Contacts of the helix formed by residues 757 - 773 (chain A) in PDB entry 1OFD
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 THR 757 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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738A GLY* 5.6 0.4 - - - -
740A GLU* 6.0 6.3 - - + +
741A LEU* 4.8 5.6 - - - +
755A GLY 4.4 5.6 - - - +
756A LEU* 1.3 73.8 - - - +
758A ILE* 1.3 65.4 + - - +
759A ALA* 3.4 10.1 + - - +
760A ASP* 3.0 40.9 + - - +
761A VAL* 3.1 18.0 + - - +
1214A THR* 5.4 0.4 - - + -
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Residues in contact with ILE 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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576A LEU* 3.6 21.7 - - + +
577A GLU* 3.8 60.3 - - + +
580A LEU* 4.3 11.7 - - + -
620A LEU* 5.4 1.3 - - + -
740A GLU* 5.5 4.3 - - + +
741A LEU* 4.3 26.3 - - + +
744A TYR* 4.6 26.7 - - + -
757A THR* 1.3 72.3 - - - +
759A ALA* 1.3 65.2 + - - +
761A VAL* 3.1 9.4 + - - -
762A ALA 3.1 17.5 + - - -
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Residues in contact with ALA 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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576A LEU* 6.0 0.2 - - - -
757A THR* 3.2 9.0 + - - +
758A ILE* 1.3 81.1 - - - +
760A ASP* 1.3 58.6 + - - +
762A ALA* 3.3 8.5 + - - +
763A GLY* 3.0 24.3 + - - -
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Residues in contact with ASP 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A LEU* 3.8 13.4 - - + +
757A THR* 3.0 35.0 + - - +
759A ALA* 1.3 78.7 - - - +
761A VAL* 1.3 62.9 + - - +
763A GLY* 3.2 3.5 + - - -
764A GLU* 3.1 23.2 + - - +
1213A LYS* 3.3 27.2 - - - +
1214A THR* 2.6 27.4 - - - +
1215A GLN 4.8 0.9 + - - -
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Residues in contact with VAL 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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491A LEU* 4.6 13.7 - - + -
576A LEU* 3.4 22.7 - - + -
617A PRO* 4.5 13.9 - - + -
620A LEU* 4.1 13.2 - - + -
741A LEU* 3.8 27.6 - - + -
756A LEU* 4.0 17.7 - - + +
757A THR 3.1 16.1 + - - +
758A ILE* 3.1 4.9 + - - +
760A ASP* 1.3 74.5 - - - +
762A ALA* 1.3 64.0 + - - +
764A GLU* 3.2 10.2 + - - +
765A VAL* 3.0 27.1 + - + +
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Residues in contact with ALA 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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568A TYR* 4.7 6.5 - - - +
576A LEU* 3.8 33.2 - - + +
758A ILE 3.1 8.1 + - - +
759A ALA* 3.5 11.9 - - - +
760A ASP 3.3 0.2 - - - -
761A VAL* 1.3 76.7 - - - +
763A GLY* 1.3 63.5 + - - +
765A VAL* 3.4 9.4 + - - +
766A MET* 3.0 31.3 + - + +
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Residues in contact with GLY 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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759A ALA 3.0 14.3 + - - -
760A ASP* 3.2 4.9 + - - -
762A ALA* 1.3 75.1 - - - +
764A GLU* 1.3 62.1 + - - +
766A MET* 3.3 9.8 + - - +
767A VAL* 3.2 25.4 + - - +
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Residues in contact with GLU 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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488A PRO* 3.6 5.0 - - + +
489A ARG 2.8 30.1 + - - +
490A LEU 5.1 0.7 - - - -
491A LEU 5.3 0.2 + - - -
494A TYR* 2.5 36.9 + - - -
756A LEU* 4.4 5.4 - - + +
760A ASP 3.1 14.5 + - - +
761A VAL* 3.2 11.7 + - - +
763A GLY* 1.3 72.6 - - - +
765A VAL* 1.3 67.5 + - + +
767A VAL* 3.1 24.2 + - + +
768A PHE* 3.6 12.3 + - - -
1213A LYS* 2.8 41.8 + - + -
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Residues in contact with VAL 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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449A ALA 4.8 2.3 - - - +
568A TYR* 5.4 2.7 - - - +
576A LEU* 5.7 0.9 - - + -
614A SER* 3.6 23.6 - - - +
615A PHE* 4.4 25.0 - - + +
617A PRO* 3.7 32.1 - - + -
646A GLN* 5.8 2.2 - - - +
761A VAL* 3.0 16.0 + - + +
762A ALA* 3.4 15.5 - - + +
764A GLU* 1.3 76.0 - - + +
766A MET* 1.3 63.0 + - + +
768A PHE* 3.2 15.5 + - - +
769A HIS* 3.0 23.6 + - - +
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Residues in contact with MET 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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568A TYR* 5.9 0.2 - - - -
570A LEU* 4.1 28.5 - - + -
614A SER* 3.9 19.7 - - - -
762A ALA* 3.0 24.6 + - + +
763A GLY* 3.6 8.1 - - - +
764A GLU 3.2 0.2 - - - -
765A VAL* 1.3 76.2 - - + +
767A VAL* 1.3 59.1 + - - +
769A HIS* 3.4 36.2 - - + +
770A GLY* 2.9 24.9 + - - -
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Residues in contact with VAL 767 (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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488A PRO* 3.8 32.8 - - + -
763A GLY 3.2 15.3 + - - +
764A GLU* 3.1 13.8 + - + +
766A MET* 1.3 75.9 - - - +
768A PHE* 1.3 61.5 + - - +
770A GLY* 3.2 3.7 + - - -
771A MET* 3.1 29.1 + - + +
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Residues in contact with PHE 768 (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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448A ALA 3.6 17.5 - - - +
449A ALA* 3.7 11.7 - - - +
450A PHE 5.4 0.2 - - - -
451A GLY* 3.6 35.0 - - - -
452A TYR 5.1 2.0 - - - -
453A THR* 4.7 11.2 - - - -
488A PRO* 3.7 38.4 - - + -
489A ARG* 3.7 22.2 - - - -
490A LEU* 3.9 15.5 - - + -
646A GLN* 5.5 2.9 - - - -
764A GLU 3.6 11.8 + - - -
765A VAL* 3.2 12.3 + - - +
767A VAL* 1.3 72.9 - - - +
769A HIS* 1.3 66.7 + - - +
771A MET* 3.2 23.8 + - + +
772A ALA* 3.1 23.7 + - - +
783A PHE* 4.9 1.1 - + - -
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Residues in contact with HIS 769 (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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449A ALA* 4.6 4.4 + - - +
570A LEU* 3.7 7.8 - - + +
609A LEU* 5.1 4.2 - - - +
611A GLU* 2.9 28.1 + - - +
613A GLN 3.0 28.5 + - - -
614A SER* 4.7 4.6 + - - +
765A VAL 3.0 13.3 + - - +
766A MET* 3.3 37.1 + - + +
768A PHE* 1.3 75.1 - - - +
770A GLY* 1.3 60.5 + - - +
772A ALA* 3.2 2.4 + - - -
773A PHE* 2.9 61.8 + + + +
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Residues in contact with GLY 770 (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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766A MET 2.9 13.6 + - - -
767A VAL* 3.7 4.5 - - - -
768A PHE 3.2 0.2 - - - -
769A HIS* 1.3 78.1 - - - +
771A MET* 1.3 62.8 + - - +
773A PHE 4.0 12.4 + - - -
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Residues in contact with MET 771 (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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448A ALA* 4.8 12.2 - - + +
452A TYR 5.9 2.5 - - - +
453A THR* 5.6 0.4 - - - +
488A PRO* 4.3 1.6 - - - -
767A VAL* 3.1 28.5 + - + +
768A PHE* 3.2 30.5 + - + +
770A GLY* 1.3 77.1 - - - +
772A ALA* 1.3 60.1 + - - +
781A GLU* 3.6 30.7 - - + +
783A PHE* 3.6 37.0 - - + -
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Residues in contact with ALA 772 (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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445A GLN* 3.1 33.0 + - + +
448A ALA* 3.8 7.6 - - + -
449A ALA* 3.6 34.8 - - + +
768A PHE 3.1 15.6 + - - +
769A HIS 3.2 3.3 + - - +
771A MET* 1.3 79.2 - - - +
773A PHE* 1.3 65.5 + - + +
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Residues in contact with PHE 773 (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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445A GLN* 3.6 37.0 - - + +
446A GLN* 4.6 4.0 - - - -
449A ALA* 3.7 27.4 - - + -
609A LEU* 3.9 19.3 - - + -
610A THR* 3.8 14.6 - - - -
611A GLU* 3.5 45.9 - - + +
769A HIS* 2.9 61.3 + + + +
770A GLY* 4.0 9.8 + - - -
771A MET 3.7 0.8 - - - -
772A ALA* 1.3 76.6 - - + +
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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