Contacts of the strand formed by residues 709 - 713 (chain A) in PDB entry 4BL8
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 VAL 709 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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615A TRP* 4.8 2.9 - - + -
616A ASP 3.8 7.2 - - - +
618A LEU* 4.3 5.0 - - - +
706A LEU* 4.3 18.2 - - + -
708A SER* 1.3 80.4 - - - +
710A HIS* 1.3 65.3 + - - +
711A LEU* 3.3 31.4 - - + -
764A TYR* 3.5 40.2 - - + -
771A LEU* 3.8 17.0 - - + -
773A ILE* 4.7 4.0 - - + -
806A GLU 4.5 4.0 + - - -
807A LYS* 3.7 10.7 - - + +
808A LYS 3.2 24.8 + - - +
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Residues in contact with HIS 710 (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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615A TRP* 3.5 1.7 - - - -
616A ASP* 3.0 42.0 + - + +
618A LEU* 3.9 26.7 - - + +
709A VAL* 1.3 73.4 - - - +
711A LEU* 1.3 74.8 + - - +
712A LYS* 3.8 23.0 + - + +
801A GLU* 4.5 6.2 + - - -
808A LYS* 3.6 18.6 - - + +
809A LEU 4.8 0.2 - - - -
810A LYS* 3.0 56.6 - - + +
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Residues in contact with LEU 711 (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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614A ALA 3.8 2.7 - - - -
615A TRP* 3.8 7.6 - - + -
709A VAL* 3.3 29.4 - - + -
710A HIS* 1.3 74.5 - - - +
712A LYS* 1.3 59.7 + - - +
713A PHE* 3.8 19.3 - - + -
746A ILE* 4.0 12.1 - - + -
748A PHE* 3.8 20.2 - - + -
771A LEU* 3.5 20.6 - - + -
773A ILE* 3.5 27.1 - - + -
807A LYS* 4.5 13.2 - - - +
808A LYS 3.3 9.2 + - - +
809A LEU* 3.3 10.2 - - + +
810A LYS 2.9 25.8 + - - -
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Residues in contact with LYS 712 (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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613A CYS* 3.3 6.7 - - - +
614A ALA* 2.8 50.4 + - + +
615A TRP 5.2 1.4 - - - -
616A ASP* 3.9 35.1 + - - +
710A HIS* 3.9 29.4 - - + +
711A LEU* 1.3 78.5 - - - +
713A PHE* 1.3 63.4 + - - +
810A LYS* 3.7 13.5 - - + -
812A SER* 5.1 8.7 - - - +
816A ASP* 5.9 2.0 - - - +
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Residues in contact with PHE 713 (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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612A LYS 3.8 3.8 - - - -
613A CYS* 3.8 14.1 - - + -
711A LEU* 3.8 13.7 - - + -
712A LYS* 1.3 74.0 - - - +
714A ASN* 1.3 70.2 + - - +
717A SER* 3.9 10.3 - - - +
718A GLY* 4.0 7.0 - - - -
721A ILE* 3.7 18.8 - - + -
737A TYR* 3.9 43.7 - + - -
746A ILE* 4.0 23.3 - - + -
748A PHE* 4.3 13.2 - + - -
809A LEU* 3.3 35.0 - - + -
810A LYS 3.2 9.5 + - - +
811A VAL* 3.5 4.3 - - + -
812A SER* 3.1 28.6 + - - +
816A ASP* 5.0 4.4 - - - +
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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