Contacts of the helix formed by residues 831 - 846 (chain D) in PDB entry 5YWB
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 SER 831 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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830D LEU* 1.3 74.0 - - - +
832D GLY* 1.3 66.5 + - - +
833D GLY* 3.5 3.5 + - - -
834D GLN* 3.1 44.2 + - - +
835D ARG* 3.2 27.9 + - - +
837D ARG* 5.1 0.5 + - - -
2502D ADP 5.5 15.0 + - - -
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Residues in contact with GLY 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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831D SER* 1.3 80.7 + - - +
833D GLY* 1.3 59.8 + - - +
835D ARG* 3.7 17.8 + - - +
836D GLN* 3.7 17.8 + - - +
859D ALA* 3.9 9.5 - - - +
1427D GLN* 5.6 6.3 - - - -
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Residues in contact with GLY 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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831D SER* 3.5 4.0 + - - -
832D GLY* 1.3 72.5 - - - +
834D GLN* 1.3 60.0 + - - +
836D GLN* 3.3 3.2 + - - +
837D ARG* 2.9 47.2 + - - +
859D ALA* 3.3 30.3 + - - +
860D LEU* 4.5 0.6 - - - +
1427D GLN* 5.8 0.4 - - - +
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Residues in contact with GLN 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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808D LEU* 4.4 3.8 - - + +
811D ASP* 3.0 40.4 + - - +
815D LEU* 4.7 8.6 - - - +
829D ASN 4.8 0.9 - - - +
830D LEU* 3.6 21.4 - - + +
831D SER* 3.1 42.4 + - - +
832D GLY 3.3 0.8 - - - -
833D GLY* 1.3 77.4 - - - +
835D ARG* 1.3 56.8 + - - +
837D ARG* 3.3 22.1 + - - +
838D ILE* 2.9 36.6 + - + +
2502D ADP 5.3 9.1 + - - -
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Residues in contact with ARG 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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777D PRO* 4.2 18.2 - - + +
778D TRP* 6.5 0.2 - - - +
779D LEU* 3.6 28.2 - - + +
826D ARG 3.4 24.2 + - - -
827D GLY 2.4 31.8 + - - -
828D ILE* 4.5 1.4 + - - +
830D LEU* 2.8 31.6 + - + -
831D SER 3.2 21.5 + - - +
832D GLY* 4.2 10.3 + - - +
833D GLY 3.4 0.6 - - - -
834D GLN* 1.3 77.3 - - - +
836D GLN* 1.3 57.0 + - - +
838D ILE* 3.2 6.8 + - - +
839D SER* 2.9 29.1 + - - -
1428D ASP* 4.5 14.3 + - - -
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Residues in contact with GLN 836 (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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775D GLN 5.0 5.2 + - - -
777D PRO* 4.1 23.5 - - + +
832D GLY 3.7 12.9 + - - +
833D GLY 3.3 6.7 + - - +
834D GLN 3.3 0.6 - - - -
835D ARG* 1.3 77.9 - - - +
837D ARG* 1.3 62.8 + - - +
839D SER* 2.8 23.8 + - - -
840D VAL* 2.9 16.3 + - + +
855D ASP 4.1 3.8 + - - +
856D PRO* 4.0 14.0 - - - +
858D SER* 2.5 36.3 + - - -
859D ALA* 3.4 23.6 + - + +
860D LEU* 4.3 9.4 - - + +
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Residues in contact with ARG 837 (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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806D CYS* 3.1 31.7 - - + +
807D SER* 3.3 21.6 + - - -
808D LEU* 3.5 19.0 - - + +
811D ASP* 4.7 9.3 - - - +
831D SER* 5.1 0.4 + - - -
833D GLY* 2.9 28.4 + - - +
834D GLN* 3.6 31.6 - - - +
836D GLN* 1.3 76.5 - - - +
838D ILE* 1.3 58.0 + - - +
840D VAL* 3.4 7.1 + - - +
841D ALA* 2.9 28.9 + - - +
859D ALA 4.9 0.8 + - - -
860D LEU* 4.2 31.1 - - + +
861D ASP* 5.3 0.6 + - - -
864D LEU* 3.3 25.7 - - - +
868D LEU* 5.4 4.7 - - + -
1381D THR* 5.0 8.3 + - - +
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Residues in contact with ILE 838 (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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779D LEU* 3.9 18.2 - - + -
784D VAL* 4.2 17.9 - - + -
787D ASN* 4.4 20.4 - - + -
788D ILE* 4.7 8.0 - - + +
808D LEU* 3.6 22.0 - - + -
812D ILE* 5.0 5.8 - - + -
823D ILE* 4.1 11.7 - - + -
830D LEU* 3.6 30.3 - - + -
834D GLN* 2.9 17.9 + - + +
835D ARG* 3.7 5.6 - - - +
836D GLN 3.2 0.2 - - - -
837D ARG* 1.3 75.2 - - - +
839D SER* 1.3 62.4 + - - +
841D ALA* 3.3 7.8 + - - +
842D ARG* 2.9 28.6 + - - +
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Residues in contact with SER 839 (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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773D ALA* 4.0 14.3 - - - +
774D SER 5.2 2.6 + - - -
777D PRO* 3.7 21.6 - - - +
778D TRP 5.1 2.5 - - - -
779D LEU* 5.4 0.2 - - - -
835D ARG 2.9 14.2 + - - -
836D GLN* 2.8 24.3 + - - -
838D ILE* 1.3 77.9 - - - +
840D VAL* 1.3 58.9 + - - +
842D ARG* 3.2 27.0 + - - +
843D ALA* 3.0 28.9 + - - +
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Residues in contact with VAL 840 (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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773D ALA* 4.5 12.1 - - + -
806D CYS* 4.9 1.8 - - - -
836D GLN* 2.9 19.7 + - + +
837D ARG* 3.8 7.0 - - - +
839D SER* 1.3 86.3 + - - +
841D ALA* 1.3 58.3 + - - +
843D ALA* 3.4 3.0 + - + +
844D LEU* 2.9 40.9 + - + +
853D LEU* 4.3 19.1 - - + -
856D PRO* 3.5 33.4 - - + +
868D LEU* 4.5 28.0 - - + -
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Residues in contact with ALA 841 (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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788D ILE* 4.0 26.0 - - + -
802D VAL* 3.6 9.2 - - + +
803D ILE* 5.6 1.1 - - + -
806D CYS* 3.5 25.3 - - + -
808D LEU* 4.8 2.7 - - + -
837D ARG 2.9 18.3 + - - +
838D ILE* 3.5 7.0 - - - +
840D VAL* 1.3 75.0 - - - +
842D ARG* 1.3 59.0 + - - +
844D LEU* 4.4 0.4 - - - -
845D TYR* 2.9 33.6 + - - +
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Residues in contact with ARG 842 (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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772D TYR 6.0 0.7 - - - -
773D ALA* 6.3 0.8 - - - +
778D TRP* 3.1 33.7 + - - +
779D LEU* 4.1 6.3 - - - +
780D LEU* 4.0 6.6 - - - +
787D ASN* 3.2 48.1 + - - +
788D ILE* 4.2 12.1 - - - +
790D PHE* 3.5 41.8 - - + -
838D ILE* 2.9 11.7 + - - +
839D SER* 3.3 36.8 + - - +
841D ALA* 1.3 77.2 - - - +
843D ALA* 1.3 62.7 + - - +
844D LEU 3.2 0.3 + - - -
845D TYR* 3.4 8.0 + - - +
846D GLN* 3.5 16.3 + - + +
1213D THR* 5.0 6.1 - - - +
1217D PHE* 4.8 14.6 - - + -
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Residues in contact with ALA 843 (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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771D ALA* 3.5 23.7 - - + +
772D TYR* 4.0 13.2 - - - +
773D ALA* 3.8 31.0 - - + +
839D SER 3.0 15.6 + - - +
840D VAL* 4.0 3.4 - - - +
842D ARG* 1.3 78.2 - - - +
844D LEU* 1.3 59.7 + - - +
846D GLN 4.3 4.6 + - - +
851D VAL* 4.1 11.8 - - + +
852D PHE 5.2 1.6 - - - +
853D LEU* 5.3 8.7 - - + -
1217D PHE* 4.8 4.0 - - - -
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Residues in contact with LEU 844 (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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798D ARG* 4.0 9.5 + - - -
802D VAL* 4.6 8.5 - - + +
805D ALA* 5.4 2.0 - - + -
806D CYS* 4.5 18.4 - - - -
840D VAL* 2.9 26.1 + - + +
841D ALA* 3.9 3.8 - - - +
843D ALA* 1.3 78.3 - - - +
845D TYR* 1.3 61.7 + - - +
846D GLN 3.4 3.3 + - - +
851D VAL* 5.8 0.9 - - + -
853D LEU* 6.5 0.4 - - + -
868D LEU* 5.0 4.5 - - + -
872D GLY* 4.1 25.8 - - - +
873D ILE* 6.0 1.8 - - + -
876D LEU* 4.5 20.5 - - + +
877D LEU* 3.5 41.5 - - + -
882D ARG* 5.0 4.0 + - - -
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Residues in contact with TYR 845 (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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788D ILE* 3.1 32.1 - - + +
789D THR* 3.8 27.1 - - + +
792D SER* 4.2 11.4 - - - -
793D PRO 2.9 24.4 + - - -
794D PHE* 3.9 9.7 - - - -
795D ASN* 4.0 7.2 + - - -
798D ARG* 2.9 45.1 + - + +
799D TYR* 3.9 23.7 - + + +
802D VAL* 3.8 31.0 - - + -
841D ALA 2.9 17.8 + - - +
842D ARG 4.0 0.9 - - - +
844D LEU* 1.3 78.3 - - - +
846D GLN* 1.3 64.5 + - + +
847D GLN* 3.7 2.1 + - - +
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Residues in contact with GLN 846 (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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771D ALA* 4.5 9.4 - - + -
788D ILE 5.4 0.2 - - - +
789D THR 2.8 28.9 + - - +
790D PHE* 3.1 22.9 + - + +
792D SER* 3.5 15.5 + - - -
798D ARG* 3.5 0.3 + - - -
842D ARG 3.5 14.5 + - - +
843D ALA 4.6 2.3 - - - +
844D LEU 3.4 4.3 - - - +
845D TYR* 1.3 84.0 - - + +
847D GLN* 1.3 72.9 + - - +
848D THR* 3.6 3.0 + - - +
882D ARG* 2.9 20.8 + - - -
1217D PHE* 3.6 30.6 - - + -
1219D TYR* 3.4 16.9 + - - -
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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
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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