Contacts of the helix formed by residues 819 - 835 (chain F) in PDB entry 6V3O
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 TRP 819 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F PHE* 4.6 2.7 - - - -
615F TRP* 3.6 30.7 - + - -
618F TYR* 4.3 10.0 + + - -
658F SER 5.8 0.2 + - - -
706F PRO* 6.0 0.7 - - + -
707F VAL* 4.3 11.6 + - + -
709F PRO* 3.5 35.6 - - + +
713F TRP* 3.5 44.2 - + + -
717F MET* 3.9 20.4 - - + -
815F MET* 2.9 28.9 + - + +
817F ASN 3.8 0.6 - - - -
818F GLU* 1.3 76.8 - - - +
820F PRO* 1.3 77.7 - - + +
821F PHE* 3.6 37.4 - + + +
822F PHE* 3.1 15.5 + - + -
823F ARG* 3.1 19.2 + - - +
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Residues in contact with PRO 820 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F PHE* 4.0 36.5 - - + -
654F LEU* 4.5 7.0 - - + -
657F LEU 5.0 1.3 - - - +
658F SER* 3.4 24.9 - - - +
706F PRO* 3.9 19.5 - - + -
707F VAL* 4.0 10.8 - - + +
818F GLU 3.5 10.5 - - - +
819F TRP* 1.3 91.6 - - + +
821F PHE* 1.3 61.3 + - - +
823F ARG* 3.1 2.7 + - + +
824F VAL* 3.0 28.8 + - - +
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Residues in contact with PHE 821 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611F LEU* 5.9 0.9 - - + -
614F ALA* 3.8 38.1 - - + -
615F TRP* 4.1 13.5 - + - -
618F TYR* 3.8 29.8 - + + -
658F SER* 3.6 16.5 + - - +
717F MET* 4.1 20.6 - - + -
819F TRP* 3.3 45.9 - + - +
820F PRO* 1.3 77.1 - - - +
822F PHE* 1.3 76.4 + + - +
824F VAL* 3.3 5.6 - - + +
825F THR* 2.6 50.3 + - + -
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Residues in contact with PHE 822 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611F LEU* 5.1 5.8 - - + -
717F MET* 3.9 21.1 - - + -
720F MET* 4.4 5.6 - - + -
798F PHE* 4.2 13.2 - + - -
812F LEU* 3.9 28.3 - - + -
815F MET* 3.4 34.3 - - + +
816F TYR* 3.6 22.9 - - + -
819F TRP* 3.1 21.7 + + + +
821F PHE* 1.3 87.7 - + - +
823F ARG* 1.3 61.8 + - - +
825F THR* 3.3 5.0 + - - -
826F LEU* 3.1 56.9 + - + +
874F ILE* 4.1 6.5 - - + -
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Residues in contact with ARG 823 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F PHE* 3.6 26.2 - - + -
132F ALA* 4.0 23.7 + - - +
654F LEU* 4.0 15.7 - - + -
816F TYR* 3.3 57.6 + - + +
817F ASN* 3.7 26.5 + - - +
819F TRP 3.1 10.3 + - - +
820F PRO* 3.1 9.1 + - + +
822F PHE* 1.3 77.8 - - - +
824F VAL* 1.3 58.2 + - + +
826F LEU* 3.4 1.9 + - - +
827F ASP* 2.9 50.9 + - - +
877F HIS* 5.9 0.4 + - - -
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Residues in contact with VAL 824 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644F THR* 3.9 26.4 - - + +
647F ARG* 5.1 1.2 + - - -
651F PRO 5.3 1.1 - - - +
654F LEU* 3.5 35.0 - - + +
655F ALA* 3.9 17.7 - - + +
658F SER* 3.6 16.4 - - - +
820F PRO 3.0 15.3 + - - +
821F PHE* 3.3 14.4 - - + +
823F ARG* 1.3 77.2 - - - +
825F THR* 1.3 68.2 + - - +
827F ASP* 3.8 7.6 - - - +
828F LEU* 3.2 22.7 + - - +
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Residues in contact with THR 825 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610F ARG* 5.6 10.1 + - + +
611F LEU* 4.5 17.3 - - + -
614F ALA* 4.2 20.7 - - + +
644F THR* 4.7 8.8 - - + +
821F PHE* 2.6 43.4 + - + -
822F PHE* 3.7 9.2 - - + -
823F ARG 3.2 0.2 - - - -
824F VAL* 1.3 81.0 - - - +
826F LEU* 1.3 68.3 + - + +
828F LEU* 3.7 4.7 + - - +
829F LEU* 3.5 23.9 + - + +
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Residues in contact with LEU 826 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611F LEU* 5.3 4.9 - - + -
798F PHE* 3.9 22.9 - - + -
816F TYR* 4.3 17.5 - - + -
822F PHE* 3.1 46.5 + - + +
823F ARG 4.1 2.0 - - - +
825F THR* 1.3 84.0 - - + +
827F ASP* 1.3 61.8 + - - +
828F LEU 3.2 2.0 - - - -
829F LEU* 3.1 23.2 + - + +
830F GLU* 2.8 31.1 + - - +
871F LEU* 3.6 26.1 - - + +
874F ILE* 4.0 14.6 - - + -
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Residues in contact with ASP 827 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F GLY* 6.0 0.7 - - - -
647F ARG* 3.7 11.0 + - - +
651F PRO* 6.5 0.4 - - + -
654F LEU* 4.6 6.9 - - - +
816F TYR* 3.4 23.2 + - - -
823F ARG* 2.9 45.2 + - - +
824F VAL* 3.4 9.2 + - - +
826F LEU* 1.3 77.0 - - - +
828F LEU* 1.3 57.7 + - - +
830F GLU* 3.7 12.4 - - - +
831F MET* 3.0 28.2 + - - +
877F HIS* 5.3 0.2 - - - -
881F LEU* 5.3 2.4 - - - +
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Residues in contact with LEU 828 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610F ARG* 4.1 18.6 - - - +
642F GLY 4.2 14.6 - - - +
643F GLY 4.5 1.8 - - - +
644F THR* 3.7 33.0 - - + -
647F ARG* 3.5 25.3 - - + +
790F VAL* 3.7 27.4 - - + -
824F VAL 3.2 16.3 + - - +
825F THR 3.9 5.2 - - - +
826F LEU 3.2 0.4 - - - -
827F ASP* 1.3 74.5 - - - +
829F LEU* 1.3 67.6 + - + +
831F MET* 3.2 7.2 + - + +
832F VAL* 3.0 28.0 + - + +
969F THR 3.9 18.8 - - - +
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Residues in contact with LEU 829 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610F ARG* 4.3 8.5 - - + -
611F LEU* 6.0 1.8 - - + -
790F VAL* 3.1 42.8 - - + +
791F TRP* 4.2 8.1 - - + -
794F VAL* 4.1 28.9 - - + -
825F THR* 3.5 14.3 + - + +
826F LEU* 3.1 31.7 + - + +
828F LEU* 1.3 76.7 - - + +
830F GLU* 1.3 58.5 + - - +
832F VAL* 3.3 4.5 + - - +
833F PHE* 3.0 41.1 + - + -
867F THR* 6.2 0.2 - - + -
871F LEU* 4.1 13.2 - - + -
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Residues in contact with GLU 830 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816F TYR* 4.2 1.6 + - - -
826F LEU 2.8 15.9 + - - +
827F ASP* 3.7 18.0 - - - +
829F LEU* 1.3 75.2 - - - +
831F MET* 1.3 65.8 + - - +
833F PHE* 3.3 3.0 + - - +
834F ALA* 3.0 18.5 + - - +
871F LEU* 3.8 17.7 - - + +
872F LEU* 4.0 8.7 - - + +
875F ALA* 4.7 4.4 - - - +
877F HIS* 2.9 37.9 + - - -
880F ILE* 3.5 16.7 - - + +
881F LEU* 2.8 43.5 + - + +
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Residues in contact with MET 831 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647F ARG* 3.3 44.0 - - - +
827F ASP 3.0 13.6 + - - +
828F LEU* 3.6 5.4 - - + +
830F GLU* 1.3 76.6 - - - +
832F VAL* 1.3 77.7 + - + +
834F ALA* 3.1 17.7 + - - +
835F LYS* 3.1 44.2 + - - +
881F LEU* 4.6 7.5 - - + +
887F LEU* 4.2 16.8 - - + -
891F LEU* 4.5 3.8 - - + -
968F ASN* 3.6 20.4 - - - +
969F THR 4.4 5.2 - - - +
1004F FLC 3.5 19.1 - - + +
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Residues in contact with VAL 832 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787F HIS* 3.4 42.8 - - + +
790F VAL* 4.0 25.6 - - + -
791F TRP* 5.3 3.8 - - + -
828F LEU* 3.0 18.8 + - + +
829F LEU 3.8 3.6 - - - +
830F GLU 3.3 0.2 - - - -
831F MET* 1.3 83.6 - - - +
833F PHE* 1.3 62.5 + - + +
835F LYS* 3.1 16.2 + - - +
836F GLY 3.2 8.1 + - - -
969F THR* 3.8 35.2 - - - +
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Residues in contact with PHE 833 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787F HIS* 5.7 0.4 - - + -
791F TRP* 3.6 39.7 - + + -
829F LEU* 3.0 29.2 + - + +
830F GLU 3.7 5.2 - - - +
832F VAL* 1.3 77.2 - - + +
834F ALA* 1.3 61.6 + - - +
836F GLY* 3.1 18.0 + - - +
864F TYR* 3.6 51.6 + + - -
867F THR* 4.0 11.4 - - + -
868F GLN* 3.6 43.9 - - + +
871F LEU* 3.6 26.2 - - + -
880F ILE* 4.3 15.0 - - + +
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Residues in contact with ALA 834 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F GLU* 5.8 0.2 - - - +
785F ARG* 5.6 0.5 + - - -
830F GLU 3.0 10.2 + - - +
831F MET 3.1 11.4 + - - +
833F PHE* 1.3 76.4 - - - +
835F LYS* 1.3 59.5 + - - +
836F GLY 3.2 4.3 + - - +
880F ILE* 3.9 16.5 - - + +
881F LEU* 3.7 28.9 - - + -
888F LYS* 4.9 7.4 - - + +
891F LEU* 4.1 13.4 - - + +
895F ASN* 4.8 9.4 + - - +
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Residues in contact with LYS 835 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785F ARG* 3.3 22.3 + - - +
787F HIS* 2.9 18.3 + - + +
831F MET* 3.1 31.6 + - - +
832F VAL* 3.1 10.3 + - - +
834F ALA* 1.3 75.2 - - - +
836F GLY* 1.3 57.5 + - - +
891F LEU* 3.9 29.4 - - + -
894F ARG* 4.5 1.3 - - - +
895F ASN* 5.8 1.6 - - - +
965F GLY 5.1 0.2 - - - -
966F MET* 2.7 55.3 + - + +
968F ASN* 2.8 21.4 + - - +
969F THR* 4.4 7.2 - - + -
1004F FLC 3.1 25.6 + - - +
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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
------------------------------------------------------------
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