Contacts of the helix formed by residues 843 - 848 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841B MET 3.3 1.2 + - - -
842B ASN* 1.3 63.7 - - - +
844B SER* 1.3 59.9 + - - +
845B SER 2.9 1.8 - - - -
846B ILE* 2.6 43.2 + - - +
847B ASP* 2.8 32.9 + - - +
973B ILE* 5.7 1.2 - - - +
974B PRO 5.4 0.9 + - - +
993B THR* 2.8 36.1 + - - +
994B TYR 2.4 37.0 + - - +
995B ARG* 3.8 10.5 - - + +
6K ARG* 3.2 32.2 - - - +
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Residues in contact with SER 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B ASN* 3.4 10.8 - - - -
843B GLN* 1.3 78.0 - - - +
845B SER* 1.3 56.7 + - - +
847B ASP* 3.3 7.3 - - - +
848B ARG* 3.0 61.9 + - - +
994B TYR 4.1 0.2 + - - -
995B ARG* 3.5 11.4 - - - +
996B ARG* 3.1 26.9 + - - +
997B GLU* 4.6 1.4 + - - -
168C ALA* 3.8 11.9 - - - +
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Residues in contact with SER 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B ASN* 2.4 43.7 + - - +
843B GLN 2.9 0.2 - - - -
844B SER* 1.3 72.4 - - - +
846B ILE* 1.3 58.4 + - - +
847B ASP 3.1 0.7 + - - -
848B ARG* 3.2 9.4 + - - +
849B GLY 3.2 0.3 + - - -
850B LEU* 2.7 46.1 + - - +
1009B ASP* 2.8 27.5 + - - -
8J PHE* 3.4 18.8 + - - -
9J SER* 4.1 0.7 - - - -
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Residues in contact with ILE 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B MET* 3.8 28.0 - - + -
842B ASN 3.1 15.7 - - - +
843B GLN* 2.6 37.3 + - - +
845B SER* 1.3 74.1 - - - +
847B ASP* 1.3 59.0 - - - +
849B GLY* 3.3 13.0 + - - -
850B LEU* 3.8 10.5 + - + +
852B ARG* 3.5 11.1 + - - +
973B ILE* 3.5 20.0 - - + -
974B PRO* 3.2 43.5 - - + +
990B ILE* 4.9 0.9 - - + -
993B THR* 4.1 12.8 - - + -
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Residues in contact with ASP 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843B GLN* 2.8 35.8 + - - -
844B SER* 3.3 10.1 - - - +
846B ILE* 1.3 75.0 - - - +
848B ARG* 1.3 51.2 + - - +
849B GLY 2.5 15.9 + - - -
852B ARG* 3.4 6.7 + - - +
995B ARG* 5.6 0.7 - - - +
65C HIS* 2.8 26.0 - - - -
167C HIS* 2.9 39.0 + - + +
168C ALA* 3.0 17.9 + - + +
169C LYS 6.2 0.2 - - - -
6K ARG* 2.6 25.4 + - - -
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Residues in contact with ARG 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B TYR* 5.3 3.1 - - - -
844B SER* 3.0 37.9 + - - +
845B SER 3.2 6.0 + - - +
847B ASP* 1.3 75.5 - - - +
849B GLY* 1.3 55.1 - - - +
850B LEU 3.6 0.2 - - - -
996B ARG* 3.3 30.2 - - - +
38C ILE* 5.7 1.6 - - - +
65C HIS* 3.7 6.4 + - - -
69C LEU* 3.5 28.3 - - + +
168C ALA* 3.8 22.1 + - + +
169C LYS* 5.6 1.1 - - - +
5J VAL 4.7 1.2 - - - +
6J ARG* 4.6 10.7 - - + +
7J CYS 3.2 20.6 - - - +
8J PHE* 2.8 54.9 + - + +
9J SER 3.1 17.2 + - - -
10J CYS 4.2 0.2 + - - -
11J GLY* 3.5 19.4 - - - -
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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