Contacts of the strand formed by residues 745 - 755 (chain A) in PDB entry 5M9O
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 TRP 745 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714A MET* 3.6 8.4 - - + +
715A ARG* 3.0 36.3 + - + +
718A ILE* 3.6 44.1 - - + +
723A PRO* 4.2 23.5 - - + +
737A ILE* 3.5 34.8 - - + -
738A ALA 3.5 17.7 - - - -
739A LYS* 3.5 36.9 - - + +
743A GLY 4.7 5.8 + - - -
744A GLU* 1.3 77.2 + - - +
746A TYR* 1.3 58.9 + - - +
775A THR 5.0 2.9 - - - -
776A ARG* 3.4 34.1 - - - -
777A LEU 3.9 10.3 - - - -
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Residues in contact with TYR 746 (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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711A MET* 4.5 6.5 - - - -
714A MET* 4.1 8.7 - - - -
715A ARG* 3.1 23.7 + - - -
737A ILE* 3.3 4.3 - - - -
738A ALA* 2.9 30.9 + - - +
740A PHE* 3.6 17.7 - - + -
742A ASP* 2.5 34.0 + - - -
744A GLU* 3.3 30.1 - - + +
745A TRP* 1.3 71.4 - - - +
747A ARG* 1.3 63.4 + - - +
763A TYR* 3.6 19.3 - - + -
765A ASP* 6.5 0.2 - - + -
766A TYR* 3.5 37.9 - + + -
113B 2MR 3.0 29.1 - - - +
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Residues in contact with ARG 747 (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 LEU* 3.6 21.3 - - - +
711A MET* 3.8 12.9 - - + +
714A MET* 3.9 12.9 - - - +
736A CYS 3.6 7.2 - - - +
737A ILE* 4.7 1.3 - - - +
746A TYR* 1.3 73.9 - - - +
748A ALA* 1.3 60.4 + - - +
763A TYR* 3.6 8.7 - - - +
764A ILE* 3.3 34.8 + - + +
765A ASP* 2.9 47.1 + - - +
766A TYR* 6.1 0.2 - - - -
780A LEU* 4.0 13.9 - - + -
784A PHE 2.9 29.9 + - - -
785A SER 3.0 12.1 + - - -
786A THR 3.7 2.0 - - - +
789A LEU* 2.9 36.8 + - - +
790A PRO 3.2 13.1 + - - -
791A ALA* 3.9 2.2 - - - +
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Residues in contact with ALA 748 (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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735A PHE* 3.3 8.5 - - - +
736A CYS* 2.8 42.5 + - - +
738A ALA* 4.0 27.1 - - + -
747A ARG* 1.3 76.9 - - - +
749A ARG* 1.3 60.1 + - - +
761A VAL* 4.2 12.1 - - + -
762A PHE 3.2 13.9 - - - +
763A TYR* 4.4 4.0 - - + -
764A ILE* 4.0 6.3 - - - +
780A LEU* 5.5 0.2 - - - +
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Residues in contact with ARG 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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733A GLY* 3.0 32.3 + - - +
734A GLU 3.4 13.7 - - - +
735A PHE* 3.7 33.5 - - + -
748A ALA* 1.3 73.9 - - - +
750A VAL* 1.3 67.7 + - - +
751A GLU* 3.4 5.5 + - + -
761A VAL* 3.3 5.4 - - - -
762A PHE* 2.8 41.7 + - + +
764A ILE* 3.9 14.1 - - + +
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Residues in contact with VAL 750 (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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728A TYR* 3.7 21.1 - - - +
730A PRO* 3.8 11.0 - - + -
731A ARG 3.5 21.1 - - - +
732A ARG* 4.0 2.4 - - - +
733A GLY* 2.8 30.3 + - - -
734A GLU 2.9 18.4 + - - +
736A CYS* 4.0 15.9 - - - -
749A ARG* 1.3 71.9 - - - +
751A GLU* 1.3 61.2 + - - +
752A LYS 4.1 3.6 - - - +
753A VAL* 3.7 27.6 - - + -
759A ILE* 3.8 18.2 - - + -
760A HIS 3.8 3.4 - - - -
761A VAL* 4.6 2.9 - - + -
777A LEU* 5.1 0.2 - - + -
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Residues in contact with GLU 751 (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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732A ARG* 3.5 23.1 + - - +
749A ARG* 3.4 7.4 + - + +
750A VAL* 1.3 77.2 - - - +
752A LYS* 1.3 60.9 + - + +
760A HIS* 2.8 21.5 + - + +
761A VAL 4.5 1.7 - - - +
762A PHE* 3.5 26.1 + - + +
769A ARG* 2.8 49.1 + - - +
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Residues in contact with LYS 752 (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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732A ARG* 4.8 6.5 - - - +
750A VAL* 3.7 1.4 - - - -
751A GLU* 1.3 82.1 - - + +
753A VAL* 1.3 72.7 + - - +
754A GLU* 3.7 12.7 + - + +
759A ILE* 3.6 4.2 - - - +
760A HIS* 2.8 77.3 + - + +
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Residues in contact with VAL 753 (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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730A PRO* 3.7 24.9 - - + +
731A ARG* 4.2 0.4 - - - -
732A ARG* 4.0 15.9 - - + +
750A VAL* 3.7 24.7 - - + -
752A LYS* 1.3 75.1 - - - +
754A GLU* 1.3 60.7 + - - +
755A SER* 4.2 10.3 - - - +
756A PRO* 5.6 0.4 - - + -
758A LYS 4.2 1.8 - - - -
759A ILE* 3.7 23.3 - - + -
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Residues in contact with GLU 754 (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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752A LYS* 3.7 14.0 + - - -
753A VAL* 1.3 75.7 - - - +
755A SER* 1.3 63.8 + - - +
758A LYS* 3.0 47.8 + - + +
760A HIS* 2.9 31.1 + - + -
771A VAL* 5.2 0.2 - - - +
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Residues in contact with SER 755 (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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753A VAL* 3.5 6.5 - - - -
754A GLU* 1.3 80.6 - - - +
756A PRO* 1.3 77.2 - - - +
757A ALA* 3.4 7.4 + - - +
758A LYS* 3.0 37.0 + - - +
759A ILE* 3.1 16.4 - - - +
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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