Contacts of the helix formed by residues 840 - 847 (chain B) in PDB entry 4Q0R
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 ALA 840 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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817B PHE* 4.7 5.3 - - + -
821B GLY 4.8 3.8 - - - +
822B THR* 3.5 35.2 + - + +
839B ASP* 1.3 75.5 - - - +
841B GLU* 1.3 58.3 + - - +
843B ILE* 3.6 11.0 + - - +
844B LEU* 3.2 26.5 + - - +
849B LEU 4.8 0.9 - - - +
854B MSE 5.4 10.7 - - + +
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Residues in contact with GLU 841 (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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839B ASP* 3.2 12.6 - - - +
840B ALA* 1.3 78.3 - - - +
842B SER* 1.3 61.8 + - - +
844B LEU* 3.9 7.7 + - + +
845B LYS* 3.3 22.5 + - + +
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Residues in contact with SER 842 (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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13B THR* 4.3 22.2 - - - -
15B ARG* 3.3 21.0 + - - -
839B ASP* 2.4 30.0 + - - -
841B GLU* 1.3 76.3 - - - +
843B ILE* 1.3 61.6 + - - +
845B LYS* 4.4 3.4 - - - +
846B LEU* 2.9 46.0 + - - +
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Residues in contact with ILE 843 (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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6B PHE* 4.9 3.1 - - + -
10B ALA* 4.1 21.3 - - + -
13B THR* 3.7 24.5 - - + +
817B PHE* 3.9 30.1 - - + -
838B TYR* 5.3 2.7 - - + -
839B ASP 3.5 15.7 + - - +
840B ALA* 3.8 8.7 - - - +
841B GLU 3.4 0.4 - - - -
842B SER* 1.3 78.5 - - - +
844B LEU* 1.3 55.8 + - - +
847B LEU* 2.9 43.1 + - + +
848B GLY 3.3 1.9 + - - -
849B LEU* 3.5 30.2 + - + +
854B MSE 4.4 17.7 - - + -
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Residues in contact with LEU 844 (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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840B ALA 3.2 15.9 + - - +
841B GLU* 4.3 7.4 - - + +
842B SER 3.3 0.4 - - - -
843B ILE* 1.3 74.2 - - - +
845B LYS* 1.3 67.9 + - + +
848B GLY* 3.3 36.3 - - - +
849B LEU 3.3 19.2 + - - +
850B ASP* 3.8 18.4 - - + +
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Residues in contact with LYS 845 (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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841B GLU* 3.3 17.7 + - + +
842B SER* 3.3 5.6 + - - +
844B LEU* 1.3 84.1 - - + +
846B LEU* 1.3 69.5 + - + +
848B GLY 4.6 0.9 + - - -
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Residues in contact with LEU 846 (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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833A ASN* 6.4 0.4 - - - +
12B PRO 5.1 2.7 - - - +
13B THR* 3.6 34.5 - - + +
842B SER* 2.9 22.1 + - - +
845B LYS* 1.3 87.2 - - + +
847B LEU* 1.3 64.6 + - + +
848B GLY 3.6 0.4 - - - -
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Residues in contact with LEU 847 (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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9B ILE* 3.3 42.4 - - + +
10B ALA* 4.1 9.2 - - - -
12B PRO* 5.4 8.7 - - + -
13B THR* 3.9 22.9 - - + -
843B ILE* 2.9 21.4 + - + +
846B LEU* 1.3 86.0 - - + +
848B GLY* 1.3 57.6 + - - +
849B LEU* 3.1 27.7 + - + +
878B ILE* 5.2 6.4 - - + +
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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