Contacts of the helix formed by residues 752 - 757 (chain B) in PDB entry 3LJ1
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 752 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751B ASN* 1.3 74.0 - - - +
753B GLN* 1.3 57.7 + - - +
755B LEU* 3.2 20.4 + - + +
756B VAL* 2.8 54.0 + - + +
777B LEU* 4.5 3.8 - - + -
781B ILE* 4.4 0.7 - - + -
800B PRO* 3.4 12.5 + - + +
803B ILE* 2.7 35.2 + - + +
804B LEU* 4.5 0.2 - - - +
805B VAL* 4.3 12.3 - - + +
824B ILE* 4.4 8.3 - - + -
909B VAL* 3.7 19.7 - - + -
912B TYR* 4.7 5.2 - - + -
913B ILE* 3.6 35.4 - - + -
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Residues in contact with GLN 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B ASN* 3.0 13.9 + - - +
752B LEU* 1.3 78.7 - - - +
754B ASP* 1.3 56.5 + - - +
757B GLU* 2.8 52.4 + - + +
800B PRO* 3.5 17.2 + - + +
801B GLN* 3.1 31.5 - - - +
912B TYR* 3.2 25.1 - - + +
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Residues in contact with ASP 754 (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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1B DKI 2.7 31.1 + - - +
750B LEU* 3.6 21.1 - - + +
751B ASN* 2.7 46.4 + - - +
753B GLN* 1.3 76.6 - - - +
755B LEU* 1.3 66.1 + - - +
757B GLU 3.4 17.4 - - - +
758B SER* 3.6 6.8 + - - -
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Residues in contact with LEU 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750B LEU* 3.5 21.2 - - + +
751B ASN 3.1 8.9 + - - +
752B LEU* 3.2 20.8 + - + +
754B ASP* 1.3 78.5 - - - +
756B VAL* 1.3 59.2 + - - +
758B SER* 3.0 23.4 + - - -
772B TYR* 3.7 35.0 - - + +
777B LEU* 4.0 10.8 - - + -
805B VAL* 4.4 13.7 - - + -
822B LEU* 3.9 26.9 - - + -
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Residues in contact with VAL 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A TYR* 4.3 6.6 + - - -
752B LEU* 2.8 45.9 + - + +
755B LEU* 1.3 74.5 - - + +
757B GLU* 1.3 58.2 + - - +
758B SER* 3.6 3.5 + - - -
772B TYR* 4.4 17.5 - - - +
912B TYR* 3.7 24.9 - - + +
913B ILE* 4.5 9.9 - - + +
916B LYS* 3.6 13.2 - - + +
917B GLY* 3.5 32.3 - - - +
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Residues in contact with GLU 757 (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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925A TYR* 3.1 38.7 + - + +
753B GLN* 2.8 36.8 + - + +
754B ASP* 3.4 10.4 - - - +
756B VAL* 1.3 70.9 - - - +
758B SER* 1.3 63.4 + - - +
912B TYR* 2.7 35.4 + - + +
917B GLY* 4.7 1.1 - - - +
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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