Contacts of the helix formed by residues 819 - 835 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 4.2 2.4 - - - -
615A TRP* 3.6 33.0 - + - -
618A TYR* 4.5 7.7 + + - -
706A PRO* 6.0 0.9 - - + -
707A VAL* 4.3 13.2 + - + -
709A PRO* 3.5 36.4 - - + +
713A TRP* 3.5 44.4 - + + -
717A MET* 3.9 20.6 - - + -
815A MET* 2.9 28.4 + - + +
817A ASN 3.9 0.4 - - - -
818A GLU* 1.3 77.0 - - - +
820A PRO* 1.3 75.0 - - + +
821A PHE* 3.7 35.4 - + + +
822A PHE* 3.0 25.1 + - + +
823A ARG* 3.0 11.0 + - - +
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Residues in contact with PRO 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 4.2 28.2 - - + -
654A LEU* 4.6 10.5 - - + -
657A LEU* 5.0 1.6 - - + +
658A SER* 3.5 25.6 - - - +
706A PRO* 3.9 18.6 - - + -
707A VAL* 4.0 9.9 - - + +
818A GLU 3.5 10.1 - - - +
819A TRP* 1.3 91.1 - - + +
821A PHE* 1.3 62.5 + - - +
823A ARG* 3.1 8.8 + - + +
824A VAL* 2.9 28.9 + - + +
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Residues in contact with PHE 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 6.2 0.2 - - + -
614A ALA* 3.6 39.9 - - + -
615A TRP* 4.0 17.0 - + - -
618A TYR* 3.9 22.4 - + + -
658A SER* 3.8 21.9 + - - +
717A MET* 4.0 24.0 - - + -
819A TRP* 3.3 37.4 - + + +
820A PRO* 1.3 78.3 - - - +
822A PHE* 1.3 64.1 + + - +
824A VAL* 3.4 6.1 - - + +
825A THR* 2.3 50.9 + - + -
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Residues in contact with PHE 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 5.1 6.3 - - + -
717A MET* 4.0 21.1 - - + -
720A MET* 5.3 2.9 - - + -
798A PHE* 4.3 17.5 - + - -
812A LEU* 3.9 25.1 - - + -
815A MET* 3.5 34.1 - - + +
816A TYR* 3.6 22.0 - - + -
819A TRP* 3.0 23.6 + + + +
821A PHE* 1.3 87.0 - + - +
823A ARG* 1.3 62.7 + - - +
825A THR* 3.4 3.7 + - - -
826A LEU* 3.1 64.9 + - + +
874A ILE* 4.4 6.5 - - + -
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Residues in contact with ARG 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 4.1 14.4 - - + -
132A ALA* 3.6 29.6 - - - +
654A LEU* 4.3 13.5 - - + -
816A TYR* 3.2 72.1 + - - +
817A ASN* 4.2 12.7 + - - +
819A TRP 3.0 10.1 + - - +
820A PRO* 3.1 12.1 + - + +
822A PHE* 1.3 77.1 - - - +
824A VAL* 1.3 59.6 + - + +
826A LEU* 3.2 2.6 + - - +
827A ASP* 2.8 51.2 + - - +
877A HIS* 5.7 2.2 + - - -
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Residues in contact with VAL 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A THR* 4.0 24.7 - - + +
647A ARG* 4.8 3.8 + - - +
651A PRO 5.6 0.7 - - - +
654A LEU* 3.5 33.9 - - + -
655A ALA* 4.1 12.6 - - + +
658A SER* 3.7 22.7 - - - +
820A PRO 2.9 13.7 + - - +
821A PHE* 3.4 14.4 - - + +
823A ARG* 1.3 74.5 - - - +
825A THR* 1.3 69.0 + - - +
827A ASP* 3.9 8.3 - - - +
828A LEU* 3.2 22.9 + - - +
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Residues in contact with THR 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A ARG* 5.9 4.9 - - + -
611A LEU* 4.4 20.2 - - + -
614A ALA* 4.1 22.4 - - + +
644A THR* 4.9 6.9 - - - +
821A PHE* 2.3 46.0 + - + -
822A PHE* 3.6 7.9 - - + -
823A ARG 3.2 0.2 - - - -
824A VAL* 1.3 82.9 - - - +
826A LEU* 1.3 66.5 + - + +
828A LEU* 3.8 4.7 + - - +
829A LEU* 3.6 22.8 + - + +
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Residues in contact with LEU 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 5.6 2.7 - - + -
798A PHE* 4.1 17.5 - - + -
816A TYR* 3.8 26.5 - - + -
822A PHE* 3.1 69.0 + - + +
825A THR* 1.3 84.7 - - + +
827A ASP* 1.3 62.2 + - - +
828A LEU 3.2 0.7 - - - -
829A LEU* 3.2 9.5 + - + +
830A GLU* 2.9 29.3 + - - +
871A LEU* 3.6 32.0 - - + +
874A ILE* 4.5 11.9 - - + -
875A ALA* 5.6 0.2 - - + -
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Residues in contact with ASP 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLY* 6.0 1.2 - - - -
647A ARG* 4.0 15.3 + - - +
654A LEU* 4.6 7.1 - - - +
816A TYR* 3.1 26.0 + - - -
823A ARG* 2.8 43.7 + - - +
824A VAL* 3.9 7.7 - - - +
825A THR 3.5 0.2 - - - -
826A LEU* 1.3 74.1 - - - +
828A LEU* 1.3 65.4 + - - +
830A GLU* 3.3 10.3 + - - +
831A MET* 3.0 22.5 + - - +
881A LEU* 5.4 1.9 - - - +
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Residues in contact with LEU 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ARG* 3.3 31.4 - - + +
642A GLY 4.4 3.6 - - - +
643A GLY 4.9 1.3 - - - +
644A THR* 3.8 24.0 - - + -
647A ARG* 4.0 22.2 - - + +
790A VAL* 3.6 29.2 - - + -
824A VAL 3.2 14.3 + - - +
825A THR 3.9 4.9 - - - +
826A LEU 3.2 0.4 - - - -
827A ASP* 1.3 77.7 - - - +
829A LEU* 1.3 67.6 + - + +
831A MET* 3.1 9.9 + - + +
832A VAL* 3.0 35.5 + - + +
969A THR 3.7 14.1 - - - +
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Residues in contact with LEU 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ARG* 4.8 7.2 - - + -
611A LEU* 6.1 2.2 - - + -
790A VAL* 3.3 42.4 - - + +
791A TRP* 4.1 10.3 - - + -
794A VAL* 4.3 28.0 - - + -
798A PHE* 5.3 2.7 - - + -
825A THR* 3.6 20.1 + - + +
826A LEU* 3.2 13.8 + - + +
828A LEU* 1.3 82.0 - - + +
830A GLU* 1.3 63.3 + - - +
832A VAL* 3.2 4.7 + - + +
833A PHE* 3.0 34.8 + - + -
871A LEU* 4.1 24.9 - - + -
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Residues in contact with GLU 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A TYR* 3.8 9.0 + - - -
826A LEU 2.9 16.0 + - - +
827A ASP* 3.6 11.6 - - - +
828A LEU 3.2 0.2 - - - -
829A LEU* 1.3 77.7 - - - +
831A MET* 1.3 61.5 + - - +
833A PHE 3.4 1.2 + - - -
834A ALA* 3.1 19.1 + - - +
871A LEU* 3.9 14.6 - - + +
872A LEU* 3.9 12.1 - - - +
875A ALA* 4.5 4.8 - - - +
877A HIS* 2.9 39.0 + - - -
880A ILE* 3.6 23.8 - - + +
881A LEU* 2.9 36.9 + - + +
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Residues in contact with MET 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A ARG* 3.5 37.9 - - - +
827A ASP 3.0 7.7 + - - +
828A LEU* 3.1 9.2 + - + +
830A GLU* 1.3 76.3 - - - +
832A VAL* 1.3 77.8 + - + +
834A ALA* 3.3 8.7 + - - +
835A LYS* 3.2 51.3 + - - +
881A LEU* 4.5 7.5 - - + +
887A LEU* 4.2 18.6 - - + -
891A LEU* 4.6 2.0 - - + -
968A ASN* 3.5 33.9 - - - +
969A THR 4.5 4.5 - - - +
1004A FLC 3.9 7.0 - - + +
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Residues in contact with VAL 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A HIS* 3.5 42.5 + - + +
790A VAL* 4.0 17.7 - - + -
791A TRP* 5.4 3.4 - - + -
828A LEU* 3.0 35.0 + - + +
829A LEU* 3.2 4.9 + - + +
831A MET* 1.3 85.5 - - - +
833A PHE* 1.3 65.4 + - + +
835A LYS* 3.0 16.1 + - - +
836A GLY 3.1 8.8 + - - -
969A THR* 3.9 20.2 - - - +
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Residues in contact with PHE 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787A HIS* 5.5 0.2 - - - -
791A TRP* 3.7 25.6 - + + -
829A LEU* 3.0 31.7 + - + +
830A GLU 3.7 4.3 - - - +
832A VAL* 1.3 77.1 - - + +
834A ALA* 1.3 58.1 + - - +
836A GLY* 2.8 24.9 + - - +
864A TYR* 3.5 51.6 + + - -
867A THR* 3.5 33.4 - - + -
868A GLN* 3.6 32.1 - - + +
871A LEU* 3.9 21.3 - - + -
880A ILE* 3.8 14.8 - - + -
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Residues in contact with ALA 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785A ARG* 5.7 0.3 + - - -
830A GLU 3.1 11.3 + - - +
831A MET 3.4 10.1 - - - +
832A VAL 3.3 0.2 - - - -
833A PHE* 1.3 76.0 - - - +
835A LYS* 1.3 59.6 + - - +
836A GLY 3.6 4.0 + - - +
880A ILE* 4.0 18.9 - - + +
881A LEU* 3.6 31.6 - - + -
888A LYS* 4.5 7.3 - - + +
891A LEU* 4.1 12.4 - - + +
892A VAL* 6.1 1.0 - - - +
895A ASN* 4.8 11.3 + - - +
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Residues in contact with LYS 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785A ARG* 3.2 22.9 + - - -
787A HIS* 3.1 12.0 - - + +
831A MET* 3.2 28.7 + - - +
832A VAL* 3.0 11.0 + - - +
834A ALA* 1.3 77.2 - - - +
836A GLY* 1.3 57.2 + - - +
891A LEU* 4.1 25.1 - - + -
894A ARG* 4.6 4.0 - - - +
895A ASN* 5.6 3.5 - - - +
965A GLY 5.3 0.2 - - - -
966A MET* 2.7 54.7 + - + +
968A ASN* 2.9 21.2 + - - +
969A THR* 4.4 4.7 - - + -
1004A FLC 2.7 29.7 + - - -
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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