Contacts of the strand formed by residues 785 - 792 (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 LEU 785 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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768A LEU* 3.8 0.8 - - + +
769A PHE* 3.4 3.5 - - - -
770A TRP* 2.8 48.0 + - + +
784A TYR* 1.3 79.8 - - - +
786A LEU* 1.3 68.3 + - - +
787A CYS* 4.5 7.6 - - - +
800A ILE* 3.6 23.6 - - + -
802A GLN 3.3 16.2 - - - +
803A SER* 4.4 7.0 - - - +
805A TYR* 3.7 19.2 - - + +
860A LEU* 3.6 39.3 - - + -
861A GLY* 3.8 21.1 - - - +
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Residues in contact with LEU 786 (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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642A PHE* 3.8 31.9 - - + -
643A ARG* 4.0 22.4 - - - +
767A GLU* 4.6 5.4 - - + +
768A LEU 3.4 22.4 - - - +
769A PHE* 4.1 4.9 - - + +
784A TYR* 4.1 16.4 - - + +
785A LEU* 1.3 74.8 - - - +
787A CYS* 1.3 61.1 + - - +
788A GLU* 3.9 15.7 - - - +
800A ILE* 3.8 1.6 - - - +
801A SER* 2.9 43.5 + - - +
802A GLN* 2.9 16.6 + - + +
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Residues in contact with CYS 787 (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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767A GLU* 3.2 8.0 - - - +
768A LEU* 3.0 50.3 + - - -
785A LEU* 4.2 14.1 - - + -
786A LEU* 1.3 75.1 - - - +
788A GLU* 1.3 68.5 + - - +
789A PHE* 3.9 27.1 - - - -
798A VAL* 4.7 4.9 - - + -
799A ASN 3.2 13.7 - - - +
800A ILE* 3.7 17.9 - - + -
813A PHE* 5.0 1.6 - - - -
860A LEU* 4.6 5.2 - - - -
861A GLY 5.6 1.1 - - - -
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Residues in contact with GLU 788 (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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643A ARG* 4.0 4.5 + - - -
766A GLY 3.6 7.2 - - - +
767A GLU* 3.2 34.4 - - - +
786A LEU* 3.9 14.9 - - - +
787A CYS* 1.3 77.9 - - - +
789A PHE* 1.3 65.2 + - - +
790A SER* 6.4 0.2 - - - -
797A GLU 3.7 0.7 - - - +
798A VAL* 3.4 5.4 - - - +
799A ASN* 2.8 45.5 + - + +
801A SER* 4.8 15.5 - - - +
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Residues in contact with PHE 789 (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 ILE* 3.7 33.4 - - + -
736A PRO* 4.3 5.4 - - + -
754A LEU* 3.7 20.9 - - + -
765A LYS* 3.3 5.0 - - - +
766A GLY* 3.0 42.9 + - - +
767A GLU 3.6 24.7 - - - -
768A LEU* 3.8 14.6 - - + -
787A CYS* 3.9 10.3 - - - -
788A GLU* 1.3 80.0 - - - +
790A SER* 1.3 63.6 + - - +
796A LEU* 4.2 5.2 - - + -
797A GLU 3.3 4.5 - - - +
798A VAL* 3.8 30.5 - - + -
813A PHE* 3.6 33.9 - + - -
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Residues in contact with SER 790 (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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764A ALA 3.5 6.1 - - - -
765A LYS* 3.7 25.4 - - - -
788A GLU* 6.4 0.2 - - - -
789A PHE* 1.3 77.0 - - - +
791A VAL* 1.3 65.4 + - - +
792A THR* 6.3 1.1 - - - -
795A ARG 3.8 0.3 - - - +
796A LEU* 3.4 2.1 - - - +
797A GLU* 2.8 51.0 + - - +
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Residues in contact with VAL 791 (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 ILE* 3.8 5.4 - - + -
756A ILE* 3.8 27.1 - - + -
758A LEU* 3.9 23.1 - - + -
762A LYS 4.0 2.5 - - - +
763A GLU* 3.3 8.3 - - - +
764A ALA 2.9 31.7 + - - +
790A SER* 1.3 77.5 - - - +
792A THR* 1.3 80.7 + - - +
795A ARG 3.2 5.8 - - - +
796A LEU* 3.6 27.8 - - + -
818A ILE* 6.3 0.2 - - + -
868A TRP* 4.2 14.1 - - + -
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Residues in contact with THR 792 (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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762A LYS 3.6 10.3 - - - +
763A GLU* 3.8 18.4 - - - +
790A SER* 5.9 1.3 - - - -
791A VAL* 1.3 90.6 - - - +
793A GLN* 1.3 83.3 + - - +
794A ASN 3.0 3.5 + - - -
795A ARG* 3.0 25.1 + - - +
868A TRP* 4.3 1.7 - - - -
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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