Contacts of the helix formed by residues 819 - 835 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 4.5 2.7 - - - -
615D TRP* 3.6 28.0 - + - -
618D TYR* 4.5 9.0 + + - -
706D PRO* 5.8 1.1 - - + +
707D VAL* 4.3 12.4 + - + -
709D PRO* 3.5 36.4 - - + +
713D TRP* 3.5 46.9 - + + -
717D MET* 3.9 22.0 - - + -
815D MET* 2.9 21.5 + - - +
817D ASN 3.9 0.6 - - - -
818D GLU* 1.3 76.5 - - - +
820D PRO* 1.3 77.8 - - + +
821D PHE* 3.6 40.2 - + + +
822D PHE* 3.1 16.4 + - + -
823D ARG* 3.0 20.4 + - - +
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Residues in contact with PRO 820 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 4.1 27.1 - - + -
654D LEU* 4.5 12.8 - - + -
657D LEU* 5.1 1.1 - - + +
658D SER* 3.4 25.1 - - - +
706D PRO* 3.9 19.1 - - + -
707D VAL* 3.9 10.1 - - + -
818D GLU 3.5 9.6 - - - +
819D TRP* 1.3 92.3 - - + +
821D PHE* 1.3 61.5 + - - +
823D ARG* 3.3 7.4 + - + +
824D VAL* 2.9 28.9 + - - +
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Residues in contact with PHE 821 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614D ALA* 3.6 37.7 - - + -
615D TRP* 4.0 17.5 - + - -
618D TYR* 3.8 30.3 - + + -
658D SER* 3.7 17.0 + - - +
717D MET* 4.0 16.6 - - + -
819D TRP* 3.2 46.6 + + + +
820D PRO* 1.3 78.7 - - - +
822D PHE* 1.3 69.3 + + - +
824D VAL* 3.5 1.8 + - - +
825D THR* 3.0 48.6 + - + -
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Residues in contact with PHE 822 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611D LEU* 5.4 5.4 - - + -
717D MET* 4.1 24.0 - - + -
720D MET* 5.5 0.9 - - - -
798D PHE* 4.3 19.5 - + - -
812D LEU* 3.8 17.5 - - + -
815D MET* 3.5 36.8 - - + +
816D TYR* 3.5 24.5 - - + -
819D TRP* 3.1 25.6 + + + +
821D PHE* 1.3 84.6 - + - +
823D ARG* 1.3 65.5 + - - +
825D THR* 3.6 3.8 + - - -
826D LEU* 3.2 54.5 + - + +
874D ILE* 4.4 4.5 - - + -
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Residues in contact with ARG 823 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 4.1 16.4 - - + -
132D ALA* 3.6 24.2 - - - +
654D LEU* 4.3 15.5 - - + -
816D TYR* 3.1 74.9 + - - +
817D ASN* 4.1 14.5 + - - +
819D TRP 3.0 11.0 + - - +
820D PRO* 3.3 12.1 + - + +
822D PHE* 1.3 79.3 - - - +
824D VAL* 1.3 56.6 + - - +
826D LEU* 3.3 1.4 + - - +
827D ASP* 2.9 49.3 + - - +
877D HIS* 5.7 2.2 + - - -
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Residues in contact with VAL 824 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644D THR* 3.4 34.9 - - + +
647D ARG* 4.6 4.4 + - - +
651D PRO* 5.0 1.8 - - + +
654D LEU* 3.5 38.1 - - + +
655D ALA* 3.8 23.8 - - + +
658D SER* 4.3 5.4 - - - +
820D PRO 2.9 16.0 + - - +
821D PHE 4.2 2.5 - - - +
823D ARG* 1.3 77.2 - - - +
825D THR* 1.3 65.6 + - - +
827D ASP* 3.3 8.0 + - - +
828D LEU* 3.2 22.3 + - - +
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Residues in contact with THR 825 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D ARG* 5.7 7.0 - - + +
611D LEU* 5.6 10.3 - - + -
614D ALA* 4.1 22.4 - - + +
644D THR* 4.6 10.3 - - + +
821D PHE* 3.0 37.4 + - + -
822D PHE* 4.1 6.3 - - - -
823D ARG 3.3 0.2 - - - -
824D VAL* 1.3 81.2 - - - +
826D LEU* 1.3 67.8 + - + +
828D LEU* 3.6 5.9 + - + +
829D LEU* 3.5 25.1 + - + +
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Residues in contact with LEU 826 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611D LEU* 5.6 3.8 - - + -
794D VAL* 5.2 0.4 - - + -
798D PHE* 3.9 25.4 - - + -
816D TYR* 3.9 25.1 - - + -
822D PHE* 3.2 49.2 + - + +
823D ARG 3.9 2.5 - - - +
825D THR* 1.3 81.7 - - + +
827D ASP* 1.3 61.5 + - - +
828D LEU 3.2 0.2 - - - -
829D LEU* 3.1 27.2 + - + +
830D GLU* 2.9 30.0 + - - +
871D LEU* 4.1 18.4 - - + +
874D ILE* 4.5 9.9 - - + -
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Residues in contact with ASP 827 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D GLY* 5.9 1.9 - - - -
647D ARG* 3.9 14.1 + - - +
654D LEU* 4.7 6.8 - - - +
816D TYR* 3.2 23.9 + - - -
823D ARG* 2.9 41.3 + - - +
824D VAL* 3.3 9.4 + - - +
826D LEU* 1.3 77.4 - - - +
828D LEU* 1.3 62.7 + - - +
830D GLU* 3.4 11.1 + - - +
831D MET* 3.0 23.7 + - - +
877D HIS* 5.5 0.2 - - - -
881D LEU* 5.1 2.5 - - - +
884D ASP* 6.0 2.0 - - - -
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Residues in contact with LEU 828 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D ARG* 3.7 25.4 - - + +
642D GLY 4.3 2.9 - - - +
643D GLY 4.7 1.3 - - - +
644D THR* 3.6 33.4 - - + -
647D ARG* 3.7 25.2 - - + +
790D VAL* 3.8 26.5 - - + -
824D VAL 3.2 12.9 + - - +
825D THR 3.7 8.7 - - - +
826D LEU 3.2 0.2 - - - -
827D ASP* 1.3 76.8 - - - +
829D LEU* 1.3 61.3 + - + +
831D MET* 3.2 7.0 + - + +
832D VAL* 2.9 40.9 + - + +
969D THR 3.9 12.6 - - - +
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Residues in contact with LEU 829 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D ARG* 4.9 5.6 - - + -
611D LEU* 5.9 1.3 - - + -
790D VAL* 3.2 44.9 - - + +
791D TRP* 4.1 9.9 - - + -
794D VAL* 4.2 26.7 - - + -
825D THR* 3.5 14.3 + - + +
826D LEU* 3.1 32.4 + - + +
828D LEU* 1.3 82.2 - - + +
830D GLU* 1.3 57.9 + - - +
832D VAL* 3.2 5.0 + - - +
833D PHE* 2.9 36.1 + - + -
867D THR* 6.0 0.4 - - + -
871D LEU* 3.5 17.9 - - + -
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Residues in contact with GLU 830 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816D TYR* 3.9 8.7 + - - -
826D LEU 2.9 15.1 + - - +
827D ASP* 3.7 11.7 - - - +
828D LEU 3.2 0.2 - - - -
829D LEU* 1.3 73.4 - - - +
831D MET* 1.3 64.0 - - - +
833D PHE* 3.1 2.2 + - - +
834D ALA* 3.0 19.4 + - - +
871D LEU* 4.1 17.8 - - + +
872D LEU* 4.0 9.9 - - - +
875D ALA* 4.6 1.7 - - - +
877D HIS* 2.8 38.8 + - - -
880D ILE* 3.6 21.6 - - + +
881D LEU* 2.8 41.0 + - + +
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Residues in contact with MET 831 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647D ARG* 3.6 33.7 - - - +
827D ASP 3.0 13.3 + - - +
828D LEU* 3.2 9.6 + - + +
830D GLU* 1.3 74.9 - - - +
832D VAL* 1.3 77.4 + - + +
834D ALA* 3.1 6.9 + - - +
835D LYS* 3.1 55.3 + - - +
881D LEU* 4.3 9.5 - - + +
887D LEU* 4.2 17.5 - - + -
891D LEU* 4.5 8.7 - - + -
968D ASN* 3.6 34.1 - - - +
969D THR 4.7 4.0 - - - +
1001D PG0 4.3 7.0 - - - +
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Residues in contact with VAL 832 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787D HIS* 3.7 37.5 + - + +
790D VAL* 4.1 21.8 - - + -
791D TRP* 5.4 3.4 - - + -
828D LEU* 2.9 37.8 + - + +
829D LEU 3.8 4.9 - - - +
831D MET* 1.3 90.7 - - - +
833D PHE* 1.3 54.7 + - + +
835D LYS* 2.4 31.3 - - - +
864D TYR* 6.1 0.2 - - - -
969D THR* 4.0 20.6 - - - +
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Residues in contact with PHE 833 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791D TRP* 3.7 36.6 - + + -
829D LEU* 2.9 28.5 + - + +
830D GLU* 3.1 5.8 + - - +
832D VAL* 1.3 78.4 - - + +
834D ALA* 1.3 65.8 + - - +
835D LYS 3.2 6.4 + - - -
836D GLY 3.7 10.0 - - - +
864D TYR* 3.6 47.1 + + - -
867D THR* 3.9 9.4 - - + -
868D GLN* 3.5 47.9 - - + +
871D LEU* 3.5 28.5 - - + -
880D ILE* 3.6 17.3 - - + -
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Residues in contact with ALA 834 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785D ARG* 5.5 0.2 + - - -
830D GLU 3.0 9.7 + - - +
831D MET 3.1 9.2 + - - +
833D PHE* 1.3 76.1 - - - +
835D LYS* 1.3 58.8 + - - +
836D GLY 3.6 5.4 + - - +
880D ILE* 3.9 24.7 - - + +
881D LEU* 3.6 27.8 - - + -
888D LYS* 5.8 2.5 - - + -
891D LEU* 4.3 12.7 - - + +
895D ASN* 4.9 10.2 + - - +
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Residues in contact with LYS 835 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785D ARG* 5.1 1.8 - - - +
787D HIS* 2.7 14.8 + - + -
831D MET* 3.1 38.2 + - - +
832D VAL* 2.4 25.3 - - - +
833D PHE 3.6 0.7 - - - -
834D ALA* 1.3 73.9 - - - +
836D GLY* 1.3 58.5 + - - +
891D LEU* 3.7 28.0 - - + -
895D ASN* 5.7 2.0 - - - -
965D GLY 4.8 3.3 + - - +
966D MET* 2.5 56.1 + - + +
968D ASN 3.2 14.8 + - - +
969D THR* 4.2 8.1 - - + -
1001D PG0 3.0 27.1 + - - -
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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