Contacts of the helix formed by residues 938 - 942 (chain B) in PDB entry 1JQO
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 LEU 938 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A TRP* 3.9 25.7 - - + -
334A ARG* 6.2 1.6 - - - +
93B ALA* 3.4 36.1 - - + +
96B ILE* 3.4 37.5 - - + -
97B LEU* 3.7 28.0 - - + -
928B GLU 6.4 2.5 - - - -
936B ALA 2.8 6.1 + - - +
937B GLY* 1.3 75.8 - - - +
939B VAL* 1.3 59.4 + - + +
941B LEU* 3.0 38.5 - - + +
953B ASP* 5.4 3.2 - - - +
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Residues in contact with VAL 939 (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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92B PRO* 3.7 12.1 - - + +
93B ALA* 3.4 40.8 - - + +
96B ILE* 4.9 3.8 - - + -
936B ALA* 2.8 15.0 + - - +
938B LEU* 1.3 70.6 - - + +
940B LYS* 1.3 58.9 + - + +
941B LEU* 2.9 11.3 + - - +
942B ASN* 3.5 16.3 + - - +
949B PRO* 3.8 36.4 - - + +
950B GLY* 3.9 5.4 - - - +
953B ASP* 5.4 4.3 - - - +
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Residues in contact with LYS 940 (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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936B ALA* 3.1 19.2 + - + +
937B GLY* 3.7 27.5 - - - +
938B LEU 3.3 0.6 - - - -
939B VAL* 1.3 75.7 - - + +
941B LEU* 1.3 60.3 + - - +
942B ASN 3.2 9.3 + - - +
943B PRO* 4.5 5.4 - - - +
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Residues in contact with LEU 941 (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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333A TRP* 4.0 49.4 - - + +
368A ASN* 4.1 22.7 - - - +
228B ASP* 4.1 23.1 - - + +
232B ARG* 2.8 29.7 + - - +
937B GLY 3.6 7.9 - - - +
938B LEU* 3.0 31.7 + - + +
939B VAL 2.9 2.0 + - - +
940B LYS* 1.3 79.4 - - - +
942B ASN* 1.3 54.1 + - - +
943B PRO* 3.3 9.5 - - - +
953B ASP* 4.9 7.4 - - - +
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Residues in contact with ASN 942 (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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232B ARG* 3.6 13.6 - - - +
939B VAL 3.5 11.4 + - - +
940B LYS* 4.4 4.0 - - - -
941B LEU* 1.3 77.5 - - - +
943B PRO* 1.3 67.9 - - - +
944B ALA 3.6 10.6 - - - +
945B SER* 3.1 22.5 - - - -
949B PRO 6.0 1.8 - - - +
952B GLU* 3.1 37.2 + - + +
953B ASP* 3.2 23.0 + - - +
956B ILE* 5.1 3.0 - - - +
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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
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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