Contacts of the helix formed by residues 737 - 741 (chain A) in PDB entry 3LLT
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 737 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A ASP* 2.8 27.3 + - - +
678A LEU 5.8 0.4 + - - -
679A LYS* 3.1 26.7 + - + +
736A ASN* 1.3 71.7 - - - +
738A ARG* 1.3 72.1 + - + +
739A GLN* 3.2 17.5 - - - +
740A TYR* 2.8 39.4 + - + +
741A ARG 3.2 7.8 + - - -
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Residues in contact with ARG 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A ASN 3.6 3.4 + - - -
737A THR* 1.3 73.8 - - + +
739A GLN* 1.3 71.2 + - - +
741A ARG* 3.2 39.9 - - - +
776A THR* 3.9 7.0 - - + +
777A HIS* 3.2 45.3 + - - +
778A GLU* 3.6 11.5 - - - +
779A HIS* 3.6 29.5 + - - +
782A HIS* 3.0 31.9 + - + -
876A ACT 4.4 9.1 - - - +
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Residues in contact with GLN 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A THR* 3.0 18.6 + - - +
738A ARG* 1.3 85.9 - - - +
740A TYR* 1.3 74.0 + - + +
741A ARG 3.4 1.3 + - - -
758A TRP* 5.6 0.2 + - - -
762A CYS* 4.2 4.0 - - - +
772A LEU* 3.8 26.3 - - + +
774A PHE* 3.2 51.8 + - - +
776A THR* 3.0 26.7 + - + +
777A HIS* 5.0 1.0 - - - +
782A HIS* 4.0 5.3 + - - -
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Residues in contact with TYR 740 (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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678A LEU 3.6 21.3 - - - +
679A LYS* 3.7 13.0 - - + -
680A PRO* 3.4 25.5 - - + +
681A GLU* 4.0 8.3 + - - -
736A ASN* 4.0 3.2 - - + +
737A THR* 2.8 35.4 + - + +
739A GLN* 1.3 83.4 - - + +
741A ARG* 1.3 63.5 + - - +
742A ALA 3.6 0.5 + - - -
758A TRP* 3.9 4.6 - - - -
759A SER* 2.7 40.7 + - - +
762A CYS* 3.7 28.0 - - + -
763A VAL* 4.3 4.5 - - + -
766A GLU* 2.5 32.8 + - - -
772A LEU* 3.1 22.7 - - + +
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Residues in contact with ARG 741 (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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734A ILE* 3.5 23.7 - - - +
735A ILE 2.8 20.7 + - - +
736A ASN* 2.9 29.2 + - + +
737A THR 3.2 3.2 + - - +
738A ARG* 3.2 52.2 + - - +
739A GLN 3.4 1.0 - - - -
740A TYR* 1.3 77.8 - - - +
742A ALA* 1.3 66.9 + - - +
745A VAL* 3.9 21.5 - - + -
746A ILE* 3.9 15.8 - - + +
758A TRP* 3.4 13.1 + - - -
779A HIS* 3.1 36.8 + - - -
782A HIS* 4.0 3.6 + - - -
786A MET* 3.6 11.1 - - - +
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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