Contacts of the strand formed by residues 752 - 760 (chain A) in PDB entry 5AMN
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 TYR 752 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A ASN 5.0 1.8 - - - -
725A VAL* 5.0 11.1 - - + +
742A THR* 3.6 36.8 - - + +
743A ALA 3.4 1.6 - - - -
744A PHE* 3.5 48.7 - + + +
750A ALA 4.4 2.6 - - - +
751A GLY* 1.3 74.0 - - - -
753A THR* 1.3 61.9 + - - +
754A THR 4.3 0.2 - - - -
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Residues in contact with THR 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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742A THR* 3.3 3.8 - - - -
743A ALA* 2.7 41.2 + - - -
746A LEU* 4.4 13.4 - - + +
749A ARG* 3.2 52.1 + - - +
750A ALA 5.0 1.4 + - - -
751A GLY 4.7 1.9 + - - -
752A TYR* 1.3 76.9 + - - +
754A THR* 1.3 75.5 + - - +
755A VAL* 3.6 11.3 + - + +
791A TYR* 4.8 4.9 - - + +
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Residues in contact with THR 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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740A LYS* 3.8 28.0 - - + -
741A ALA 3.6 11.7 - - - +
742A THR* 4.3 7.0 + - - +
753A THR* 1.3 80.2 - - - +
755A VAL* 1.3 70.9 + - - +
791A TYR* 5.2 0.3 - - - -
806A TYR* 3.8 28.3 + - + +
2017A FMT 3.0 32.7 + - - +
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Residues in contact with VAL 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A LEU* 4.5 1.3 - - + -
740A LYS* 3.8 3.3 - - - +
741A ALA* 2.8 52.8 + - + +
742A THR 4.3 1.1 - - - +
743A ALA* 4.3 8.1 - - + -
746A LEU* 3.8 13.2 - - + -
753A THR* 3.8 10.1 - - + +
754A THR* 1.3 81.8 - - - +
756A ALA* 1.3 61.3 + - - +
757A VAL* 4.5 1.1 - - + -
791A TYR* 3.7 32.5 - - + -
803A ILE* 3.8 18.4 - - + -
804A VAL 3.3 9.2 - - - +
805A GLU* 5.0 0.2 - - - -
806A TYR* 3.8 16.6 - - - +
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Residues in contact with ALA 756 (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 LEU* 4.6 1.8 - - + -
738A VAL* 4.1 5.4 - - + -
739A VAL 3.5 7.6 - - - +
755A VAL* 1.3 76.4 - - - +
757A VAL* 1.3 66.2 + - - +
758A LYS 4.3 0.2 - - - -
802A LEU 3.5 0.7 - - - +
803A ILE* 3.5 1.0 - - - -
804A VAL* 3.0 35.7 + - + +
806A TYR* 4.2 5.5 - - + +
2018A DTQ 3.2 50.3 - - + +
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Residues in contact with VAL 757 (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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724A LEU* 4.2 7.6 - - + -
726A LEU* 4.0 22.4 - - + -
737A LYS 3.8 1.0 - - - +
738A VAL* 3.3 4.4 - - - -
739A VAL* 2.7 45.5 + - + +
741A ALA* 3.5 23.1 - - + -
755A VAL* 4.5 1.8 - - + -
756A ALA* 1.3 80.3 - - - +
758A LYS* 1.3 64.2 + - - +
759A MET* 4.1 5.2 + - + +
801A LEU* 3.8 29.4 - - + -
802A LEU 3.0 11.0 - - - +
803A ILE* 4.2 15.3 - - + -
2018A DTQ 5.4 0.2 - - - -
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Residues in contact with LYS 758 (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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736A GLY 6.0 0.2 - - - -
737A LYS 3.4 9.6 - - - +
738A VAL* 3.7 19.5 - - + +
757A VAL* 1.3 73.2 - - - +
759A MET* 1.3 69.5 + - - +
772A LEU* 3.6 24.2 - - + +
775A GLU* 2.8 19.6 + - - +
800A LEU 4.0 0.5 - - - +
801A LEU* 3.5 4.9 - - - -
802A LEU* 2.9 38.1 + - + +
892A ASP* 3.6 16.3 + - - +
2018A DTQ 2.8 47.5 + - + -
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Residues in contact with MET 759 (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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726A LEU* 4.4 20.4 - - + -
736A GLY* 3.3 2.9 - - - -
737A LYS* 3.0 61.9 + - + +
739A VAL* 4.5 15.9 - - - -
757A VAL* 5.0 3.8 - - - +
758A LYS* 1.3 79.5 - - - +
760A LEU* 1.3 72.7 + - - +
768A GLU* 5.1 0.2 - - - +
772A LEU* 4.5 5.4 - - - -
799A PRO* 4.8 14.1 - - + -
800A LEU 3.9 5.4 - - - +
801A LEU* 3.4 32.5 - - + -
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Residues in contact with LEU 760 (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 3.5 2.9 - - - -
736A GLY* 4.0 0.2 - - - -
737A LYS* 5.1 2.3 - - - +
759A MET* 1.3 92.4 - - - +
761A LYS* 1.3 65.9 + - - +
764A ALA* 3.8 16.8 - - + -
768A GLU* 3.3 46.7 - - + +
769A LEU* 3.9 31.4 - - + +
772A LEU* 3.7 25.1 - - + +
799A PRO* 6.1 0.7 - - - +
800A LEU* 4.6 8.3 + - + +
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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