Contacts of the helix formed by residues 743 - 748 (chain A) in PDB entry 3L4U
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 THR 743 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A TYR 4.0 11.2 - - - +
322A ASP* 3.4 9.6 - - - -
357A ASN 3.5 23.1 + - - +
358A GLY* 3.5 21.8 + - - +
359A GLN* 4.3 2.5 - - + -
631A TYR* 4.2 3.8 - - - -
741A ASN* 3.2 2.2 - - - +
742A THR* 1.3 91.6 + - - +
744A THR* 1.3 59.3 + - - +
745A LEU* 3.6 6.3 + - - +
746A ALA* 3.3 23.0 + - - +
747A SER* 2.8 27.7 + - - -
2001A NAG 5.3 3.5 + - - +
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Residues in contact with THR 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A TYR* 3.7 29.1 - - + +
290A TRP* 3.3 19.6 + - - +
293A GLY 4.6 3.1 - - - +
322A ASP* 2.7 34.3 + - - +
631A TYR* 4.1 5.4 - - + -
634A LEU* 3.6 31.6 - - + -
743A THR* 1.3 69.6 - - - +
745A LEU* 1.3 71.3 + - - +
746A ALA 3.1 0.2 - - - -
747A SER* 3.2 8.3 - - - +
748A ARG* 3.1 27.4 + - - +
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Residues in contact with LEU 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ASP* 4.2 0.8 + - - -
355A HIS 5.2 2.7 - - - +
356A ASN 6.1 0.2 - - - +
358A GLY* 3.6 33.0 - - - +
743A THR* 3.3 9.0 - - - +
744A THR* 1.3 84.5 + - - +
746A ALA* 1.3 61.9 + - + +
748A ARG* 4.0 7.8 + - - +
749A LYS* 3.8 31.7 - - - +
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Residues in contact with ALA 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A ASN* 3.3 28.7 - - - +
743A THR* 3.3 13.5 + - - +
744A THR 3.1 0.4 - - - -
745A LEU* 1.3 80.4 - - + +
747A SER* 1.3 65.9 + - - +
748A ARG 3.2 2.2 - - - -
749A LYS* 3.1 27.5 + - + +
750A ASN* 4.0 8.0 + - - +
2001A NAG 3.6 19.2 - - - +
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Residues in contact with SER 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A TYR* 4.6 4.5 + - - -
631A TYR* 4.7 8.5 + - - -
634A LEU* 5.0 2.4 - - - +
738A GLN* 3.0 20.4 + - - +
739A GLN 4.0 6.3 - - - -
740A PRO* 4.3 2.5 - - - -
741A ASN* 3.7 26.4 - - - +
743A THR 2.8 18.2 + - - -
744A THR* 3.2 22.9 + - - +
746A ALA* 1.3 72.9 - - - +
748A ARG* 1.3 60.9 + - - +
750A ASN* 2.9 24.4 + - - +
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Residues in contact with ARG 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A TYR* 3.4 64.6 - - + -
638A TYR* 4.8 3.0 - - - -
738A GLN* 3.1 20.6 + - - -
744A THR* 3.1 21.8 + - - +
745A LEU* 4.2 7.2 - - - +
746A ALA 3.2 0.2 - - - -
747A SER* 1.3 75.9 + - - +
749A LYS* 1.3 58.5 + - + +
750A ASN 3.4 0.4 - - - -
770A TRP* 3.8 26.0 - - + +
771A ASP 3.0 25.5 + - - -
772A ASP* 3.4 20.4 + - - +
773A GLY* 3.6 11.2 - - - -
805A TYR* 5.0 1.0 + - - -
807A ASP* 4.1 9.8 + - - +
809A ASN* 4.9 1.9 - - - +
811A LEU* 3.6 16.3 - - - +
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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
------------------------------------------------------------
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