Contacts of the helix formed by residues 830 - 845 (chain B) in PDB entry 2XWU
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 GLU 830 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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787B PRO* 3.9 33.1 - - + +
828B PHE* 3.8 7.4 - - - +
829B PRO* 1.3 92.1 - - - +
831B ALA* 1.3 64.9 + - - +
832B PRO* 3.9 10.5 - - + -
833B THR* 3.4 16.4 + - - +
834B VAL* 3.0 25.3 + - - +
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Residues in contact with ALA 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829B PRO 3.5 4.2 + - - +
830B GLU* 1.3 71.4 - - - +
832B PRO* 1.4 63.5 - - + +
834B VAL* 2.8 3.6 + - - +
835B LYS* 2.8 39.6 + - + +
878B SER* 6.2 1.6 - - - -
880B SER* 6.2 2.0 - - - -
881B LEU* 3.9 30.1 - - + -
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Residues in contact with PRO 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791B ASP* 3.1 22.2 - - + +
830B GLU* 3.4 12.1 - - + -
831B ALA* 1.4 92.3 - - + +
833B THR* 1.3 63.0 - - - +
835B LYS* 3.5 8.4 + - + +
836B ALA* 3.2 18.9 + - - +
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Residues in contact with THR 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787B PRO* 3.1 33.6 + - - +
790B VAL* 3.6 22.0 - - + -
791B ASP* 3.9 10.7 - - - +
794B MET* 4.7 1.4 - - - +
825B ALA* 4.4 3.3 - - + +
828B PHE* 3.5 34.1 - - + -
830B GLU* 3.4 16.1 + - - +
831B ALA 3.2 0.8 - - - -
832B PRO* 1.3 82.1 - - - +
834B VAL* 1.3 60.5 + - - +
836B ALA* 3.7 2.9 + - - +
837B SER* 3.2 19.6 + - - -
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Residues in contact with VAL 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825B ALA 3.8 11.0 - - - +
826B LEU* 3.6 25.6 - - - +
828B PHE* 3.2 23.3 - - + +
830B GLU 3.0 17.3 - - - +
831B ALA 2.8 7.3 + - - +
833B THR* 1.3 73.0 - - - +
835B LYS* 1.3 66.8 + - - +
836B ALA 3.1 1.8 - - - -
837B SER* 2.8 14.6 + - - -
838B CYS* 2.9 18.7 + - - -
881B LEU* 4.0 22.7 - - + -
885B PHE* 3.7 22.2 - - + -
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Residues in contact with LYS 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831B ALA* 2.8 24.8 + - + +
832B PRO* 3.9 7.4 - - + +
834B VAL* 1.3 72.6 - - - +
836B ALA* 1.3 57.2 + - - +
838B CYS* 3.3 10.1 + - - +
839B GLY* 2.9 26.2 + - - -
881B LEU* 3.8 20.2 - - + -
884B CYS* 3.9 21.7 - - - -
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Residues in contact with ALA 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791B ASP* 3.7 31.6 - - - +
794B MET* 3.4 17.2 - - + +
795B GLN* 4.2 15.1 - - + +
798B ALA* 5.5 0.7 - - - +
832B PRO 3.2 15.2 + - - +
833B THR 3.7 5.4 - - - +
834B VAL 3.1 0.6 - - - -
835B LYS* 1.3 79.3 - - - +
837B SER* 1.3 60.9 + - - +
839B GLY* 3.3 2.7 + - - +
840B PHE* 3.2 16.5 + - - +
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Residues in contact with SER 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B MET* 3.3 22.6 - - - +
822B ALA* 2.5 30.1 + - - -
825B ALA* 3.9 10.5 - - - -
826B LEU* 3.4 15.6 - - - +
833B THR 3.2 11.6 + - - -
834B VAL 2.8 14.9 + - - -
836B ALA* 1.3 72.2 - - - +
838B CYS* 1.3 65.2 + - - -
840B PHE* 3.0 13.7 + - - +
841B PHE* 3.2 15.6 + - - -
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Residues in contact with CYS 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826B LEU* 3.7 15.0 - - - +
834B VAL* 2.9 27.7 + - - -
835B LYS 3.5 7.4 - - - +
837B SER* 1.3 76.8 - - - +
839B GLY* 1.3 57.9 + - - +
841B PHE* 3.2 4.0 + - - +
842B THR* 2.9 32.7 + - - +
884B CYS* 3.7 42.4 - - + +
885B PHE* 4.3 7.9 - - - -
888B ILE* 4.0 22.8 - - + +
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Residues in contact with GLY 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B ALA* 3.9 7.2 - - - +
835B LYS 2.9 15.3 + - - -
836B ALA* 3.7 5.6 - - - -
837B SER 3.1 0.4 - - - -
838B CYS* 1.3 74.3 - - - +
840B PHE* 1.3 63.5 + - - +
842B THR* 3.5 10.1 - - - -
843B GLU* 3.4 25.8 + - - +
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Residues in contact with PHE 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B MET* 3.3 23.1 - - + +
797B LEU* 3.8 25.8 - - + -
798B ALA* 3.9 10.3 - - - +
801B LEU* 3.6 25.3 - - + +
808B PHE* 4.7 4.0 - + - -
818B VAL* 4.0 22.9 - - + -
819B PHE* 4.6 7.2 - - - -
822B ALA* 3.4 31.2 - - + -
836B ALA 3.2 7.3 + - - +
837B SER 3.0 7.5 + - - +
839B GLY* 1.3 76.3 - - - +
841B PHE* 1.3 82.9 + + - +
843B GLU* 3.1 4.7 + - - +
844B LEU* 2.8 49.2 + - + +
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Residues in contact with PHE 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819B PHE* 3.7 21.8 - + - -
822B ALA* 3.3 35.2 - - + -
823B VAL* 3.5 7.6 - - + -
826B LEU* 3.5 23.1 - - + -
837B SER* 3.2 21.5 + - - -
838B CYS 3.2 4.5 + - - +
840B PHE* 1.3 97.9 - + - +
842B THR* 1.3 61.7 + - - +
844B LEU* 3.7 13.0 - - + -
845B LEU* 3.2 32.8 + - + +
865B LEU* 3.5 33.0 - - + -
888B ILE* 3.9 28.0 - - + -
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Residues in contact with THR 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838B CYS* 2.9 17.9 + - - +
839B GLY* 3.5 14.7 - - - +
841B PHE* 1.3 76.2 - - - +
843B GLU* 1.3 70.5 + - + +
846B PRO* 3.0 23.9 - - - +
887B ASP* 3.9 27.4 + - + +
888B ILE* 4.8 2.6 + - - +
891B ALA* 4.7 11.7 - - - +
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Residues in contact with GLU 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B ALA* 4.0 16.2 - - + +
801B LEU* 4.0 19.5 - - + +
802B LYS* 2.9 56.8 + - - +
839B GLY 3.4 12.8 + - - +
840B PHE 3.1 6.6 + - - +
842B THR* 1.3 89.7 - - + +
844B LEU* 1.3 64.8 + - - +
845B LEU 3.4 0.4 - - - -
846B PRO* 3.3 16.2 - - - +
847B ARG* 3.6 17.7 + - - +
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Residues in contact with LEU 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801B LEU* 3.8 19.9 - - + +
808B PHE* 5.2 4.3 - - + -
815B VAL* 6.0 4.0 - - + -
819B PHE* 3.7 35.7 - - + -
840B PHE* 2.8 35.9 + - + +
841B PHE* 3.3 17.7 + - + +
843B GLU* 1.3 77.4 - - - +
845B LEU* 1.3 65.4 + - + +
847B ARG* 3.1 20.3 + - - +
854B VAL* 3.3 39.1 - - + +
857B VAL* 6.4 0.4 - - + -
858B VAL* 4.4 11.0 - - + -
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Residues in contact with LEU 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841B PHE* 3.2 18.1 + - + +
844B LEU* 1.3 75.7 - - + +
846B PRO* 1.3 74.8 - - + +
847B ARG 2.7 6.9 + - - -
848B CYS* 2.7 24.6 + - - +
858B VAL* 3.9 22.7 - - + -
865B LEU* 4.9 6.5 - - + -
888B ILE* 3.9 11.2 - - + +
891B ALA* 3.4 33.9 - - + +
892B LEU* 3.5 38.1 - - + +
895B HIS* 3.9 4.6 - - - +
896B CYS* 3.9 13.9 - - - -
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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