Contacts of the helix formed by residues 827 - 838 (chain A) in PDB entry 1LUF
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 PRO 827 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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698A CYS* 4.4 15.7 - - - -
702A LEU* 5.1 0.4 - - + -
795A PHE* 3.7 17.0 - - + -
825A ASN 3.3 10.0 - - - +
826A CYS* 1.3 85.4 - - - +
828A LEU* 1.3 60.7 + - - +
829A GLU* 4.5 5.4 - - + +
830A LEU* 2.9 43.4 + - + +
831A TYR 3.0 9.9 + - - -
858A MET* 4.4 12.1 - - + -
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Residues in contact with LEU 828 (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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822A CYS* 5.2 4.3 - - + -
826A CYS 3.2 4.6 + - - -
827A PRO* 1.3 71.6 - - - +
829A GLU* 1.3 59.0 + - + +
831A TYR* 3.0 18.3 + - + +
832A ASN* 2.8 56.7 + - - +
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Residues in contact with GLU 829 (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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827A PRO* 3.2 5.5 - - + +
828A LEU* 1.3 78.5 - - + +
830A LEU* 1.3 61.3 + - - +
832A ASN* 3.6 10.3 + - - +
833A LEU* 3.4 17.8 + - - +
854A ILE* 6.0 1.6 - - - +
858A MET* 4.8 21.7 - - + +
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Residues in contact with LEU 830 (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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702A LEU* 3.7 15.0 - - + -
791A LEU* 3.6 28.9 - - + -
795A PHE* 3.0 45.8 - - + -
826A CYS* 4.2 6.5 - - - -
827A PRO* 2.9 19.5 + - + +
829A GLU* 1.3 77.6 - - - +
831A TYR* 1.3 66.9 + - - +
832A ASN 3.2 0.4 - - - -
833A LEU* 3.0 28.9 + - + +
834A MET* 3.1 15.0 + - + +
855A LEU* 4.0 14.6 - - + -
858A MET* 4.1 11.7 - - + +
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Residues in contact with TYR 831 (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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819A ILE* 3.7 12.1 - - + +
820A LEU 2.8 22.4 + - - -
821A ALA* 3.5 10.6 - - - -
822A CYS* 3.3 58.3 - - + -
827A PRO 3.0 7.2 + - - +
828A LEU* 3.0 17.8 + - + +
830A LEU* 1.3 76.4 - - - +
832A ASN* 1.3 64.4 + - - +
834A MET* 3.0 28.1 + - + +
835A ARG* 2.9 61.3 + - + +
838A TRP* 4.2 11.7 - + - -
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Residues in contact with ASN 832 (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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828A LEU* 2.8 43.4 + - - +
829A GLU* 3.7 9.5 - - - +
830A LEU 3.2 0.2 - - - -
831A TYR* 1.3 80.6 - - - +
833A LEU* 1.3 61.6 + - - +
835A ARG* 3.3 24.7 - - - +
836A LEU* 3.1 28.4 + - + +
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Residues in contact with LEU 833 (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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791A LEU* 4.3 7.6 - - + -
829A GLU 3.4 10.0 + - - +
830A LEU* 3.0 29.1 + - + +
832A ASN* 1.3 75.4 - - - +
834A MET* 1.3 68.8 + - - +
836A LEU* 3.0 12.8 + - + +
837A CYS* 2.9 38.5 + - - -
846A PRO* 4.2 15.5 - - + -
851A ILE* 4.3 27.8 - - + -
854A ILE* 4.0 35.4 - - + -
855A LEU* 4.6 4.7 - - + -
858A MET* 5.6 0.2 - - - -
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Residues in contact with MET 834 (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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788A GLY* 3.7 15.7 - - - +
791A LEU* 3.9 18.4 - - + +
792A TRP* 3.9 30.5 - - - +
795A PHE* 5.1 0.2 - - + -
823A PRO* 4.2 6.3 - - + -
826A CYS* 3.2 35.4 - - - -
830A LEU* 3.1 13.7 + - + +
831A TYR* 3.0 28.4 + - + +
833A LEU* 1.3 76.2 - - - +
835A ARG* 1.3 63.1 + - - +
837A CYS* 2.9 18.6 + - - +
838A TRP* 3.0 50.3 + - + -
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Residues in contact with ARG 835 (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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819A ILE* 4.1 20.5 - - + +
831A TYR* 2.9 47.9 + - + +
832A ASN* 3.3 26.6 - - - +
834A MET* 1.3 77.0 - - - +
836A LEU* 1.3 64.0 + - + +
838A TRP* 3.1 28.2 + - - +
839A SER* 3.5 3.3 + - - -
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Residues in contact with LEU 836 (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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832A ASN* 3.2 16.4 - - + +
833A LEU* 3.0 16.4 + - + +
835A ARG* 1.3 78.7 - - + +
837A CYS* 1.3 61.7 + - - +
839A SER* 2.7 28.2 + - - +
844A ASP 5.1 5.2 - - - +
845A ARG* 3.5 10.4 - - - +
846A PRO* 3.6 25.1 - - + -
854A ILE* 6.0 4.5 - - + -
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Residues in contact with CYS 837 (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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784A VAL* 3.5 37.5 - - - +
785A TRP* 3.4 12.3 - - - +
787A TYR* 4.6 3.8 - - - -
788A GLY* 3.8 19.5 - - - -
791A LEU* 5.5 0.4 - - - -
833A LEU* 2.9 35.1 + - - -
834A MET* 2.9 9.7 + - - +
836A LEU* 1.3 75.7 - - - +
838A TRP* 1.3 59.6 + - + +
839A SER 3.3 0.9 - - - -
845A ARG* 3.2 23.4 + - - -
846A PRO* 4.0 6.7 - - - -
851A ILE* 4.2 8.1 - - - -
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Residues in contact with TRP 838 (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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785A TRP* 3.2 69.5 + + + -
788A GLY 3.4 24.0 - - - -
789A VAL* 3.4 13.8 - - + +
792A TRP* 4.4 2.9 - + + -
802A TYR* 5.7 2.2 - - - -
819A ILE* 3.9 36.3 - - + +
820A LEU* 3.8 50.5 - - + -
831A TYR* 4.2 8.5 - + - -
834A MET* 3.0 46.9 + - + +
835A ARG* 3.1 8.6 + - - +
837A CYS* 1.3 78.8 - - + +
839A SER* 1.3 62.2 + - - +
840A LYS 3.5 1.6 + - - -
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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