Contacts of the helix formed by residues 847 - 861 (chain A) in PDB entry 5LUQ
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 SER 847 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767A GLU* 3.7 4.7 - - - -
846A ILE* 1.3 79.2 - - - +
848A LEU* 1.3 69.1 + - - +
849A GLU* 3.2 16.5 + - - -
850A GLU* 2.9 30.4 + - - +
851A ILE 2.9 8.7 + - - -
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Residues in contact with LEU 848 (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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764A PRO* 2.9 51.4 - - + +
765A LEU* 6.1 0.9 - - + -
767A GLU* 3.7 9.1 + - - +
807A ASP* 5.4 10.3 - - - +
846A ILE 3.6 0.6 + - - -
847A SER* 1.3 73.1 + - - +
849A GLU* 1.3 80.1 + - - +
851A ILE* 3.0 29.7 + - + +
852A ARG* 3.1 11.8 + - - +
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Residues in contact with GLU 849 (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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847A SER* 3.2 17.7 + - - +
848A LEU* 1.3 92.9 - - - +
850A GLU* 1.3 59.0 + - - +
852A ARG* 3.2 11.7 + - - +
853A ILE* 2.9 35.7 + - + +
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Residues in contact with GLU 850 (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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846A ILE* 3.9 3.5 + - - -
847A SER* 2.9 34.5 + - - +
849A GLU* 1.3 75.8 - - - +
851A ILE* 1.3 62.8 + - - +
853A ILE* 2.9 17.5 + - + +
854A ARG* 2.5 63.7 + - + +
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Residues in contact with ILE 851 (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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767A GLU* 3.3 28.5 - - + -
770A LEU* 3.5 44.9 - - + -
771A ASN* 5.2 2.5 - - - +
774A GLU* 3.0 28.3 - - + +
803A SER* 6.5 1.1 - - - -
807A ASP* 5.8 2.2 - - - +
846A ILE* 3.6 14.6 - - + +
847A SER 2.9 8.5 + - - +
848A LEU* 3.0 29.8 + - + +
850A GLU* 1.3 75.3 - - - +
852A ARG* 1.3 64.0 + - - +
854A ARG* 3.3 4.6 + - - +
855A VAL* 3.0 25.6 + - + +
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Residues in contact with ARG 852 (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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803A SER 4.2 7.9 - - - +
804A ALA* 3.8 20.7 - - - +
807A ASP* 4.9 12.4 + - + +
808A GLU* 2.7 45.5 + - - +
848A LEU 3.1 8.0 + - - +
849A GLU* 3.3 14.4 - - - +
851A ILE* 1.3 81.2 - - - +
853A ILE* 1.3 65.6 + - + +
855A VAL* 2.9 27.6 - - - +
856A VAL* 2.9 35.8 + - - +
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Residues in contact with ILE 853 (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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849A GLU* 2.9 25.4 + - + +
850A GLU* 2.9 18.3 + - + +
852A ARG* 1.3 79.5 - - + +
854A ARG* 1.3 59.8 + - + +
856A VAL* 2.8 29.2 + - + +
857A GLN* 2.9 25.3 + - + +
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Residues in contact with ARG 854 (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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771A ASN* 3.7 15.4 + - - +
774A GLU* 3.0 40.2 + - - +
778A ILE* 5.8 1.6 - - + +
846A ILE* 3.0 37.9 - - - +
850A GLU* 2.5 58.3 + - + +
851A ILE* 3.6 2.8 - - - +
853A ILE* 1.3 75.6 - - + +
855A VAL* 1.3 60.6 + - - +
857A GLN* 3.7 9.3 - - + +
858A MSE 2.9 27.7 + - - +
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Residues in contact with VAL 855 (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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774A GLU* 4.1 8.9 + - + +
800A LEU* 5.2 7.4 - - + +
803A SER* 4.0 28.5 - - - +
804A ALA* 4.4 16.6 - - + -
851A ILE* 3.0 21.0 + - + +
852A ARG* 2.9 22.4 - - - +
854A ARG* 1.3 74.4 - - - +
856A VAL* 1.3 63.3 + - + +
858A MSE 3.0 10.8 - - - +
859A LEU* 2.9 47.5 + - + +
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Residues in contact with VAL 856 (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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804A ALA* 6.3 0.2 - - + -
852A ARG* 2.9 45.3 - - - +
853A ILE* 2.8 19.3 + - + +
855A VAL* 1.3 72.4 - - + +
857A GLN* 1.3 66.0 + - + +
859A LEU* 3.2 12.7 + - + +
860A GLY* 2.9 20.8 + - - -
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Residues in contact with GLN 857 (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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853A ILE* 2.9 27.5 + - + +
854A ARG* 3.7 11.9 - - + +
856A VAL* 1.3 76.1 - - + +
858A MSE 1.3 65.0 + - - +
860A GLY* 2.9 14.5 + - - -
861A SER* 3.0 15.1 + - - -
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Residues in contact with MSE 858 (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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774A GLU* 4.7 7.2 - - + +
777A SER* 3.0 32.1 - - - +
778A ILE* 3.6 35.9 - - + +
781A ASP* 3.0 35.0 - - - +
800A LEU* 5.3 8.1 - - - -
854A ARG 2.9 17.9 + - - +
855A VAL* 3.0 12.6 - - - +
857A GLN* 1.3 77.7 - - - +
859A LEU* 1.3 65.4 + - + +
861A SER* 3.0 20.2 + - - +
862A LEU* 3.2 18.0 - - + +
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Residues in contact with LEU 859 (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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800A LEU* 3.5 41.5 - - + -
804A ALA* 5.3 7.0 - - + -
855A VAL* 2.9 36.4 + - + +
856A VAL* 3.7 9.4 - - + +
858A MSE 1.3 81.4 - - - +
860A GLY* 1.3 68.4 + - - +
861A SER 3.2 1.6 - - - -
862A LEU* 3.0 27.1 + - + +
863A GLY 3.7 3.8 + - - -
866A ILE* 4.3 23.5 - - + +
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Residues in contact with GLY 860 (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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856A VAL 2.9 10.9 + - - -
857A GLN* 2.9 7.3 + - - -
859A LEU* 1.3 77.2 - - - +
861A SER* 1.3 53.6 + - - +
862A LEU 2.7 17.3 + - - -
863A GLY* 3.8 3.5 + - - -
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Residues in contact with SER 861 (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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781A ASP* 4.3 2.9 + - - -
782A ARG* 5.5 10.8 + - - -
857A GLN 3.0 9.7 + - - -
858A MSE 3.0 22.7 + - - +
860A GLY* 1.3 74.3 - - - +
862A LEU* 1.3 71.5 + - - +
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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