Contacts of the helix formed by residues 878 - 888 (chain B) in PDB entry 7JUR
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 PRO 878 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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876B THR 4.5 2.0 - - - +
877B GLN* 1.3 93.9 - - + +
879B ALA* 1.3 67.8 + - - +
880B GLU* 4.6 1.6 - - - +
881B ALA* 3.2 18.8 + - + +
882B ILE* 3.0 20.9 + - - +
230C MET* 4.1 22.7 - - + -
234C ARG* 4.0 24.5 - - - +
402C QOM 3.8 23.3 - - + -
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Residues in contact with ALA 879 (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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824B ILE* 4.4 6.3 - - + -
829B LEU* 3.7 20.9 - - + +
878B PRO* 1.3 73.8 - - - +
880B GLU* 1.3 59.8 + - - +
882B ILE* 3.1 8.7 + - - +
883B ILE* 2.9 33.6 + - - +
222C SER* 3.6 26.4 + - - +
224C VAL* 3.9 19.7 - - + -
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Residues in contact with GLU 880 (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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878B PRO* 3.3 1.6 - - - +
879B ALA* 1.3 77.0 + - - +
881B ALA* 1.3 63.2 + - - +
883B ILE* 3.2 4.6 + - - +
884B TRP* 3.1 20.8 + - - +
223C PHE 5.9 0.9 - - - -
224C VAL* 3.9 32.9 - - + +
227C ARG 5.2 0.5 - - - +
228C SER* 3.1 29.8 + - - -
229C TYR 4.8 0.7 + - - -
230C MET* 3.3 25.2 - - - +
235C LEU* 3.7 18.8 - - + -
314C LEU* 3.3 24.1 - - + +
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Residues in contact with ALA 881 (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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877B GLN* 4.1 4.9 - - + +
878B PRO* 3.2 29.4 + - + +
880B GLU* 1.3 77.8 - - - +
882B ILE* 1.3 57.6 + - - +
885B GLN* 2.9 45.5 + - - +
230C MET* 4.8 0.4 - - - -
234C ARG 3.6 24.2 - - - +
235C LEU* 3.5 19.2 - - - +
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Residues in contact with ILE 882 (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 LEU* 3.8 24.7 - - + -
830B CYS* 4.6 5.6 - - + +
873B PRO 5.2 0.9 - - - +
874B PHE* 3.6 37.5 - - + +
877B GLN* 3.5 25.8 - - + +
878B PRO 3.0 12.7 + - - +
879B ALA* 3.5 10.5 - - - +
881B ALA* 1.3 72.4 - - - +
883B ILE* 1.3 68.8 + - - +
885B GLN* 4.5 4.3 - - - -
886B MET* 2.8 50.5 + - + +
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Residues in contact with ILE 883 (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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824B ILE* 4.2 23.1 - - + -
829B LEU* 3.8 20.2 - - + -
837B ILE* 3.6 25.6 - - + +
840B LEU* 4.9 6.5 - - + -
879B ALA 2.9 19.6 + - - +
880B GLU* 3.2 7.6 + - - +
882B ILE* 1.3 76.8 - - - +
884B TRP* 1.3 58.7 + - - +
887B GLY* 2.7 29.6 + - - -
224C VAL* 4.5 8.1 - - + -
310C ILE* 3.7 26.7 - - + -
311C PHE* 3.9 27.1 - - + +
314C LEU* 4.1 6.7 - - + -
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Residues in contact with TRP 884 (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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880B GLU 3.1 15.1 + - - +
881B ALA 4.1 1.8 - - - +
883B ILE* 1.3 77.9 - - - +
885B GLN* 1.3 67.5 + - - +
888B THR* 3.1 55.6 + - + +
890B MET* 4.3 17.3 - - - -
235C LEU* 3.8 20.4 - - + +
236C GLN* 3.6 31.4 - - + -
311C PHE* 4.0 14.1 - + - -
314C LEU* 3.8 15.9 - - + +
315C ASP* 2.7 51.1 + - - +
318C VAL* 3.5 31.0 - - + +
319C ASN* 4.4 3.6 - - - -
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Residues in contact with GLN 885 (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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874B PHE* 3.2 27.1 - - + -
877B GLN* 3.0 41.4 + - - +
881B ALA* 2.9 22.0 + - - +
882B ILE 4.0 0.4 - - - +
884B TRP* 1.3 88.1 - - + +
886B MET* 1.3 60.1 + - - +
888B THR* 3.7 1.6 + - - -
889B GLY 3.3 3.6 + - - -
890B MET* 2.8 56.1 + - + +
235C LEU 3.5 18.5 - - - +
236C GLN 3.9 13.5 + - - +
237C GLY* 3.6 3.9 + - - -
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Residues in contact with MET 886 (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 LEU 3.4 17.5 - - - +
830B CYS* 3.7 14.1 - - + +
832B LEU 3.2 27.1 - - - +
834B PRO* 3.7 21.4 - - + +
837B ILE* 4.5 12.8 - - + -
858B PHE* 3.8 23.6 - - + -
874B PHE* 3.9 27.1 - - + -
882B ILE* 2.8 39.2 + - + +
883B ILE 4.1 1.1 - - - +
885B GLN* 1.3 74.2 - - - +
887B GLY* 1.3 66.3 + - - +
889B GLY* 3.3 10.7 + - - -
890B MET 4.3 5.6 - - - +
911B TRP* 6.4 0.2 - - + -
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Residues in contact with GLY 887 (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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834B PRO* 4.8 2.2 - - - -
837B ILE* 4.1 6.1 - - - +
838B ARG* 3.1 33.2 + - - -
883B ILE 2.7 17.0 + - - -
886B MET* 1.3 73.5 - - - +
888B THR* 1.3 54.8 + - - +
889B GLY 3.2 0.2 - - - -
913B PHE* 3.2 13.2 - - - -
311C PHE* 3.4 26.9 - - - -
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Residues in contact with THR 888 (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 ARG* 4.6 5.4 - - - +
884B TRP* 3.1 62.0 + - + +
885B GLN 3.8 3.8 + - - -
887B GLY* 1.3 75.5 - - - +
889B GLY* 1.3 59.3 + - - +
890B MET* 4.0 10.7 - - - +
913B PHE* 4.2 5.2 - - - -
311C PHE* 3.6 15.0 - - + -
315C ASP* 3.9 4.3 - - - +
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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