Contacts of the strand formed by residues 745 - 749 (chain A) in PDB entry 5W6V
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 ASP 745 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 2.9 38.0 + - - +
735A ASP* 4.0 0.3 - - - +
739A THR* 3.3 13.3 - - - +
740A HIS* 3.0 28.8 + - - +
743A GLU 3.2 3.4 + - - +
744A PHE* 1.3 74.4 - - - +
746A PHE* 1.3 68.3 + - - +
747A TYR* 5.1 0.2 - - - -
762A HIS* 2.9 23.4 + - - +
763A TYR 3.2 6.7 - - - +
764A TYR* 3.4 26.3 - - + -
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Residues in contact with PHE 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A ILE* 5.7 1.1 - - + -
733A THR* 4.3 1.6 - - + -
734A VAL 3.3 13.9 - - - +
735A ASP* 3.7 13.0 - - + -
739A THR* 4.1 3.4 - - - -
744A PHE* 4.5 9.2 - + - -
745A ASP* 1.3 80.7 - - - +
747A TYR* 1.3 73.3 + - - +
748A LEU* 4.0 13.5 - - + -
762A HIS* 3.6 5.4 - - - -
763A TYR* 2.9 68.8 + + + +
765A VAL* 4.7 4.9 - - + -
777A LEU* 4.3 21.8 - - + -
778A GLN* 3.7 42.6 - - + +
781A THR* 4.1 16.4 - - + -
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Residues in contact with TYR 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 3.3 10.3 + - - -
205A ARG* 5.7 0.5 - - - -
709A HIS* 3.6 15.6 + + - +
711A THR* 2.9 47.1 + - + -
713A LEU* 4.5 7.2 - - + -
732A THR 4.5 0.4 - - - -
733A THR* 3.2 8.4 - - - +
734A VAL* 2.7 44.2 + - + +
738A ILE* 4.3 24.9 + - + -
739A THR* 4.1 18.6 - - + -
746A PHE* 1.3 73.5 - - - +
748A LEU* 1.3 59.8 + - - +
749A CYS 4.2 0.7 - - - -
760A PRO* 4.0 23.3 - - + -
761A SER 3.5 1.8 - - - +
762A HIS* 3.4 41.4 + + + -
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Residues in contact with LEU 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 4.5 1.8 - - + -
731A GLY* 3.8 15.0 - - - +
732A THR 3.5 4.9 - - - +
733A THR* 3.5 21.5 - - + +
746A PHE* 4.0 12.1 - - + -
747A TYR* 1.3 75.7 - - - +
749A CYS* 1.3 61.6 + - - +
750A SER* 3.3 15.7 + - - +
760A PRO* 4.6 0.4 - - - -
761A SER* 3.0 33.3 + - - +
763A TYR* 3.9 11.4 - - + +
778A GLN 4.1 6.1 - - - +
781A THR* 3.8 28.5 - - + -
782A TYR* 3.8 39.3 - - + +
785A CYS* 5.0 0.2 - - - -
796A SER 4.8 0.2 - - - +
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Residues in contact with CYS 749 (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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713A LEU* 5.5 0.4 - - + +
728A ILE* 3.7 39.9 - - + -
729A PRO 3.8 0.8 - - - +
730A ALA* 3.7 1.7 - - - -
731A GLY 2.8 28.0 + - - -
732A THR* 2.9 14.1 + - - +
747A TYR 4.2 0.4 - - - -
748A LEU* 1.3 70.0 - - - +
750A SER* 1.3 52.9 + - - +
751A HIS* 3.4 38.0 + - - -
758A SER* 4.0 13.7 - - - -
760A PRO* 3.8 19.6 - - + +
761A SER 4.5 0.4 - - - +
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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
------------------------------------------------------------
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