Contacts of the helix formed by residues 788 - 805 (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 HIS 788 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LYS* 3.4 22.6 + - + +
39A TYR* 4.7 10.5 - - + -
302A GTP 4.0 13.5 + + - -
746B PRO* 3.6 31.3 - - + +
747B ASP* 5.3 1.6 - - - -
750B ASP* 6.0 0.9 - - + -
786B LEU* 3.1 26.2 + - + +
787B ASP* 1.3 76.9 + - - +
789B ARG* 1.3 61.8 + - - +
790B ASP* 4.0 20.9 - - + -
791B ALA* 3.4 22.4 + - + +
792B ASN* 2.9 31.6 + - - +
848B TYR* 4.5 2.9 + - - -
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Residues in contact with ARG 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASP* 4.9 6.9 + - - -
93A THR* 4.7 14.6 + - - -
94A SER* 4.7 16.2 + - - -
788B HIS* 1.3 74.2 + - - +
790B ASP* 1.3 65.9 + - - +
792B ASN* 3.8 3.3 - - - +
793B CYS* 2.8 32.1 + - - +
846B PRO* 5.9 0.4 - - - +
848B TYR* 3.3 52.6 + - + +
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Residues in contact with ASP 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LYS* 5.9 0.7 + - - -
750B ASP* 3.7 21.0 - - - +
754B ARG* 6.1 1.1 - - - +
788B HIS* 3.7 16.8 + - + -
789B ARG* 1.3 78.3 - - - +
791B ALA* 1.3 59.1 + - - +
793B CYS* 3.3 6.4 + - - +
794B SER* 2.9 30.8 + - - -
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Residues in contact with ALA 791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746B PRO 3.6 20.0 - - - +
749B VAL* 4.2 6.9 - - + +
750B ASP* 3.9 14.0 - - - +
786B LEU* 3.8 21.3 - - + -
788B HIS* 3.4 21.6 + - - +
790B ASP* 1.3 78.2 - - - +
792B ASN* 1.3 57.8 + - - +
794B SER* 3.1 4.7 + - - -
795B VAL* 2.8 33.4 + - - +
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Residues in contact with ASN 792 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B SER 4.8 1.7 + - - -
784B THR* 3.6 12.7 + - - +
786B LEU* 4.0 10.8 + - - +
788B HIS 2.9 24.0 + - - +
789B ARG* 3.8 4.9 - - - +
791B ALA* 1.3 70.3 - - - +
793B CYS* 1.3 61.9 + - - +
795B VAL* 3.2 7.4 + - - +
796B MET* 2.8 62.4 + - - +
845B LEU* 3.4 21.9 - - - +
848B TYR* 4.6 4.2 - - + +
849B THR* 3.2 22.8 - - - +
852B ASP* 5.2 2.6 - - - +
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Residues in contact with CYS 793 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789B ARG 2.8 22.6 + - - +
790B ASP* 3.5 7.0 - - - +
792B ASN* 1.3 73.0 + - - +
794B SER* 1.3 58.6 + - - +
796B MET* 3.4 1.0 + - - +
797B ARG* 2.8 44.2 + - - +
852B ASP* 4.4 18.6 - - - +
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Residues in contact with SER 794 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750B ASP* 2.8 47.8 + - - -
753B PHE* 3.4 4.5 - - - +
754B ARG* 3.3 17.9 + - - +
757B THR* 4.5 2.3 - - - +
790B ASP 2.9 7.1 + - - -
791B ALA 3.3 8.7 - - - -
793B CYS* 1.3 78.8 - - - +
795B VAL* 1.3 57.0 - - - +
797B ARG* 3.3 5.5 + - - +
798B PHE* 2.8 30.3 + - - +
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Residues in contact with VAL 795 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749B VAL* 3.6 13.9 - - + -
753B PHE* 3.5 31.4 - - + -
780B ALA* 3.7 35.0 - - + +
783B SER* 3.8 10.1 - - - +
784B THR* 4.3 11.2 - - + +
791B ALA 2.8 23.9 + - - +
792B ASN* 3.6 9.4 - - - +
794B SER* 1.3 72.2 - - - +
796B MET* 1.3 60.5 + - + +
798B PHE* 3.2 5.0 + - - +
799B LEU* 2.9 37.4 + - + +
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Residues in contact with MET 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B THR* 4.6 11.9 - - + +
792B ASN* 2.8 58.8 + - - +
793B CYS 4.0 2.2 - - - +
795B VAL* 1.3 72.5 - - + +
797B ARG* 1.3 61.5 + - - +
799B LEU* 3.3 21.3 + - - +
800B ARG* 2.9 30.4 + - - +
837B LEU* 4.2 11.2 - - + -
840B THR* 6.1 0.2 - - + -
845B LEU* 4.7 4.3 - - + -
849B THR* 4.7 4.0 - - + -
852B ASP* 3.5 45.7 - - + +
853B VAL* 4.0 21.3 - - + +
856B VAL* 3.7 7.3 - - + +
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Residues in contact with ARG 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B THR* 4.3 9.0 - - + -
793B CYS* 2.8 30.9 + - - +
794B SER* 3.6 6.3 - - - +
796B MET* 1.3 77.1 - - - +
798B PHE* 1.3 57.6 + - - +
800B ARG* 3.1 51.2 + - - +
801B ASP* 2.9 42.8 + - - +
852B ASP* 5.4 2.6 + - - -
855B GLU* 4.9 3.0 + - - -
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Residues in contact with PHE 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B PHE* 3.7 22.9 - + + -
756B ALA* 3.5 27.1 - - + -
757B THR* 3.3 24.6 - - + +
760B ILE* 3.9 21.8 - - + -
767B LEU* 4.8 5.4 - - + -
773B VAL* 5.5 3.4 - - + -
776B ILE* 3.9 24.7 - - + -
777B LEU* 4.6 6.7 - - + -
780B ALA* 4.2 19.3 - - + -
794B SER 2.8 14.2 + - - +
795B VAL 3.4 7.6 - - - +
797B ARG* 1.3 76.9 - - - +
799B LEU* 1.3 59.4 + - - +
801B ASP* 4.0 0.8 - - - +
802B LEU* 2.8 63.8 + - + +
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Residues in contact with LEU 799 (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* 3.7 30.1 - - + -
780B ALA* 4.0 16.8 - - + -
781B ILE 5.2 0.4 - - - +
784B THR* 4.1 22.9 - - + -
795B VAL* 2.9 21.6 + - + +
796B MET* 3.6 20.6 - - - +
798B PHE* 1.3 78.5 - - + +
800B ARG* 1.3 65.3 + - - +
802B LEU* 3.6 4.5 - - + +
803B ILE* 2.9 31.4 + - + +
833B LEU* 3.9 32.5 - - + -
837B LEU* 4.6 3.8 - - + -
856B VAL* 3.9 14.8 - - + -
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Residues in contact with ARG 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B MET 2.9 17.9 + - - +
797B ARG* 3.1 53.0 - - - +
799B LEU* 1.3 77.7 - - - +
801B ASP* 1.3 74.5 + - - +
803B ILE* 3.7 1.1 - - - -
804B HIS* 2.8 33.0 + - + +
852B ASP 5.6 0.2 - - - +
855B GLU* 2.8 45.5 + - + +
856B VAL* 3.9 15.1 - - + +
859B GLU* 3.8 20.9 - - - +
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Residues in contact with ASP 801 (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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757B THR* 4.3 12.2 - - + +
760B ILE* 3.8 18.4 - - + +
761B GLN* 6.0 1.7 - - - +
797B ARG* 2.9 38.3 + - - +
798B PHE* 4.0 3.6 - - - +
800B ARG* 1.3 99.4 + - - +
802B LEU* 1.3 57.8 + - - +
804B HIS* 3.5 9.8 - - - +
805B THR* 2.8 32.9 + - - -
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Residues in contact with LEU 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760B ILE* 3.4 31.9 - - + +
768B LEU* 3.9 15.7 - - + -
773B VAL* 4.6 11.2 - - + -
777B LEU* 3.6 38.8 - - + -
798B PHE* 2.8 47.6 + - + +
799B LEU* 3.6 5.4 - - + +
801B ASP* 1.3 72.7 - - - +
803B ILE* 1.3 69.2 + - + +
805B THR* 3.2 8.7 - - - +
822B ILE* 3.1 31.0 - - + +
825B VAL* 5.2 4.9 - - + -
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Residues in contact with ILE 803 (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* 5.9 3.4 - - + -
799B LEU* 2.9 23.2 + - + +
800B ARG 4.0 2.2 - - - +
802B LEU* 1.3 88.9 - - + +
804B HIS* 1.3 62.7 + - - +
806B GLY* 3.3 10.4 + - - -
822B ILE* 4.3 7.2 - - + +
825B VAL* 6.5 0.9 - - + -
826B MET* 3.4 37.2 - - + -
833B LEU* 4.4 13.7 - - + -
856B VAL* 4.8 3.8 - - + -
859B GLU* 3.5 37.0 - - + +
860B ILE* 3.6 15.7 - - + +
863B VAL* 3.7 21.6 - - + +
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Residues in contact with HIS 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B ARG* 2.8 20.7 + - + +
801B ASP* 3.1 12.8 + - - +
803B ILE* 1.3 73.4 - - - +
805B THR* 1.3 57.8 + - - +
806B GLY 2.9 5.4 - - - -
807B VAL* 2.9 33.3 + - + +
808B ALA* 3.2 28.9 + - + +
859B GLU* 2.8 37.5 + - + +
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Residues in contact with THR 805 (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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760B ILE* 4.4 11.9 + - + -
764B PRO* 3.5 24.9 - - + +
768B LEU* 4.0 17.3 - - + -
801B ASP 2.8 13.9 + - - -
802B LEU* 3.2 21.3 - - - +
804B HIS* 1.3 74.5 - - - +
806B GLY* 1.3 58.1 + - - +
807B VAL 3.3 1.1 - - - -
808B ALA* 4.1 9.0 - - - -
818B ARG* 3.3 36.9 + - + +
822B ILE* 3.5 17.7 - - + -
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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
------------------------------------------------------------
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