Contacts of the helix formed by residues 847 - 863 (chain A) in PDB entry 1Q2L
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 LYS 847 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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845A ALA 4.2 6.5 + - - +
846A MET* 1.3 75.2 - - - +
848A PRO* 1.3 76.6 - - + +
849A ASP* 3.3 26.2 - - - +
850A GLU* 2.7 25.0 + - - +
851A PHE* 3.1 21.2 + - - +
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Residues in contact with PRO 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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846A MET 3.9 2.4 - - - +
847A LYS* 1.3 87.8 - - + +
849A ASP* 1.3 61.4 + - - +
851A PHE* 3.6 6.4 - - + +
852A ALA* 2.9 31.8 + - - +
902A PRO* 6.1 1.3 - - + -
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Residues in contact with ASP 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 LYS* 3.3 29.5 - - - +
848A PRO* 1.3 78.0 - - - +
850A GLU* 1.3 78.1 + - - +
852A ALA* 3.2 7.4 + - - +
853A GLN* 3.1 21.7 + - - +
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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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845A ALA 4.4 0.7 - - - +
846A MET* 3.5 19.2 - - + +
847A LYS* 2.7 55.9 + - - +
849A ASP* 1.3 89.3 + - - +
851A PHE* 1.3 60.9 + - - +
853A GLN* 3.3 8.3 + - - +
854A ILE* 3.0 29.6 + - + +
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Residues in contact with PHE 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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778A LEU* 4.0 18.4 - - + -
782A ILE* 4.7 2.9 - - + -
846A MET* 3.7 26.5 - - + -
847A LYS 3.1 18.6 + - - +
848A PRO* 3.6 6.7 - - + +
850A GLU* 1.3 75.9 - - - +
852A ALA* 1.3 67.2 + - + +
854A ILE* 3.0 6.8 + - + +
855A GLN* 3.0 40.2 + - - +
900A LEU* 3.2 31.6 - - + -
901A THR* 3.6 14.4 - - - -
902A PRO* 3.7 24.5 - - + -
905A LEU* 3.5 27.4 - - + -
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Residues in contact with ALA 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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848A PRO 2.9 18.1 + - - +
849A ASP* 3.6 6.3 - - - +
851A PHE* 1.3 77.7 - - + +
853A GLN* 1.3 57.5 + - - +
855A GLN* 3.3 16.1 + - - +
856A GLN* 2.9 49.0 + - - +
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Residues in contact with GLN 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 ASP 3.1 12.8 + - - +
850A GLU* 3.5 11.7 - - - +
852A ALA* 1.3 75.1 - - - +
854A ILE* 1.3 67.2 + - + +
856A GLN* 3.8 13.3 - - - +
857A ALA* 3.0 24.9 + - - +
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Residues in contact with ILE 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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778A LEU* 3.5 23.1 - - + -
781A GLN* 4.1 22.2 - - + +
782A ILE* 3.6 37.7 - - + -
846A MET* 4.4 5.8 - - - -
850A GLU* 3.0 19.2 + - + +
851A PHE* 3.0 12.9 + - + +
853A GLN* 1.3 76.3 - - + +
855A GLN* 1.3 66.2 + - - +
857A ALA* 3.2 6.1 + - + +
858A VAL* 3.0 22.7 + - - +
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Residues in contact with GLN 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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778A LEU* 4.0 15.7 - - + -
851A PHE* 3.0 40.4 + - + +
852A ALA* 3.5 16.2 - - - +
854A ILE* 1.3 77.6 - - - +
856A GLN* 1.3 59.4 + - + +
858A VAL* 3.3 1.6 + - - +
859A ILE* 2.9 39.8 + - + +
897A ILE* 2.9 34.6 + - + +
898A LYS* 3.5 16.6 + - - +
900A LEU 3.4 18.0 + - - -
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Residues in contact with GLN 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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852A ALA* 2.9 34.2 + - - +
853A GLN* 3.8 12.4 - - - +
855A GLN* 1.3 79.1 - - + +
857A ALA* 1.3 53.7 + - - +
859A ILE* 3.8 8.6 - - + +
860A THR* 2.6 41.9 + - - +
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Residues in contact with ALA 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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781A GLN* 4.0 18.6 - - - +
853A GLN 3.0 19.4 + - - +
854A ILE* 3.2 6.0 + - + +
856A GLN* 1.3 76.4 - - - +
858A VAL* 1.3 57.5 + - - +
860A THR* 3.6 6.2 - - - -
861A GLN* 2.9 38.3 + - - +
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Residues in contact with VAL 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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777A SER* 4.0 20.6 - - - +
778A LEU* 3.6 20.0 - - + -
781A GLN* 3.9 31.6 - - + +
854A ILE 3.0 16.1 + - - +
855A GLN 3.8 3.4 - - - +
857A ALA* 1.3 72.8 - - - +
859A ILE* 1.3 62.6 + - - +
861A GLN* 3.2 12.3 + - - +
862A MET* 2.9 36.0 + - + +
897A ILE* 3.7 24.5 - - + -
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Residues in contact with ILE 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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855A GLN* 2.9 28.8 + - + +
856A GLN* 3.8 7.6 - - + +
858A VAL* 1.3 74.3 - - - +
860A THR* 1.3 65.3 + - - +
862A MET* 3.2 6.7 + - - +
863A LEU* 3.0 38.3 + - + +
894A VAL* 3.9 25.6 - - + -
897A ILE* 3.8 23.1 - - + -
898A LYS* 3.8 37.2 - - + -
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Residues in contact with THR 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 GLN* 2.6 27.7 + - - +
857A ALA* 3.6 6.9 - - - -
859A ILE* 1.3 79.6 - - - +
861A GLN* 1.3 63.9 + - + +
863A LEU* 3.3 4.7 + - - +
864A GLN* 3.1 23.0 + - + +
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Residues in contact with GLN 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 GLN* 3.3 34.4 + - - +
857A ALA* 2.9 30.2 + - + +
858A VAL* 3.2 12.4 + - - +
860A THR* 1.3 78.5 - - + +
862A MET* 1.3 62.6 + - + +
864A GLN* 3.3 25.9 + - - +
875A LYS* 5.3 2.4 + - - -
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Residues in contact with MET 862 (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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777A SER* 4.8 5.2 - - - -
858A VAL* 2.9 24.9 + - + +
859A ILE* 3.2 5.8 + - - +
861A GLN* 1.3 78.6 - - + +
863A LEU* 1.3 60.7 + - - +
864A GLN 3.3 2.4 + - - +
875A LYS* 5.0 2.3 + - - -
890A ARG* 3.6 57.0 + - + +
893A ILE* 3.7 34.3 - - + -
894A VAL* 4.4 10.1 - - + -
897A ILE* 3.6 31.2 - - - -
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Residues in contact with LEU 863 (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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541A TYR* 5.3 2.8 + - - -
859A ILE* 3.0 36.3 + - + +
860A THR* 3.7 5.2 - - - +
862A MET* 1.3 78.8 - - - +
864A GLN* 1.3 66.3 + - - +
865A ALA* 3.3 3.3 + - - -
890A ARG* 5.1 8.5 - - + -
891A ASP* 4.4 15.7 - - - +
894A VAL* 4.2 22.4 - - + -
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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