Contacts of the helix formed by residues 862 - 868 (chain A) in PDB entry 5HG1
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 GLY 862 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677A ILE* 4.5 0.2 - - - -
678A VAL 3.2 16.1 - - - +
679A GLY* 4.2 0.2 - - - -
861A ASP* 1.3 92.3 + - - +
863A THR* 1.3 66.3 + - - -
865A TYR* 3.2 11.3 + - - +
866A LYS* 3.4 16.5 + - - +
1003A BG6 3.2 21.9 + - - -
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Residues in contact with THR 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A THR* 5.2 10.3 - - + +
678A VAL 3.7 0.4 + - - -
679A GLY* 4.4 3.6 - - - -
680A THR* 4.8 1.4 + - - -
862A GLY* 1.3 71.9 - - - -
864A LEU* 1.3 64.4 + - - +
865A TYR 3.3 0.2 + - - -
866A LYS* 3.3 10.6 + - + -
867A LEU* 2.9 44.1 + - + +
1003A BG6 2.8 25.2 + - - +
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Residues in contact with LEU 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678A VAL* 3.6 20.1 + - + +
679A GLY* 4.3 6.2 - - - +
745A ILE 4.0 3.1 - - - +
746A SER* 4.2 6.5 - - - -
747A GLY 4.9 0.9 - - - +
750A LEU* 3.5 31.0 - - + -
784A THR* 4.0 24.5 - - + +
787A LEU* 6.0 0.9 - - + -
788A SER* 4.4 6.3 - - - +
827A ALA* 6.3 0.4 - - + -
862A GLY 3.4 0.8 - - - -
863A THR* 1.3 81.4 + - - +
865A TYR* 1.3 63.1 + - - +
867A LEU* 5.5 0.2 - - - -
868A HIS* 3.2 46.9 + - + +
871A PHE* 3.8 26.8 - - + -
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Residues in contact with TYR 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678A VAL* 3.4 21.1 + - + +
860A VAL* 3.2 44.9 - - + -
861A ASP* 4.3 2.9 - - - +
862A GLY 3.2 8.4 + - - +
863A THR 3.2 0.8 - - - -
864A LEU* 1.3 81.7 - - - +
866A LYS* 1.3 66.4 + - + +
868A HIS* 4.1 8.8 + - - +
871A PHE* 4.3 18.6 - + - -
872A ALA* 3.5 42.2 + - + +
875A MET* 4.6 10.8 - - - -
876A HIS* 2.9 30.3 + - - -
890A PHE* 3.5 13.5 - - - +
891A LEU 5.3 0.3 + - - -
892A GLN* 4.0 26.6 - - + +
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Residues in contact with LYS 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861A ASP* 3.2 31.2 + - - +
862A GLY 3.4 16.2 - - - +
863A THR* 3.6 11.9 - - + +
865A TYR* 1.3 82.9 - - + +
867A LEU* 1.3 77.1 + - + +
868A HIS 4.7 2.2 - - - +
892A GLN* 2.9 51.9 + - - +
893A SER 5.3 0.2 - - - +
894A GLU* 4.9 13.1 - - - +
1003A BG6 5.1 3.2 + - - -
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Residues in contact with LEU 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788A SER* 3.8 16.5 - - - +
792A SER* 5.2 1.2 + - - -
863A THR* 2.9 33.6 + - + +
864A LEU* 5.5 0.4 - - - -
866A LYS* 1.3 94.8 - - + +
868A HIS* 1.3 65.0 + - - +
869A PRO* 3.6 3.1 - - - +
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Residues in contact with HIS 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787A LEU* 4.2 8.4 + - + -
788A SER* 3.4 28.4 + - - +
791A GLU* 3.4 26.3 + - - -
827A ALA* 3.4 30.5 - - + +
864A LEU* 3.2 35.6 + - + +
865A TYR 4.1 7.0 + - - +
866A LYS 3.5 2.5 - - - +
867A LEU* 1.3 80.6 - - - +
869A PRO* 1.3 74.9 - - + +
870A HIS* 3.0 30.7 + - + -
871A PHE* 3.1 25.9 + - + +
872A ALA* 5.1 1.7 + - - +
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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