4 5.1 - - - -
759A LEU* 2.8 33.0 + - - +
761A VAL* 3.5 28.4 - - + +
778A PHE* 3.7 43.7 - + + -
780A LEU* 4.3 3.6 - - + -
796A LEU* 3.8 18.6 - - + -
800A PHE* 4.7 1.3 - + - -
808A HIS* 3.6 48.2 + + + -
811A SER* 5.7 0.4 - - - -
812A LEU* 4.2 11.0 - - + -
840A ALA* 4.0 9.5 - - + +
841A VAL* 1.3 85.9 - - - +
843A GLU* 1.3 62.9 + - - +
844A VAL* 3.6 8.7 + - + +
875A PHE* 3.7 26.9 - + + -
877A ARG 3.6 9.0 - - - +
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Residues in contact with GLU 843 (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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756A THR* 3.7 34.5 + - - +
757A LEU 3.3 3.8 - - - -
758A ASP* 3.8 15.7 - - - +
842A TRP* 1.3 71.3 - - - +
844A VAL* 1.3 63.4 + - - +
875A PHE* 3.9 2.1 - - - -
876A ILE* 2.9 46.9 + - + +
877A ARG* 2.6 68.3 + - + +
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Residues in contact with VAL 844 (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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755A ASP 4.1 0.3 - - - +
756A THR* 3.1 4.3 - - - -
757A LEU* 2.8 43.8 + - - +
759A LEU* 4.1 11.7 - - + -
780A LEU* 3.6 26.5 - - + -
796A LEU* 3.9 26.7 - - + -
842A TRP* 3.9 14.1 - - + +
843A GLU* 1.3 79.9 - - - +
845A LYS* 1.3 71.0 + - - +
870A LEU* 4.0 21.3 - - + -
873A PRO* 4.1 2.5 - - + -
874A ARG 3.4 12.8 - - - +
876A ILE* 4.4 1.8 - - - -
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Residues in contact with LYS 845 (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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748A ASP* 3.0 26.6 + - - +
749A TYR 4.5 0.4 - - - -
750A LEU 2.6 21.8 + - - -
751A ASP* 4.3 2.2 - - - +
752A GLY 4.3 4.9 - - - +
753A VAL 2.6 33.9 + - - +
754A GLY* 4.2 5.6 - - - -
755A ASP 3.7 10.1 - - - +
756A THR* 4.0 16.9 - - + +
844A VAL* 1.3 76.3 - - - +
846A CYS* 1.3 69.0 + - - +
873A PRO* 3.2 4.5 - - - +
874A ARG* 2.9 48.9 + - - +
876A ILE* 3.8 27.9 - - + +
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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