Contacts of the helix formed by residues 860 - 871 (chain C) in PDB entry 2HEN
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 860 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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728C VAL* 3.9 26.5 - - + -
828C MET* 4.3 2.5 - - + -
858C ASP 3.7 8.3 - - - +
859C CYS* 1.3 85.9 - - - +
861C SER* 1.3 67.1 + - - +
862C ALA 3.0 3.6 - - - +
863C LEU* 2.9 41.8 + - + -
864C HIS* 3.2 8.7 + - - +
898C LEU* 3.1 37.2 - - + +
900C ALA 3.6 8.1 - - - +
901C MET* 4.3 8.5 - - - -
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Residues in contact with SER 861 (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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855C PRO* 6.1 2.2 - - - -
859C CYS 3.4 4.5 + - - -
860C PRO* 1.3 71.0 - - - +
862C ALA* 1.3 57.1 + - - +
864C HIS* 3.3 9.4 + - - +
865C GLN* 2.9 29.9 + - - +
900C ALA* 3.0 26.2 + - - +
901C MET 3.7 18.2 + - - -
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Residues in contact with ALA 862 (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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860C PRO* 2.9 2.1 + - + +
861C SER* 1.3 82.8 + - - +
863C LEU* 1.3 61.7 + - - +
865C GLN* 3.3 9.2 + - - +
866C LEU* 3.2 19.2 + - - +
891C MET* 4.0 20.1 - - + +
897C SER* 3.7 24.9 - - - +
898C LEU* 4.6 6.3 - - + -
900C ALA* 4.3 1.1 + - + +
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Residues in contact with LEU 863 (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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728C VAL* 4.2 2.9 - - + -
732C VAL* 3.9 24.0 - - + -
735C LEU* 5.3 6.7 - - + -
824C MET* 4.4 4.6 - - - +
828C MET* 3.7 34.1 - - + -
859C CYS* 3.9 7.4 - - - -
860C PRO* 2.9 24.4 + - + +
862C ALA* 1.3 75.8 - - - +
864C HIS* 1.3 63.3 + - - +
866C LEU* 3.1 18.2 + - + +
867C MET* 3.1 19.6 + - + +
888C LEU* 4.4 9.6 - - + -
891C MET* 3.0 38.6 - - + -
898C LEU* 3.8 9.0 - - + -
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Residues in contact with HIS 864 (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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853C LEU 2.8 28.1 + - - -
854C PRO* 3.5 5.1 - - + -
855C PRO* 3.4 47.4 - - + +
859C CYS* 4.4 1.1 - - - -
860C PRO 3.2 10.7 + - - +
861C SER* 3.7 10.3 + - - +
863C LEU* 1.3 76.6 - - - +
865C GLN* 1.3 58.1 + - - +
867C MET* 3.0 31.4 + - + +
868C LEU* 2.9 55.9 + - + +
871C TRP* 4.6 0.6 - + - -
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Residues in contact with GLN 865 (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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861C SER 2.9 17.0 + - - +
862C ALA* 3.5 9.4 - - - +
863C LEU 3.2 0.4 - - - -
864C HIS* 1.3 76.6 + - - +
866C LEU* 1.3 63.1 + - - +
868C LEU* 3.3 24.7 + - - +
869C ASP* 2.9 58.1 + - - +
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Residues in contact with LEU 866 (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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824C MET* 3.8 15.0 - - + -
862C ALA 3.2 10.9 + - - +
863C LEU* 3.1 14.4 + - + +
865C GLN* 1.3 73.2 - - - +
867C MET* 1.3 66.0 + - - +
869C ASP* 3.2 14.6 + - + +
870C CYS* 3.0 34.5 + - - -
879C PRO* 5.0 4.3 - - + -
884C ILE* 4.3 24.7 - - + -
887C THR* 4.0 29.4 - - + +
888C LEU* 4.1 28.3 - - + -
891C MET* 4.5 4.7 - - + -
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Residues in contact with MET 867 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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821C GLY 4.1 1.3 - - - +
824C MET* 3.5 30.5 - - + +
825C TRP* 4.0 21.1 - - - -
828C MET* 4.3 13.9 - - + -
856C PRO* 4.1 8.5 - - + -
859C CYS* 3.5 23.8 - - - -
863C LEU* 3.1 8.2 + - + +
864C HIS* 3.0 38.5 + - + +
866C LEU* 1.3 76.5 - - - +
868C LEU* 1.3 58.6 + - - +
870C CYS* 2.8 22.2 + - - +
871C TRP* 2.9 48.9 + - + -
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Residues in contact with LEU 868 (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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852C ARG* 3.8 34.6 + - + -
864C HIS* 2.9 47.7 + - + +
865C GLN* 3.3 30.0 + - - +
867C MET* 1.3 75.5 - - - +
869C ASP* 1.3 62.1 + - - +
871C TRP* 3.2 26.7 + - + +
872C GLN* 3.6 6.8 + - - +
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Residues in contact with ASP 869 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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865C GLN* 2.9 46.5 + - - +
866C LEU* 3.5 17.0 - - + +
868C LEU* 1.3 74.2 - - - +
870C CYS* 1.3 65.1 + - - +
871C TRP 3.3 0.3 + - - -
872C GLN* 3.2 35.2 + - - +
878C ARG* 3.8 1.4 - - - +
879C PRO* 3.5 25.2 - - + +
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Residues in contact with CYS 870 (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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817C VAL* 3.2 41.1 - - - +
818C TRP* 3.5 10.7 - - - -
820C TYR* 4.1 0.9 - - - -
821C GLY* 3.7 10.3 - - - -
824C MET* 3.3 29.2 - - - -
866C LEU* 3.0 18.5 + - - -
867C MET 2.8 8.3 + - - +
869C ASP* 1.3 77.5 - - - +
871C TRP* 1.3 59.4 + - - +
872C GLN 3.3 0.4 - - - -
878C ARG* 3.3 23.7 + - - -
879C PRO* 4.4 2.7 - - - -
884C ILE* 4.0 12.1 - - - -
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Residues in contact with TRP 871 (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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818C TRP* 3.4 43.1 - + + -
821C GLY* 3.1 27.3 - - - -
822C ILE* 3.2 39.0 - - + +
825C TRP* 4.1 7.9 - + + -
835C TYR* 5.6 2.0 - - - -
852C ARG* 2.8 52.8 + - - +
853C LEU* 3.7 43.5 - - + -
864C HIS* 4.6 1.6 - - - -
867C MET* 2.9 44.3 + - + +
868C LEU* 3.2 17.9 + - + +
869C ASP 3.1 0.8 - - - -
870C CYS* 1.3 80.7 - - - +
872C GLN* 1.3 58.4 + - - +
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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