Contacts of the helix formed by residues 756 - 766 (chain A) in PDB entry 4REC
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 SER 756 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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752A ARG* 2.8 33.9 + - - -
753A LEU* 4.1 4.0 + - - +
754A ARG 3.8 0.6 - - - -
755A GLU* 1.3 80.0 - - - +
757A PRO* 1.3 77.2 - - - +
758A SER* 2.9 14.8 + - - -
759A CYS* 2.9 15.4 + - - +
760A LYS* 3.8 6.6 + - - -
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Residues in contact with PRO 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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755A GLU 4.8 0.7 - - - +
756A SER* 1.3 86.0 - - - +
758A SER* 1.3 63.9 + - - +
759A CYS 3.1 1.6 + - - -
760A LYS* 3.4 18.0 + - + +
761A LYS* 6.0 0.2 - - - +
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Residues in contact with SER 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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722A LEU* 3.1 36.6 - - - +
752A ARG* 5.6 5.6 - - - -
753A LEU* 6.0 0.4 - - - -
756A SER* 2.9 14.8 + - - -
757A PRO* 1.3 76.6 - - - +
759A CYS* 1.3 65.5 + - - +
760A LYS 4.1 0.5 + - - -
761A LYS* 4.2 11.1 - - - +
762A PHE* 4.2 4.9 - - - -
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Residues in contact with CYS 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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722A LEU* 3.7 25.4 - - - -
726A ILE* 4.7 7.0 - - - -
753A LEU* 3.1 45.9 - - - +
754A ARG 4.9 4.9 - - - +
756A SER* 2.9 8.1 + - - +
758A SER* 1.3 84.8 - - - +
760A LYS* 1.3 63.7 + - - +
761A LYS 3.3 2.2 - - - +
762A PHE* 3.7 31.6 + - + -
763A LYS* 4.4 1.9 + - - +
766A PHE* 4.1 15.0 - - + -
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Residues in contact with LYS 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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754A ARG 5.8 1.6 - - - -
756A SER 3.8 3.4 + - - +
757A PRO* 3.4 17.2 + - + +
758A SER 4.1 0.2 + - - -
759A CYS* 1.3 76.6 - - - +
761A LYS* 1.3 64.0 + - - +
763A LYS* 3.3 51.0 + - - +
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Residues in contact with LYS 761 (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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722A LEU* 5.8 1.6 - - - -
758A SER 4.2 10.1 - - - +
760A LYS* 1.3 79.1 - - - +
762A PHE* 1.3 95.3 + - + +
763A LYS* 2.9 13.4 + - - +
764A HIS* 3.5 15.5 + - - -
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Residues in contact with PHE 762 (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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722A LEU* 3.9 23.1 - - + -
723A GLU* 3.2 41.1 - - + -
726A ILE* 4.8 3.8 - - + -
758A SER 4.2 3.1 - - - -
759A CYS* 3.7 26.7 + - + +
760A LYS 3.3 1.6 - - - -
761A LYS* 1.3 107.7 - - + +
763A LYS* 1.3 51.5 + - - +
764A HIS* 3.0 13.5 - + - -
765A LEU* 2.7 56.7 + - + +
766A PHE* 3.5 20.7 - - + -
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Residues in contact with LYS 763 (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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754A ARG* 3.7 38.3 + - + +
755A GLU* 5.9 1.2 - - - +
759A CYS 4.4 2.4 + - - +
760A LYS* 3.3 45.0 + - - +
761A LYS 2.9 5.6 + - - +
762A PHE* 1.3 75.8 - - - +
764A HIS* 1.3 60.1 + - - +
765A LEU 3.1 1.8 + - - -
766A PHE* 3.3 21.4 + - + +
767A GLN* 4.2 9.2 - - - +
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Residues in contact with HIS 764 (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 GLU* 5.3 2.4 + - - -
761A LYS 3.5 21.6 + - - -
762A PHE* 2.8 14.5 + + - -
763A LYS* 1.3 77.8 - - - +
765A LEU* 1.3 82.0 + - + +
766A PHE 3.7 0.2 + - - -
767A GLN* 2.8 28.0 + - - +
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Residues in contact with LEU 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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723A GLU* 3.7 31.2 - - + +
726A ILE* 3.7 32.6 - - + +
727A LYS* 5.8 5.6 - - + -
730A THR* 4.2 3.8 - - - +
762A PHE* 2.7 37.8 + - + +
764A HIS* 1.3 103.2 - - + +
766A PHE* 1.3 60.1 + - - +
767A GLN 3.5 2.0 - - - -
768A GLN* 3.0 14.3 - - - +
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Residues in contact with PHE 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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726A ILE* 3.4 43.5 - - + -
729A ILE* 6.5 0.2 - - + -
750A ALA* 3.9 16.8 - - + -
753A LEU* 4.1 4.3 - - + -
754A ARG* 3.5 63.4 + - + -
759A CYS* 4.1 9.6 - - + -
762A PHE* 3.5 37.0 - - + -
763A LYS* 3.3 16.1 + - + +
765A LEU* 1.3 77.9 - - - +
767A GLN* 1.3 62.3 + - - +
768A GLN* 3.2 11.7 - - - -
769A LEU* 3.3 31.6 - - + +
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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