Contacts of the helix formed by residues 876 - 888 (chain C) in PDB entry 3RMD
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 PHE 876 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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741C VAL* 4.3 8.1 - - + -
744C ALA* 3.6 25.4 - - + -
745C LEU* 3.6 31.0 - - + +
748C CYS* 4.1 13.9 - - - -
763C TYR* 5.0 0.9 - + - -
764C PHE* 3.5 35.4 - + - -
767C PHE* 3.4 34.1 - + + -
768C GLU* 5.0 2.0 - - + -
872C LEU* 2.9 42.5 + - + -
874C LYS 3.7 0.2 - - - -
875C THR* 1.3 75.6 + - - +
877C ILE* 1.3 76.8 + - + +
879C PRO* 3.0 16.2 - - - +
880C LEU* 3.0 16.9 + - + +
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Residues in contact with ILE 877 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764C PHE* 3.5 31.0 - - + -
768C GLU* 4.7 3.8 - - + +
872C LEU* 3.1 27.2 + - + +
873C GLU* 3.5 26.0 - - - +
876C PHE* 1.3 82.7 - - + +
878C LYS* 1.3 70.1 + - - +
880C LEU* 2.8 6.6 + - - -
881C GLU* 2.7 29.0 + - - +
891C TYR* 3.3 33.4 - - + +
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Residues in contact with LYS 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873C GLU* 2.9 36.8 + - + +
874C LYS* 3.7 9.6 - - + +
877C ILE* 1.3 78.3 - - - +
879C PRO* 1.3 68.6 - - + +
881C GLU* 3.3 10.3 + - - +
882C GLY* 3.2 14.4 + - - -
9I G 3.7 34.8 + - - +
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Residues in contact with PRO 879 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707C ARG* 5.6 2.0 + - - +
731C GLU* 3.8 35.2 - - + +
745C LEU* 3.9 12.3 - - + -
874C LYS 3.7 6.7 - - - +
875C THR 3.2 22.0 - - - +
876C PHE* 3.0 20.9 - - - +
878C LYS* 1.3 95.8 - - + +
880C LEU* 1.3 64.2 + - - +
882C GLY* 2.9 11.2 + - - +
883C PHE* 3.1 23.3 + - + -
9I G 5.2 5.2 - - - +
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Residues in contact with LEU 880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745C LEU* 4.0 8.7 - - + +
748C CYS* 3.7 32.1 - - + -
752C MET* 4.9 1.8 - - - -
760C LEU* 4.6 4.7 - - + -
764C PHE* 3.5 36.3 - - + -
876C PHE* 3.0 22.0 + - + +
877C ILE* 2.8 9.5 + - - +
879C PRO* 1.3 70.9 - - - +
881C GLU* 1.3 65.2 + - - +
883C PHE* 2.8 32.9 + - + +
884C THR* 2.9 34.5 + - + -
891C TYR* 4.1 14.6 - - + -
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Residues in contact with GLU 881 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873C GLU* 5.8 0.2 - - - +
877C ILE* 2.7 19.4 + - - +
878C LYS* 3.4 14.3 - - - +
880C LEU* 1.3 72.3 - - - +
882C GLY* 1.3 56.8 + - - +
884C THR* 3.3 7.8 + - - +
885C SER* 2.9 34.3 + - - -
891C TYR* 2.9 35.9 + - + -
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Residues in contact with GLY 882 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703C THR* 3.8 9.8 - - - +
707C ARG* 5.7 4.7 - - - -
878C LYS 3.2 7.2 + - - -
879C PRO* 2.9 9.2 + - - -
880C LEU 2.9 2.0 + - - -
881C GLU* 1.3 76.7 - - - +
883C PHE* 1.3 66.8 + - - +
885C SER* 3.3 13.4 + - - -
886C ALA* 3.6 12.5 + - - +
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Residues in contact with PHE 883 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701C PHE* 3.6 23.2 - + + -
703C THR* 4.1 8.5 - - + -
707C ARG* 4.6 4.7 - - - -
730C LEU* 3.8 31.2 - - + -
731C GLU* 3.5 25.4 - - - -
732C THR* 5.3 0.4 - - + -
745C LEU* 3.8 34.5 - - + -
748C CYS* 5.5 0.7 - - + -
749C ILE* 4.1 25.4 - - + -
752C MET* 3.7 11.5 - - + +
879C PRO 3.1 19.5 - - - -
880C LEU* 2.8 23.8 + - + +
882C GLY* 1.3 73.8 - - - +
884C THR* 1.3 63.1 + - - +
886C ALA* 3.2 5.7 + - - +
887C ALA* 3.1 22.5 + - - +
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Residues in contact with THR 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752C MET* 4.0 12.3 - - + -
760C LEU* 3.5 31.9 - - + -
880C LEU* 2.9 28.2 + - + -
881C GLU* 3.3 12.1 + - - +
883C PHE* 1.3 77.3 - - - +
885C SER* 1.3 60.2 + - - -
887C ALA 3.3 0.5 + - - -
888C LYS 2.7 24.8 + - - -
889C LEU* 2.8 30.4 + - + +
891C TYR* 3.5 18.1 - - + +
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Residues in contact with SER 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881C GLU* 2.9 25.0 + - - -
882C GLY* 3.3 9.0 + - - -
884C THR* 1.3 76.5 + - - +
886C ALA* 1.3 65.8 + - - +
888C LYS* 3.1 20.4 + - - +
889C LEU 4.8 1.6 - - - -
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Residues in contact with ALA 886 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C PRO* 4.3 13.5 - - + -
402C ASN* 3.0 24.8 + - - -
701C PHE* 4.7 2.7 - - + -
702C TRP 3.6 23.8 - - - +
703C THR* 4.0 13.2 - - + +
882C GLY 3.6 10.5 + - - +
883C PHE 3.2 9.1 + - - +
884C THR 3.2 0.2 - - - -
885C SER* 1.3 82.8 + - - +
887C ALA* 1.3 57.4 + - - +
888C LYS* 3.2 14.9 + - - +
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Residues in contact with ALA 887 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C ASN 4.3 0.7 - - - -
403C ARG* 3.3 31.5 + - - +
698C ILE* 3.6 21.5 - - + -
701C PHE* 4.0 7.6 - - + -
752C MET* 3.6 30.5 - - + -
883C PHE 3.1 6.0 + - - +
884C THR 3.9 2.0 - - - +
886C ALA* 1.3 73.8 - - - +
888C LYS* 1.3 74.7 + - - +
889C LEU* 4.1 4.9 - - + -
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Residues in contact with LYS 888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C PRO* 3.4 17.8 + - - +
402C ASN* 3.5 21.3 - - - +
403C ARG* 3.3 21.9 + - - +
884C THR 2.7 8.6 + - - -
885C SER* 3.1 13.0 + - - +
886C ALA* 3.1 18.0 + - - +
887C ALA* 1.3 84.4 - - - +
889C LEU* 1.3 55.7 + - - +
890C ASP* 5.8 0.4 - - - -
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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