Contacts of the helix formed by residues 772 - 784 (chain B) in PDB entry 4OL0
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 772 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722B LEU* 4.4 0.7 - - + -
725B LEU* 4.2 13.2 - - + -
726B GLN* 3.6 44.2 - - + +
729B CYS* 4.6 12.6 - - + -
733B PHE* 5.3 2.0 - - + -
767B LEU* 3.9 12.1 - - + -
770B SER* 3.2 18.2 - - - +
771B GLN* 1.3 81.2 - - + +
773B VAL* 1.3 64.3 + - - +
774B ILE 3.3 2.5 - - - -
775B PRO* 3.3 10.5 - - + +
776B ILE* 3.0 37.2 + - + +
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Residues in contact with VAL 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767B LEU* 3.4 37.5 - - + +
768B LEU* 4.0 24.5 - - + +
770B SER* 3.5 19.9 + - - +
772B VAL* 1.3 81.1 - - - +
774B ILE* 1.3 71.0 + - + +
776B ILE* 3.7 4.9 - - - +
777B LEU* 2.8 29.0 + - + +
798B PHE* 5.5 2.9 - - + -
802B LEU* 4.6 15.0 - - + -
825B VAL* 4.7 19.5 - - + -
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Residues in contact with ILE 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770B SER 5.6 1.6 - - - +
771B GLN* 4.5 5.6 + - - +
773B VAL* 1.3 87.2 - - + +
775B PRO* 1.3 69.4 - - + +
777B LEU* 3.1 7.8 + - - +
778B GLN* 2.8 40.3 + - - +
825B VAL* 5.4 12.1 - - + -
828B GLN* 3.8 29.6 - - + +
829B LEU* 4.1 18.4 - - + -
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Residues in contact with PRO 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B PHE* 3.8 23.6 - - + -
771B GLN 3.2 23.3 - - - +
772B VAL* 3.3 18.2 - - + +
774B ILE* 1.3 94.6 - - + +
776B ILE* 1.3 55.4 + - - +
778B GLN* 3.2 17.3 + - - +
779B TRP* 2.8 38.4 + - + -
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Residues in contact with ILE 776 (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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725B LEU* 4.3 15.0 - - + -
729B CYS* 3.9 20.0 - - - -
733B PHE* 3.8 20.9 - - + -
752B LEU* 5.0 7.6 - - + -
753B PHE* 3.5 26.9 - - + -
756B ALA* 4.3 11.7 - - + -
767B LEU* 4.4 8.7 - - + -
772B VAL* 3.0 39.9 + - + +
773B VAL* 3.7 3.6 - - - +
775B PRO* 1.3 75.0 - - - +
777B LEU* 1.3 59.0 + - - +
779B TRP* 3.2 4.4 + - - +
780B ALA 2.8 24.4 + - - -
798B PHE* 3.9 19.5 - - + -
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Residues in contact with LEU 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B VAL 2.8 19.1 + - - +
774B ILE* 3.4 6.1 - - - +
776B ILE* 1.3 77.6 - - - +
778B GLN* 1.3 56.3 + - - +
780B ALA* 3.2 5.5 + - - +
781B ILE* 2.9 41.4 + - + +
798B PHE* 4.6 2.9 - - + -
799B LEU* 3.7 23.1 - - + -
802B LEU* 3.6 27.4 - - + -
803B ILE* 5.9 1.6 - - + -
825B VAL* 3.4 38.4 - - + +
826B MET* 6.1 3.8 - - + -
829B LEU* 3.7 25.8 - - + +
833B LEU* 5.4 6.3 - - + -
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Residues in contact with GLN 778 (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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774B ILE* 2.8 28.7 + - - +
775B PRO* 3.2 24.6 + - - +
777B LEU* 1.3 72.0 - - - +
779B TRP* 1.3 59.7 + - + +
781B ILE* 3.2 11.1 + - + +
782B ALA* 2.8 28.9 + - - +
829B LEU* 3.7 26.7 - - + +
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Residues in contact with TRP 779 (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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733B PHE* 3.3 50.6 - + + +
736B LEU* 3.5 42.8 - - + -
737B GLU* 3.7 29.3 + - + -
742B LEU* 4.1 28.0 - - + -
752B LEU* 5.1 3.8 - - + -
753B PHE* 3.7 8.3 - - + -
775B PRO* 2.8 27.4 + - + +
776B ILE* 3.6 6.5 - - - +
778B GLN* 1.3 75.6 - - + +
780B ALA* 1.3 54.0 + - - +
782B ALA* 3.6 11.5 - - + +
783B SER* 2.6 43.1 + - - +
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Residues in contact with ALA 780 (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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753B PHE* 3.3 23.3 - - + -
776B ILE 2.8 13.5 + - - +
777B LEU* 3.2 10.7 + - - +
779B TRP* 1.3 72.8 - - - +
781B ILE* 1.3 59.8 + - - +
783B SER* 2.8 18.6 + - - -
784B THR* 2.8 20.4 + - - +
795B VAL* 3.7 11.3 - - + +
798B PHE* 4.2 7.0 - - + -
799B LEU* 4.0 21.8 - - + -
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Residues in contact with ILE 781 (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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777B LEU* 2.9 27.1 + - + +
778B GLN* 3.5 9.0 - - + +
780B ALA* 1.3 74.3 - - + +
782B ALA* 1.3 58.7 + - - +
784B THR* 2.4 33.4 + - - -
799B LEU* 5.2 0.4 - - - +
829B LEU* 3.9 42.6 - - + +
832B GLN* 4.4 10.8 - - + +
833B LEU* 4.0 26.7 - - + +
836B GLN* 3.5 33.9 - - + +
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Residues in contact with ALA 782 (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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742B LEU* 3.6 13.6 - - + +
778B GLN 2.8 16.9 + - - +
779B TRP* 3.6 22.9 - - + +
781B ILE* 1.3 76.9 - - - +
783B SER* 1.3 58.6 + - - +
784B THR 3.4 0.3 + - - -
785B THR* 3.2 27.6 + - - +
836B GLN* 5.8 0.9 - - - -
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Residues in contact with SER 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B LEU* 5.4 0.9 - - - +
742B LEU* 3.6 26.2 - - - +
749B VAL* 3.6 15.0 - - - +
753B PHE* 3.7 5.0 - - - -
779B TRP* 2.6 27.8 + - - +
780B ALA 2.8 3.8 + - - -
782B ALA* 1.3 69.2 - - - +
784B THR* 1.3 66.5 + - - +
785B THR 3.0 3.1 - - - -
786B LEU* 3.0 23.4 + - - +
792B ASN* 4.8 3.3 + - - -
795B VAL* 3.8 26.5 - - - +
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Residues in contact with THR 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780B ALA 2.8 19.3 + - - +
781B ILE* 2.4 33.1 + - - +
783B SER* 1.3 77.3 - - - +
785B THR* 1.3 59.0 + - - +
786B LEU 3.4 0.5 + - - -
792B ASN* 3.6 9.2 + - - +
795B VAL* 4.3 7.1 - - + +
796B MET* 4.6 5.8 - - - -
799B LEU* 4.1 21.8 - - + -
833B LEU* 5.3 1.3 - - + -
836B GLN* 3.3 18.5 + - + +
837B LEU* 4.2 16.8 - - + -
840B THR* 3.3 13.2 - - - +
845B LEU* 3.2 27.7 - - - +
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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
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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