Contacts of the helix formed by residues 819 - 835 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H PHE* 4.4 2.0 - - - -
615H TRP* 3.6 29.8 - + - -
618H TYR* 4.4 7.9 + + - -
706H PRO* 6.0 1.1 - - + -
707H VAL* 4.3 11.9 + - + -
709H PRO* 3.4 37.1 - - + +
713H TRP* 3.7 43.5 - + + -
717H MET* 3.8 24.5 - - + -
815H MET* 2.9 27.9 + - - +
817H ASN 3.8 0.8 - - - -
818H GLU* 1.3 76.9 - - - +
820H PRO* 1.3 75.8 - - + +
821H PHE* 3.6 36.0 - + + +
822H PHE* 3.0 16.8 + - + -
823H ARG* 3.0 19.8 + - - +
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Residues in contact with PRO 820 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H PHE* 4.1 27.6 - - + -
654H LEU* 4.6 11.9 - - + -
657H LEU* 4.9 1.3 - - + +
658H SER* 3.6 25.4 - - - +
706H PRO* 3.9 20.4 - - + -
707H VAL* 4.1 9.9 - - + -
818H GLU 3.5 10.5 - - - +
819H TRP* 1.3 90.7 - - + +
821H PHE* 1.3 63.3 + - - +
823H ARG* 3.1 8.1 + - + +
824H VAL* 3.0 28.2 + - + +
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Residues in contact with PHE 821 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611H LEU* 6.0 0.2 - - + -
614H ALA* 3.8 33.9 - - + -
615H TRP* 3.9 21.8 - + - -
618H TYR* 3.8 29.8 - + + -
658H SER* 3.8 18.1 + - - +
717H MET* 3.9 23.3 - - + -
819H TRP* 3.1 37.6 + + - +
820H PRO* 1.3 78.5 - - - +
822H PHE* 1.3 66.0 + + - +
824H VAL* 3.4 4.8 - - + +
825H THR* 2.7 51.4 + - + -
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Residues in contact with PHE 822 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611H LEU* 5.3 4.7 - - + -
717H MET* 3.9 26.7 - - + -
720H MET* 5.2 2.0 - - - -
798H PHE* 4.4 14.8 - + - -
812H LEU* 3.8 23.8 - - + -
815H MET* 3.5 35.0 - - + +
816H TYR* 3.6 21.5 - - + -
819H TRP* 3.0 25.7 + + + +
821H PHE* 1.3 84.9 - + - +
823H ARG* 1.3 63.0 + - - +
825H THR* 3.7 4.0 - - + -
826H LEU* 3.2 64.1 + - + +
874H ILE* 4.2 7.0 - - + -
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Residues in contact with ARG 823 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H PHE* 4.1 17.4 - - + -
132H ALA* 3.6 26.0 - - - +
654H LEU* 4.3 13.2 - - + -
816H TYR* 3.1 70.6 + - - +
817H ASN* 4.2 12.9 + - - +
819H TRP 3.0 11.5 + - - +
820H PRO* 3.1 12.3 + - + +
822H PHE* 1.3 77.8 - - - +
824H VAL* 1.3 58.8 + - + +
826H LEU* 3.2 2.8 + - - +
827H ASP* 2.8 50.0 + - - +
877H HIS* 5.7 2.4 + - - -
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Residues in contact with VAL 824 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644H THR* 4.0 26.8 - - + +
647H ARG* 5.0 2.0 + - - +
651H PRO 5.7 0.4 - - - +
654H LEU* 3.6 33.7 - - + -
655H ALA* 4.1 11.9 - - + +
658H SER* 3.8 22.2 - - - +
820H PRO 3.0 13.9 + - - +
821H PHE* 3.4 13.5 - - + +
823H ARG* 1.3 75.5 - - - +
825H THR* 1.3 69.2 + - - +
827H ASP* 3.8 8.1 - - - +
828H LEU* 3.2 23.9 + - - +
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Residues in contact with THR 825 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610H ARG* 5.8 7.6 - - + +
611H LEU* 4.3 20.2 - - + -
614H ALA* 4.2 22.5 - - + +
644H THR* 4.9 6.8 - - - +
821H PHE* 2.7 41.3 + - + -
822H PHE* 3.7 8.3 - - + -
823H ARG 3.2 0.2 - - - -
824H VAL* 1.3 83.6 - - - +
826H LEU* 1.3 65.0 + - + +
828H LEU* 3.9 3.6 + - - +
829H LEU* 3.5 25.1 + - + +
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Residues in contact with LEU 826 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611H LEU* 5.5 2.7 - - + -
798H PHE* 3.9 24.9 - - + -
816H TYR* 4.0 21.1 - - + -
822H PHE* 3.2 48.2 + - + +
823H ARG 4.1 2.0 - - - +
825H THR* 1.3 84.3 - - + +
827H ASP* 1.3 61.6 + - - +
828H LEU 3.2 0.7 - - - -
829H LEU* 3.1 11.6 + - + +
830H GLU* 2.8 31.0 + - - +
871H LEU* 3.6 28.4 - - + +
874H ILE* 4.0 25.4 - - + -
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Residues in contact with ASP 827 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H GLY* 5.9 1.7 - - - -
647H ARG* 4.0 12.9 + - - +
654H LEU* 4.6 8.1 - - - +
816H TYR* 3.3 23.9 + - - -
823H ARG* 2.8 42.6 + - - +
824H VAL* 3.4 9.3 + - - +
826H LEU* 1.3 77.4 - - - +
828H LEU* 1.3 57.4 + - - +
830H GLU* 3.4 11.1 + - - +
831H MET* 3.0 27.4 + - - +
881H LEU* 5.2 2.3 - - - +
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Residues in contact with LEU 828 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610H ARG* 4.0 21.1 - - - +
642H GLY 4.5 6.3 - - - +
643H GLY 4.6 1.6 - - - +
644H THR* 3.8 28.5 - - + -
647H ARG* 3.8 31.9 - - + +
790H VAL* 3.9 14.8 - - + -
824H VAL 3.2 16.0 + - - +
825H THR 4.1 4.7 - - - +
826H LEU 3.2 0.2 - - - -
827H ASP* 1.3 74.0 - - - +
829H LEU* 1.3 66.7 + - + +
831H MET* 3.1 7.9 + - + +
832H VAL* 2.9 37.8 + - + +
968H ASN* 6.1 0.2 - - - +
969H THR 3.5 25.6 - - - +
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Residues in contact with LEU 829 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610H ARG* 4.5 8.5 - - + -
611H LEU* 5.9 2.5 - - + -
790H VAL* 3.3 42.4 - - + +
791H TRP* 4.1 10.3 - - + -
794H VAL* 4.0 32.8 - - + -
825H THR* 3.5 19.3 - - + +
826H LEU* 3.1 22.7 + - + +
828H LEU* 1.3 77.2 - - + +
830H GLU* 1.3 62.5 + - - +
832H VAL* 3.3 4.8 + - + +
833H PHE* 3.0 35.7 + - + -
867H THR* 6.0 0.4 - - + -
871H LEU* 4.3 13.0 - - + -
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Residues in contact with GLU 830 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816H TYR* 3.7 9.9 + - - -
826H LEU 2.8 15.8 + - - +
827H ASP* 3.6 12.6 - - - +
828H LEU 3.2 0.2 - - - -
829H LEU* 1.3 77.2 - - - +
831H MET* 1.3 62.5 + - - +
833H PHE 3.3 1.4 + - - -
834H ALA* 3.0 19.4 + - - +
871H LEU* 3.9 16.4 - - + +
872H LEU* 3.9 7.3 - - - +
875H ALA* 4.6 4.7 - - - +
877H HIS* 2.8 36.1 + - - -
880H ILE* 3.4 28.3 - - + +
881H LEU* 2.7 37.2 + - + +
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Residues in contact with MET 831 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647H ARG* 3.4 40.8 - - - +
827H ASP 3.0 9.1 + - - +
828H LEU* 3.1 13.2 + - + +
830H GLU* 1.3 77.0 - - - +
832H VAL* 1.3 74.5 + - + +
834H ALA* 3.2 11.0 + - - +
835H LYS* 3.1 47.3 + - - +
881H LEU* 4.5 7.1 - - + +
887H LEU* 4.1 17.7 - - + -
891H LEU* 4.4 7.9 - - + -
968H ASN* 3.5 35.9 - - - +
969H THR 4.6 0.9 - - - +
1001H GOL 4.1 5.6 - - - +
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Residues in contact with VAL 832 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787H HIS* 3.5 42.3 - - + +
790H VAL* 4.0 20.4 - - + -
791H TRP* 5.3 2.9 - - + -
828H LEU* 2.9 38.6 + - + +
829H LEU* 3.9 3.8 - - - +
830H GLU 3.3 0.2 - - - -
831H MET* 1.3 84.6 - - - +
833H PHE* 1.3 60.8 + - + +
835H LYS* 2.9 20.0 + - - +
836H GLY 3.0 9.4 + - - -
969H THR* 4.0 23.3 - - - +
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Residues in contact with PHE 833 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787H HIS* 6.6 0.2 - - + -
791H TRP* 3.6 35.7 - + + -
829H LEU* 3.0 31.3 + - + +
830H GLU 3.3 0.2 + - - -
832H VAL* 1.3 74.1 - - + +
834H ALA* 1.3 66.1 + - - +
836H GLY* 3.0 16.8 + - - +
864H TYR* 3.4 56.6 + + - -
867H THR* 4.0 20.6 - - + -
868H GLN* 3.5 27.2 - - + +
871H LEU* 3.6 24.5 - - + -
880H ILE* 3.3 21.6 - - + +
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Residues in contact with ALA 834 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830H GLU 3.0 9.9 + - - +
831H MET 3.3 10.3 - - - +
833H PHE* 1.3 76.2 - - - +
835H LYS* 1.3 60.1 + - - +
836H GLY 3.6 3.6 + - - +
880H ILE* 4.2 18.5 - - + +
881H LEU* 3.7 30.1 - - + -
888H LYS* 5.9 2.9 - - + -
891H LEU* 4.0 13.8 - - + +
895H ASN* 4.7 13.2 + - - +
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Residues in contact with LYS 835 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785H ARG* 3.6 11.5 + - - +
787H HIS* 3.1 7.5 + - + +
831H MET* 3.1 32.8 + - - +
832H VAL* 2.9 12.4 + - - +
834H ALA* 1.3 78.1 - - - +
836H GLY* 1.3 56.6 + - - +
891H LEU* 3.7 35.2 - - + -
894H ARG* 4.5 2.5 - - - +
895H ASN* 5.7 1.6 - - - -
965H GLY 5.2 0.2 - - - -
966H MET* 2.6 72.5 + - - +
967H GLN* 4.4 0.4 - - - +
968H ASN* 2.9 21.8 + - - +
969H THR* 4.4 7.6 - - + -
1001H GOL 3.9 16.7 + - - -
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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