Contacts of the helix formed by residues 843 - 848 (chain N) 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 GLN 843 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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841N MET 3.2 2.2 + - - -
842N ASN* 1.3 62.9 - - - +
844N SER* 1.3 59.8 - - - +
845N SER 3.0 1.6 - - - -
846N ILE* 2.7 40.5 + - - +
847N ASP* 2.8 34.1 + - - +
973N ILE* 5.7 1.2 - - - +
974N PRO 5.4 1.5 + - - +
993N THR* 2.8 36.6 + - - +
994N TYR 2.4 37.0 + - - +
995N ARG* 3.8 11.7 - - + +
6W ARG* 3.4 27.7 - - - +
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Residues in contact with SER 844 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842N ASN* 3.6 9.1 + - - -
843N GLN* 1.3 76.1 - - - +
845N SER* 1.3 62.3 + - - +
847N ASP* 3.2 6.9 + - - +
848N ARG* 3.0 55.9 + - - +
995N ARG* 3.4 10.7 - - - +
996N ARG* 2.8 33.4 + - - +
997N GLU* 4.7 0.5 + - - -
168O ALA* 3.8 11.8 - - - +
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Residues in contact with SER 845 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842N ASN* 2.3 44.3 + - - +
843N GLN 3.0 0.4 - - - -
844N SER* 1.3 77.6 - - - +
846N ILE* 1.3 55.7 + - - +
847N ASP 3.1 0.7 + - - -
848N ARG* 3.2 10.4 + - - +
849N GLY 3.2 0.3 + - - -
850N LEU* 2.8 43.6 + - - +
1009N ASP* 2.6 28.3 + - - -
8V PHE* 3.4 16.6 + - - +
9V SER* 4.1 0.2 - - - -
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Residues in contact with ILE 846 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841N MET* 3.7 32.1 - - + -
842N ASN 3.2 17.7 + - - +
843N GLN* 2.7 26.0 + - - +
845N SER* 1.3 73.3 - - - +
847N ASP* 1.3 61.1 + - - +
849N GLY* 3.3 9.2 + - - -
850N LEU* 3.8 11.6 + - + +
852N ARG* 3.5 14.6 + - - -
973N ILE* 3.4 20.6 - - + -
974N PRO* 3.4 38.8 - - + +
990N ILE* 5.0 0.4 - - + -
993N THR* 4.0 20.9 - - + -
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Residues in contact with ASP 847 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843N GLN* 2.8 34.8 + - - +
844N SER* 3.3 10.3 - - - +
846N ILE* 1.3 76.2 - - - +
848N ARG* 1.3 52.1 + - - +
849N GLY 2.5 15.6 + - - -
852N ARG* 3.5 6.3 + - - +
995N ARG* 5.6 0.2 - - - +
65O HIS* 2.8 26.2 - - - -
69O LEU* 5.8 0.2 - - - -
167O HIS* 3.0 37.4 + - + +
168O ALA* 3.1 17.2 + - + +
169O LYS 6.1 0.2 - - - -
6W ARG* 2.3 27.2 + - - -
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Residues in contact with ARG 848 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798N TYR* 5.0 3.1 - - - -
844N SER* 3.0 40.3 + - - +
845N SER 3.2 6.0 + - - +
847N ASP* 1.3 75.1 - - - +
849N GLY* 1.3 56.2 + - - +
850N LEU 3.6 0.4 - - - -
996N ARG* 3.4 23.0 - - - +
38O ILE* 5.9 0.4 - - - +
65O HIS* 3.7 5.8 + - - -
69O LEU* 3.7 27.5 - - + +
168O ALA* 3.8 21.8 + - + +
169O LYS* 5.7 0.9 - - - +
5V VAL 4.7 0.7 - - - +
6V ARG* 4.5 11.9 - - + +
7V CYS 3.2 20.0 - - - +
8V PHE* 2.5 56.1 + - + +
9V SER 3.0 18.4 + - - -
10V CYS 4.1 0.4 - - - -
11V GLY* 3.4 20.4 - - - -
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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