Contacts of the helix formed by residues 843 - 854 (chain A) in PDB entry 1MQB
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 843 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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713A VAL* 3.4 32.3 - - + -
811A MET* 4.0 13.2 - - + -
841A ASP 3.3 9.8 - - - +
842A CYS* 1.3 88.5 - - + +
844A SER* 1.3 64.4 + - - +
845A ALA 4.3 1.8 - - - +
846A ILE* 3.1 12.5 + - + +
847A TYR* 3.1 19.8 + - - +
880A SER 5.0 0.4 - - - +
881A LEU* 3.5 41.5 - - + +
883A THR 3.4 9.4 - - - +
884A LEU* 4.0 4.2 - - + -
885A ALA 3.9 0.2 - - - -
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Residues in contact with SER 844 (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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843A PRO* 1.3 70.2 - - - +
845A ALA* 1.3 57.8 + - - +
847A TYR* 3.6 1.0 + - - +
848A GLN* 3.0 39.7 + - - +
883A THR* 2.9 26.2 + - - -
884A LEU 3.9 13.2 - - - -
885A ALA* 3.5 17.8 - - - +
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Residues in contact with ALA 845 (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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843A PRO* 3.2 3.6 - - + +
844A SER* 1.3 77.6 - - - +
846A ILE* 1.3 61.5 + - + +
848A GLN* 4.1 4.3 - - - +
849A LEU* 3.0 30.3 + - - +
870A ILE* 5.7 1.8 - - + +
874A LEU* 3.8 36.8 - - + +
880A SER* 5.1 9.1 + - - +
881A LEU* 5.2 0.4 - - + -
883A THR 4.8 0.2 + - - -
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Residues in contact with ILE 846 (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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717A VAL* 3.9 28.7 - - + -
720A LEU* 4.7 11.2 - - + -
807A MET* 3.4 7.2 - - + +
811A MET* 3.8 31.9 - - + -
842A CYS* 3.9 8.1 - - - -
843A PRO* 3.1 27.0 + - + +
845A ALA* 1.3 74.2 - - - +
847A TYR* 1.3 64.8 + - - +
849A LEU* 3.6 3.0 - - + +
850A MET* 3.1 28.7 + - + +
871A LEU* 4.1 17.3 - - + -
874A LEU* 4.0 21.8 - - + -
881A LEU* 4.2 4.5 - - + -
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Residues in contact with TYR 847 (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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835A ARG* 5.0 1.2 + - - +
836A LEU 3.1 23.1 + - - -
837A PRO* 3.8 4.2 - - - +
838A THR* 3.4 39.8 + - - -
839A PRO* 4.2 2.0 - - + -
842A CYS* 3.7 7.4 - - - -
843A PRO 3.1 10.1 + - - +
844A SER 4.0 1.8 - - - +
846A ILE* 1.3 76.3 - - - +
848A GLN* 1.3 76.3 + - - +
850A MET* 3.2 24.9 + - - +
851A MET* 3.1 50.3 + - + +
854A TRP* 4.7 0.2 - + - -
885A ALA* 3.8 29.6 - - + -
886A ASP 5.5 4.0 - - - -
887A PHE* 5.7 9.2 - + - -
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Residues in contact with GLN 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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844A SER* 3.0 28.0 + - - +
845A ALA* 4.1 5.4 - - - +
847A TYR* 1.3 95.5 - - + +
849A LEU* 1.3 58.2 + - - +
851A MET* 3.1 14.8 + - - +
852A GLN* 2.8 44.8 + - - +
885A ALA* 5.8 0.7 - - + +
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Residues in contact with LEU 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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807A MET* 3.7 21.1 - - - -
845A ALA 3.0 18.8 + - - +
846A ILE* 3.6 6.1 - - + +
848A GLN* 1.3 78.1 - - - +
850A MET* 1.3 56.4 + - - +
852A GLN* 3.1 21.3 + - - +
853A CYS* 3.0 23.9 + - - -
862A PRO* 4.2 17.3 - - + -
867A ILE* 4.3 17.3 - - + -
870A ILE* 4.1 27.4 - - + -
871A LEU* 3.4 33.7 - - + -
874A LEU* 5.7 0.2 - - + -
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Residues in contact with MET 850 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804A GLY* 3.9 3.1 - - - +
807A MET* 2.7 38.0 - - + +
808A TRP* 3.5 40.4 - - + +
811A MET* 4.2 7.9 - - + -
839A PRO* 4.1 18.4 - - + -
842A CYS* 4.5 2.5 - - - -
846A ILE* 3.1 11.2 + - + +
847A TYR* 3.2 28.0 - - + +
849A LEU* 1.3 73.5 - - - +
851A MET* 1.3 59.7 + - - +
853A CYS* 3.0 6.8 + - - +
854A TRP* 3.0 64.7 + - + -
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Residues in contact with MET 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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835A ARG* 3.6 28.3 - - + +
847A TYR* 3.1 51.4 + - + +
848A GLN* 3.1 20.6 + - - +
850A MET* 1.3 76.5 - - - +
852A GLN* 1.3 60.6 + - + +
854A TRP* 3.3 32.9 + - - +
855A GLN* 3.5 14.0 + - - +
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Residues in contact with GLN 852 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848A GLN* 2.8 29.3 + - + +
849A LEU* 3.3 29.3 + - - +
850A MET 3.1 0.4 - - - -
851A MET* 1.3 78.8 - - + +
853A CYS* 1.3 58.4 + - - +
855A GLN* 3.1 35.4 + - - +
860A ARG 6.0 0.2 - - - +
861A ARG* 3.7 2.6 - - - -
862A PRO* 3.4 26.0 - - + +
870A ILE* 4.4 9.7 - - - +
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Residues in contact with CYS 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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800A VAL* 3.4 40.4 - - + +
801A TRP* 3.3 19.2 - - - -
803A PHE* 4.3 6.7 - - - -
804A GLY* 3.8 19.3 - - - -
807A MET* 4.5 0.4 - - - -
849A LEU* 3.0 26.4 + - - -
850A MET* 3.0 8.7 + - - +
852A GLN* 1.3 77.7 - - - +
854A TRP* 1.3 58.4 + - + +
855A GLN 3.5 0.4 - - - -
861A ARG* 3.3 15.5 + - - -
862A PRO* 4.3 4.9 - - - -
867A ILE* 4.2 14.1 - - - -
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Residues in contact with TRP 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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801A TRP* 3.3 43.1 + + + -
804A GLY* 3.4 23.7 - - - -
805A ILE* 3.3 39.6 - - + +
808A TRP* 4.2 5.8 - + + -
818A TYR* 5.5 1.8 - - - -
835A ARG* 2.8 48.8 + - + +
836A LEU* 3.9 35.2 - - + -
847A TYR* 4.7 0.7 - + - -
850A MET* 3.0 41.0 + - + +
851A MET* 3.3 35.6 + - - +
852A GLN 3.2 0.6 - - - -
853A CYS* 1.3 79.9 - - - +
855A GLN* 1.3 59.0 + - - -
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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