Contacts of the strand formed by residues 764 - 770 (chain A) in PDB entry 3L4U
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 ALA 764 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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732A GLY* 3.3 20.2 - - - -
733A TYR 3.8 0.2 - - - +
734A ILE* 3.6 22.4 - - + -
756A ILE* 4.0 13.2 - - + -
757A ALA 3.6 12.3 - - - +
758A LEU* 4.5 0.4 - - + -
763A GLU* 1.3 80.1 - - - +
765A LYS* 1.3 70.6 + - - +
790A SER* 4.1 0.2 - - - -
791A VAL* 2.9 30.7 + - + +
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Residues in contact with LYS 765 (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 GLY 3.0 10.1 + - - +
733A TYR* 3.4 13.9 - - + -
734A ILE* 3.0 19.8 + - - -
763A GLU* 6.3 0.4 - - + -
764A ALA* 1.3 81.7 - - - +
766A GLY* 1.3 59.9 + - - +
789A PHE 3.3 9.0 - - - +
790A SER* 3.7 21.5 - - - -
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Residues in contact with GLY 766 (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 TYR* 6.0 0.7 - - - -
734A ILE* 3.5 23.1 - - - +
765A LYS* 1.3 76.7 - - - +
767A GLU* 1.3 65.2 + - - +
788A GLU* 3.6 7.3 - - - +
789A PHE* 3.0 30.8 + - - +
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Residues in contact with GLU 767 (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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636A TYR* 5.7 1.0 - - - -
639A THR* 3.7 21.0 - - + +
643A ARG* 2.6 56.0 + - - +
647A ARG* 4.9 2.1 + - - -
734A ILE 4.3 1.6 + - - -
736A PRO* 3.6 19.1 - - - +
766A GLY* 1.3 75.6 - - - +
768A LEU* 1.3 65.2 + - - +
786A LEU* 4.6 3.6 - - + -
787A CYS 3.2 6.5 - - - +
788A GLU* 3.2 25.1 - - - +
789A PHE* 3.6 8.3 - - - -
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Residues in contact with LEU 768 (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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635A PRO* 3.7 27.1 - - + +
639A THR* 3.7 11.4 - - - +
736A PRO* 3.8 13.2 - - + -
752A LEU* 4.9 7.4 - - + -
767A GLU* 1.3 76.7 - - - +
769A PHE* 1.3 79.5 + - - +
770A TRP* 4.3 12.8 - - + -
785A LEU* 3.8 1.4 - - - +
786A LEU* 3.4 7.9 - - - +
787A CYS* 3.0 36.2 + - - -
789A PHE* 3.8 14.3 - - + -
813A PHE* 3.8 18.8 - - + -
860A LEU* 3.7 29.2 - - + -
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Residues in contact with PHE 769 (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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286A LEU* 3.9 10.8 - - + -
638A TYR* 3.7 28.2 - + - -
639A THR* 3.0 18.3 + - + +
642A PHE* 3.4 55.9 - + + -
768A LEU* 1.3 86.6 - - - +
770A TRP* 1.3 67.9 + - - +
771A ASP* 3.5 37.2 - - + -
778A THR* 4.5 0.4 - - - -
779A VAL* 3.8 18.4 - - + -
784A TYR* 3.4 42.6 - + + -
785A LEU 3.4 2.9 - - - -
786A LEU* 4.1 3.1 - - + -
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Residues in contact with TRP 770 (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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289A TYR* 4.1 24.0 - + - -
635A PRO* 4.4 14.6 - - + -
638A TYR* 5.1 3.1 - + - -
738A GLN* 3.3 25.8 - - - -
748A ARG* 3.8 37.9 - - + +
752A LEU* 5.0 3.8 - - + -
768A LEU* 4.3 16.4 - - + -
769A PHE* 1.3 89.7 - - - +
771A ASP* 1.3 70.0 + - - +
784A TYR* 3.7 1.4 - - - -
785A LEU* 2.8 60.3 + - + +
805A TYR* 4.0 9.4 - + - -
807A ASP* 2.8 31.1 + - + -
811A LEU* 3.7 20.9 - - + +
860A LEU* 3.8 20.0 - - + -
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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