Contacts of the helix formed by residues 757 - 773 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740B GLU* 6.2 3.6 - - + -
741B LEU* 4.6 6.1 - - - +
755B GLY 4.2 6.3 - - - +
756B LEU* 1.3 74.9 - - - +
758B ILE* 1.3 64.9 + - - +
759B ALA* 3.3 10.4 + - - +
760B ASP* 3.0 41.1 + - - +
761B VAL* 3.1 18.1 + - - +
1214B THR* 5.3 0.2 - - + -
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Residues in contact with ILE 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B LEU* 3.6 31.5 - - + +
577B GLU* 3.8 51.4 - - + +
580B LEU* 4.2 12.6 - - + -
620B LEU* 5.2 0.9 - - + -
740B GLU* 5.5 4.7 - - + +
741B LEU* 3.9 28.6 - - + +
744B TYR* 4.8 24.5 - - + -
757B THR* 1.3 73.0 - - - +
759B ALA* 1.3 62.3 + - - +
761B VAL* 3.1 9.8 + - - -
762B ALA* 3.1 18.4 + - - +
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Residues in contact with ALA 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B LEU* 6.1 0.2 - - - -
577B GLU* 5.8 0.6 + - - -
757B THR* 3.2 9.2 + - - +
758B ILE* 1.3 77.3 - - - +
760B ASP* 1.3 59.3 + - - +
762B ALA* 3.4 8.7 + - - +
763B GLY* 3.1 23.7 + - - -
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Residues in contact with ASP 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756B LEU* 3.7 13.0 - - + +
757B THR* 3.0 38.1 + - - +
759B ALA* 1.3 76.4 - - - +
761B VAL* 1.3 64.6 + - - +
763B GLY* 3.3 2.5 + - - -
764B GLU* 3.2 22.7 + - - +
1213B LYS* 3.2 25.5 - - - +
1214B THR* 2.4 31.3 - - - +
1215B GLN 4.8 0.7 + - - -
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Residues in contact with VAL 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B LEU* 4.6 13.9 - - + -
576B LEU* 3.6 19.1 - - + -
617B PRO* 4.3 16.4 - - + -
620B LEU* 4.1 11.9 - - + -
741B LEU* 3.7 28.3 - - + -
756B LEU* 4.3 14.1 - - + -
757B THR 3.1 16.0 + - - +
758B ILE* 3.1 8.7 + - - +
760B ASP* 1.3 76.7 - - - +
762B ALA* 1.3 62.5 + - - +
764B GLU* 3.2 9.3 + - + +
765B VAL* 3.1 27.4 + - + +
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Residues in contact with ALA 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568B TYR* 4.7 6.3 - - - +
576B LEU* 3.7 34.1 - - + +
758B ILE 3.1 8.0 + - - +
759B ALA* 3.6 11.4 - - - +
760B ASP 3.3 0.2 - - - -
761B VAL* 1.3 77.9 - - - +
763B GLY* 1.3 57.2 + - - +
765B VAL* 3.2 9.9 + - + +
766B MET* 2.9 36.7 + - + +
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Residues in contact with GLY 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759B ALA 3.1 14.3 + - - -
760B ASP* 3.3 4.2 + - - -
761B VAL 3.3 0.4 - - - -
762B ALA* 1.3 75.4 - - - +
764B GLU* 1.3 62.6 + - - +
766B MET* 3.4 9.5 + - - +
767B VAL* 3.2 25.4 + - - +
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Residues in contact with GLU 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B PRO* 3.4 5.5 - - + +
489B ARG 2.6 45.0 + - - +
490B LEU 5.0 0.7 - - - -
494B TYR* 2.7 31.7 + - - -
756B LEU* 4.5 5.3 - - + +
760B ASP 3.2 12.9 + - - +
761B VAL* 3.5 10.5 - - - +
762B ALA 3.2 0.2 - - - -
763B GLY* 1.3 75.6 - - - +
765B VAL* 1.3 66.8 + - + +
767B VAL* 3.1 22.5 + - + +
768B PHE* 3.6 13.6 + - - -
1213B LYS* 2.8 33.2 + - + -
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Residues in contact with VAL 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B ALA 4.9 1.7 - - - +
568B TYR* 5.5 2.0 - - - +
576B LEU* 5.5 0.7 - - + -
614B SER* 3.4 26.5 - - - +
615B PHE* 4.2 28.4 - - + +
617B PRO* 3.7 31.0 - - + -
646B GLN* 6.0 1.6 - - - +
761B VAL* 3.1 19.6 + - + +
762B ALA* 3.2 10.9 + - + +
764B GLU* 1.3 75.9 - - + +
766B MET* 1.3 60.9 + - - +
768B PHE* 3.2 15.4 + - + +
769B HIS* 2.9 23.8 + - + +
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Residues in contact with MET 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568B TYR* 5.9 1.1 - - - +
570B LEU* 4.1 22.2 - - + -
614B SER* 4.1 22.4 - - - -
762B ALA* 2.9 23.3 + - + +
763B GLY* 3.6 9.0 - - - +
764B GLU 3.1 0.2 - - - -
765B VAL* 1.3 74.7 - - + +
767B VAL* 1.3 58.9 + - - +
769B HIS* 3.5 38.5 - - + +
770B GLY* 2.9 24.3 + - - -
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Residues in contact with VAL 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B PRO* 3.6 32.8 - - + -
763B GLY 3.2 16.4 + - - +
764B GLU* 3.1 13.5 + - + +
766B MET* 1.3 76.1 - - - +
768B PHE* 1.3 62.0 + - - +
770B GLY* 3.2 4.4 + - - -
771B MET* 3.2 28.1 + - + +
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Residues in contact with PHE 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B ALA 3.7 16.7 - - - +
449B ALA* 3.8 11.2 - - - +
450B PHE 5.5 0.4 - - - -
451B GLY* 3.7 33.4 - - - -
452B TYR 5.4 1.3 - - - -
453B THR* 5.4 2.5 - - - -
488B PRO* 3.4 40.8 - - + -
489B ARG 3.6 22.0 - - - -
490B LEU* 4.1 15.9 - - + -
646B GLN* 5.6 2.2 - - - -
764B GLU 3.6 12.9 + - - -
765B VAL* 3.2 12.8 + - + +
767B VAL* 1.3 73.7 - - - +
769B HIS* 1.3 66.7 + - - +
771B MET* 3.0 35.7 + - + +
772B ALA* 3.1 14.9 + - - +
783B PHE* 4.9 5.6 - + - -
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Residues in contact with HIS 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B ALA* 4.7 5.1 + - - +
570B LEU* 3.7 7.7 - - + +
609B LEU* 5.1 3.8 - - - +
611B GLU* 3.0 26.8 + - - +
613B GLN 3.0 28.3 + - - -
614B SER* 4.7 5.1 + - - +
765B VAL* 2.9 14.7 + - + +
766B MET* 3.5 36.5 - - + +
767B VAL 3.2 0.2 - - - -
768B PHE* 1.3 75.7 - - - +
770B GLY* 1.3 58.7 + - - +
772B ALA* 3.2 1.9 + - - -
773B PHE* 3.0 61.8 + + + +
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Residues in contact with GLY 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766B MET 2.9 13.9 + - - -
767B VAL* 3.6 4.9 - - - -
768B PHE 3.2 0.2 - - - -
769B HIS* 1.3 81.1 - - - +
771B MET* 1.3 59.8 + - - +
773B PHE 3.9 13.5 + - - -
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Residues in contact with MET 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B ALA* 4.8 14.5 - - + +
452B TYR 5.8 3.1 - - - +
453B THR* 5.7 0.7 - - - +
488B PRO* 4.3 0.9 - - - -
767B VAL* 3.2 27.5 + - + +
768B PHE* 3.0 31.7 + - + +
770B GLY* 1.3 77.5 - - - +
772B ALA* 1.3 59.4 + - - +
781B GLU* 4.0 25.6 - - + +
783B PHE* 3.8 35.0 - - + -
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Residues in contact with ALA 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B GLN* 3.0 38.6 + - + +
448B ALA* 3.9 7.2 - - + -
449B ALA* 3.6 40.2 - - + +
768B PHE 3.1 6.9 + - - +
769B HIS 3.2 0.2 + - - -
771B MET* 1.3 78.8 - - - +
773B PHE* 1.3 67.2 + - + +
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Residues in contact with PHE 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B GLN* 3.6 36.8 - - + +
446B GLN* 4.8 2.2 - - - -
449B ALA* 3.8 28.0 - - + -
609B LEU* 3.9 26.9 - - + -
610B THR* 3.9 6.1 - - - -
611B GLU* 3.5 45.6 - - + +
769B HIS* 3.0 56.3 + + + +
770B GLY* 3.9 11.6 + - - -
771B MET 3.6 1.0 - - - -
772B ALA* 1.3 79.7 - - + +
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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
------------------------------------------------------------
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