Contacts of the helix formed by residues 867 - 871 (chain M) in PDB entry 3HOU
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 ILE 867 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853M ASP 6.0 0.2 - - - +
854M ASN* 3.3 8.3 - - + +
865M GLN* 4.0 8.9 - - - +
866M PHE* 1.3 108.8 + - + +
868M TYR* 1.3 57.9 + - - +
869M GLY 3.2 0.3 + - - -
870M GLU* 2.8 25.8 + - - +
871M ASP* 3.6 9.9 - - - +
872M GLY* 3.2 33.7 - - - +
999M VAL* 4.6 8.5 - - + -
1000M LEU* 3.7 41.1 - - + -
1010M ALA* 4.7 5.4 - - + +
1014M ALA* 4.9 6.7 - - + -
168Q TYR* 4.1 15.9 - - + +
208Q TYR* 4.0 12.5 + - + -
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Residues in contact with TYR 868 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850M VAL* 3.5 16.2 - - + -
854M ASN 3.8 7.0 + - - +
856M THR* 3.5 16.5 + - - +
865M GLN* 3.4 12.1 - - - -
867M ILE* 1.3 70.6 - - - +
869M GLY* 1.3 62.9 + - - +
870M GLU 3.1 0.2 + - - -
871M ASP* 3.5 2.3 - - - +
872M GLY* 2.7 33.7 + - - -
873M MET 3.4 11.9 - - - -
874M ASP* 4.7 2.7 - - - -
875M ALA* 4.9 1.4 + - - +
1058M VAL* 3.2 31.0 - - + -
1064M VAL* 3.1 46.9 + - + +
1067M LEU* 4.6 7.8 - - - +
1366M ARG* 3.1 45.8 - - + +
1367M HIS* 4.0 14.5 + - - -
1370M LEU* 4.8 2.9 - - + -
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Residues in contact with GLY 869 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865M GLN* 2.7 20.2 + - - -
868M TYR* 1.3 70.1 - - - +
870M GLU* 1.3 61.1 + - - +
871M ASP* 2.8 9.7 + - - +
1365M TYR* 4.4 3.9 - - - -
1366M ARG* 3.9 33.6 + - - -
204Q THR* 2.8 30.7 + - - +
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Residues in contact with GLU 870 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865M GLN* 4.5 6.1 + - + +
867M ILE* 2.8 18.6 + - - +
869M GLY* 1.3 77.8 - - - +
871M ASP* 1.3 54.4 + - - +
1014M ALA* 4.6 3.5 - - - -
1345M ARG* 3.5 12.5 + - - -
1365M TYR* 2.6 33.3 + - - -
1369M ALA* 4.8 1.2 - - - +
1373M ASP* 4.4 3.8 - - - +
200Q ARG* 3.1 27.5 + - - -
201Q LYS 4.5 0.3 - - - +
202Q SER* 2.8 25.7 + - - +
204Q THR* 3.3 8.1 - - + -
205Q SER* 2.5 29.3 + - - -
208Q TYR* 3.2 39.9 - - + +
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Residues in contact with ASP 871 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867M ILE* 3.6 8.0 - - - +
868M TYR 3.5 0.2 - - - +
869M GLY 2.8 2.0 + - - -
870M GLU* 1.3 82.8 - - - +
872M GLY* 1.3 59.7 + - - +
873M MET* 2.9 46.2 + - + +
878M ILE* 4.6 2.8 - - - +
957M PRO* 4.5 8.0 - - - +
999M VAL* 4.0 11.1 - - - +
1014M ALA* 4.2 11.8 - - - +
1366M ARG* 2.5 26.4 + - - -
204Q THR* 3.0 30.5 + - - +
205Q SER* 3.6 15.0 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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