Contacts of the strand formed by residues 736 - 744 (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 GLY 736 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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732A GLU 3.6 0.5 - - - -
733A GLY* 2.8 27.3 + - - -
735A PHE* 1.3 80.7 - - - +
737A LYS* 1.3 61.3 + - - -
758A LYS* 6.0 0.4 - - - -
759A MET 3.3 12.8 - - - -
761A LYS* 3.4 12.8 - - - +
768A GLU* 3.3 14.2 + - - -
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Residues in contact with LYS 737 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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729A THR* 4.1 24.6 + - + +
731A GLY 3.3 14.1 - - - +
732A GLU* 4.0 20.9 - - + +
736A GLY* 1.3 75.9 - - - +
738A VAL* 1.3 65.3 + - - +
739A VAL* 4.3 11.0 - - + +
757A VAL 3.8 0.9 - - - +
758A LYS* 3.4 4.3 - - - +
759A MET* 3.0 60.0 + - + +
760A LEU 5.1 2.2 - - - -
761A LYS* 4.4 13.9 - - + +
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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
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729A THR* 3.8 2.6 - - - +
730A LEU* 2.8 27.4 + - + -
731A GLY 2.9 17.6 + - - +
737A LYS* 1.3 74.3 - - - +
739A VAL* 1.3 63.5 + - - +
756A ALA* 4.1 9.6 - - + -
757A VAL 3.3 7.4 - - - +
758A LYS* 3.7 32.5 - - + -
2018A DTQ 3.6 57.0 - - + +
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Residues in contact with VAL 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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726A LEU* 4.1 19.7 - - + -
727A GLY 3.6 21.5 - - - +
728A LYS 3.6 8.3 - - - +
729A THR* 4.1 14.4 - - - +
730A LEU* 3.9 5.5 - - - +
737A LYS* 4.3 19.7 - - + +
738A VAL* 1.3 78.8 - - - +
740A LYS* 1.3 78.2 + - - +
756A ALA* 3.5 4.2 - - - -
757A VAL* 2.7 41.6 + - + +
759A MET* 4.5 14.8 - - - -
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Residues in contact with LYS 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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727A GLY* 2.5 37.0 + - - -
728A LYS* 2.9 30.7 + - + +
730A LEU* 3.7 15.7 - - + +
739A VAL* 1.3 74.9 - - - +
741A ALA* 1.3 59.3 + - - +
754A THR* 3.8 16.8 - - + -
755A VAL 3.9 4.5 - - - +
806A TYR* 3.3 35.9 + - + +
2013A FMT 2.9 31.0 + - - +
2017A FMT 3.9 14.3 + - - -
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Residues in contact with ALA 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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724A LEU* 3.8 10.1 - - + -
725A VAL 3.3 13.5 - - - +
726A LEU* 3.9 6.7 - - + -
727A GLY 4.3 0.4 - - - +
740A LYS* 1.3 79.1 - - - +
742A THR* 1.3 63.5 + - - +
754A THR* 3.6 8.7 - - - +
755A VAL* 2.8 34.7 + - + +
757A VAL* 3.5 31.2 - - + -
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Residues in contact with THR 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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723A ASN 3.7 1.6 - - - +
724A LEU* 3.5 5.9 - - - +
725A VAL* 3.0 49.4 + - + +
741A ALA* 1.3 76.0 - - - +
743A ALA* 1.3 60.4 + - - +
744A PHE 4.3 0.2 - - - -
752A TYR* 3.6 34.7 - - + +
753A THR 3.3 12.2 + - - -
754A THR* 4.3 5.5 + - - -
755A VAL* 4.5 0.4 - - - -
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Residues in contact with ALA 743 (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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719A PHE* 3.9 21.3 - - + -
723A ASN 3.5 3.6 - - - -
724A LEU* 4.4 4.5 - - + -
742A THR* 1.3 75.3 + - - +
744A PHE* 1.3 61.9 + - - +
745A HIS 3.7 0.7 + - - -
746A LEU* 4.0 25.5 - - + +
751A GLY 3.5 1.6 - - - +
752A TYR* 3.4 3.8 - - - -
753A THR* 2.7 42.3 + - - +
755A VAL* 4.3 10.3 - - + +
803A ILE* 5.2 2.2 - - + -
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Residues in contact with PHE 744 (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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719A PHE* 3.5 5.0 - - - -
723A ASN* 2.9 57.0 + - + +
743A ALA* 1.3 70.3 - - - +
745A HIS* 1.3 77.9 + + + +
751A GLY* 3.6 26.0 - - - -
752A TYR* 3.5 47.2 - + + +
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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