Contacts of the strand formed by residues 734 - 742 (chain A) in PDB entry 5L73
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 GLY 734 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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728A MET* 3.5 5.0 - - - +
732A HIS* 3.1 4.4 - - - +
733A VAL* 1.3 79.8 - - - +
735A THR* 1.3 63.2 + - - -
756A ILE* 4.7 0.2 - - - +
757A GLY* 2.9 26.9 + - - -
784A GLU* 3.3 13.2 - - - -
786A GLY* 3.5 13.9 - - - -
793A ILE* 4.0 4.5 - - - -
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Residues in contact with THR 735 (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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734A GLY* 1.3 75.7 + - - -
736A LEU* 1.3 62.9 + - - +
737A ARG* 3.7 28.6 + - + +
754A MET* 3.6 24.5 - - + -
755A ALA 3.3 13.0 - - - +
756A ILE* 3.6 20.8 - - + +
782A GLU 3.7 0.9 - - - +
783A GLY* 3.7 0.5 - - - -
784A GLU* 2.8 49.5 + - - +
793A ILE* 3.3 7.7 - - - +
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Residues in contact with LEU 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A TRP* 4.0 27.4 - - + -
724A PHE* 4.5 5.8 - - + -
726A TYR* 3.8 28.0 - - + -
728A MET* 3.7 18.7 - - - +
735A THR* 1.3 73.7 - - - +
737A ARG* 1.3 68.3 + - - +
738A VAL* 5.4 0.2 - - + -
753A TRP* 3.7 25.2 - - + -
754A MET* 3.2 4.3 - - - -
755A ALA 2.7 35.4 + - - +
781A PHE* 4.4 10.3 - - + -
782A GLU 3.5 14.8 - - - +
783A GLY* 4.6 0.2 - - - -
793A ILE* 4.1 10.3 - - + -
795A VAL* 3.9 14.4 - - + -
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Residues in contact with ARG 737 (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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705A VAL* 4.9 1.4 - - - +
735A THR* 3.7 18.1 + - + +
736A LEU* 1.3 80.2 - - - +
738A VAL* 1.3 64.1 + - - +
739A LYS* 4.1 7.4 - - - +
751A LEU* 3.7 25.6 - - + +
753A TRP 3.4 2.9 - - - -
754A MET* 3.3 26.9 - - + -
756A ILE* 6.2 0.4 - - - +
780A ILE 3.6 0.5 - - - +
781A PHE* 3.7 2.3 - - - -
782A GLU* 2.8 73.2 + - + +
784A GLU* 2.8 45.2 + - - +
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Residues in contact with VAL 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A MET* 3.9 12.8 - - + -
724A PHE* 4.1 9.2 - - + -
736A LEU* 5.4 0.2 - - + -
737A ARG* 1.3 75.7 - - - +
739A LYS* 1.3 63.8 + - - +
740A LEU* 5.2 0.9 - - + -
751A LEU* 3.7 2.3 - - - +
752A VAL* 3.1 37.3 + - + +
753A TRP* 2.8 44.9 + - + +
768A VAL* 4.5 3.4 - - + -
779A VAL* 3.8 21.8 - - + -
780A ILE 3.3 9.6 - - - +
781A PHE* 3.9 27.4 - - + -
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Residues in contact with LYS 739 (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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707A ARG* 3.5 13.5 - - - +
737A ARG* 4.3 14.1 - - + +
738A VAL* 1.3 78.1 - - - +
740A LEU* 1.3 70.3 + - - +
749A ASP* 4.3 24.0 + - + +
750A GLN 3.1 13.2 - - - +
751A LEU* 3.9 18.8 - - + +
752A VAL 4.6 0.2 - - - +
779A VAL* 3.5 4.9 - - - +
780A ILE* 2.7 51.3 + - + +
782A GLU* 2.7 42.5 + - + +
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Residues in contact with LEU 740 (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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738A VAL* 5.2 0.4 - - + -
739A LYS* 1.3 81.4 - - - +
741A ARG* 1.3 59.6 + - - +
742A TYR* 3.7 13.3 + - + +
748A TYR 3.5 2.4 - - - +
749A ASP* 3.3 2.8 - - - -
750A GLN* 2.8 36.9 + - + +
752A VAL* 4.1 30.1 - - + -
768A VAL* 6.1 0.2 - - + -
769A LEU 5.3 2.0 - - - +
770A LEU* 3.9 16.4 - - + -
771A HIS* 3.6 35.2 - - + +
777A TYR* 4.1 25.6 - - + +
778A GLN 3.3 3.6 - - - +
779A VAL* 3.8 26.2 - - + -
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Residues in contact with ARG 741 (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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666A ASP* 2.9 33.3 + - - -
668A HIS* 6.0 1.4 - - - -
707A ARG* 4.1 15.4 - - - +
709A VAL* 4.5 12.0 - - - +
739A LYS 4.0 1.0 - - - -
740A LEU* 1.3 68.9 - - - +
742A TYR* 1.3 71.1 + - - +
743A GLN* 3.8 0.5 + - - +
747A GLU* 3.5 25.5 + - + +
749A ASP* 2.9 41.2 + - - +
777A TYR* 3.2 1.5 - - - -
778A GLN* 2.7 55.4 + - + +
780A ILE* 3.5 29.9 - - + +
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Residues in contact with TYR 742 (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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740A LEU* 3.9 10.5 - - + +
741A ARG* 1.3 77.2 - - - +
743A GLN* 1.3 66.1 + - - +
747A GLU* 3.3 22.0 - - - +
748A TYR* 2.8 67.4 + + + +
750A GLN* 2.6 37.5 + - + -
771A HIS* 3.0 24.0 + + - -
773A SER* 3.9 12.6 - - - -
775A LYS* 3.9 27.1 - - + -
776A LEU 3.5 3.6 - - - -
777A TYR* 3.7 26.9 - + + -
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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