Contacts of the helix formed by residues 874 - 886 (chain B) in PDB entry 1M8X
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 874 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A ARG* 4.7 4.2 + - - -
847B ARG* 5.2 2.0 - - - +
872B ARG 3.6 2.4 + - - -
873B ALA* 1.3 76.0 - - - +
875B PRO* 1.3 81.2 - - - +
876B ALA* 3.7 10.8 + - + +
877B GLU* 3.0 51.5 + - + +
878B ARG* 2.9 20.3 + - - +
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Residues in contact with PRO 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A ARG* 3.9 31.6 - - - +
873B ALA 4.5 1.1 - - - +
874B THR* 1.3 94.5 - - - +
876B ALA* 1.3 56.6 + - - +
878B ARG* 3.2 19.9 + - + +
879B GLN* 2.8 30.1 + - - +
913B GLN* 5.1 1.7 + - - -
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Residues in contact with ALA 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847B ARG* 3.9 20.6 - - - +
874B THR* 3.3 7.7 - - + +
875B PRO* 1.3 78.1 - - - +
877B GLU* 1.3 64.1 + - - +
879B GLN* 3.1 9.0 + - - +
880B LEU* 3.0 28.2 + - + +
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Residues in contact with GLU 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845B GLN* 5.7 1.6 - - - +
846B LEU* 4.2 27.2 - - + +
847B ARG* 4.4 28.2 + - + +
869B LYS* 5.0 3.2 - - - +
873B ALA* 3.6 9.1 - - + +
874B THR* 3.0 41.0 + - + +
876B ALA* 1.3 77.8 - - - +
878B ARG* 1.3 63.4 - - - +
880B LEU* 3.1 21.7 + - - +
881B VAL* 3.2 17.5 + - - +
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Residues in contact with ARG 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870B LEU* 3.1 38.7 + - + +
871B GLU 3.5 10.7 + - - -
873B ALA* 2.8 30.1 + - + +
874B THR 2.9 14.6 + - - +
875B PRO* 3.5 20.6 - - + +
877B GLU* 1.3 77.8 - - - +
879B GLN* 1.3 55.7 + - - +
881B VAL* 3.1 5.2 + - - +
882B PHE* 2.9 26.8 + - - +
905B PHE* 3.4 25.4 - - + -
908B PHE* 3.4 32.5 + - - +
909B GLY* 4.1 3.7 - - - -
910B SER* 4.9 1.5 - - - +
913B GLN* 3.6 19.7 - - - +
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Residues in contact with GLN 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875B PRO 2.8 13.6 + - - +
876B ALA* 3.1 12.5 + - - +
878B ARG* 1.3 72.0 - - - +
880B LEU* 1.3 62.8 + - + +
882B PHE* 3.5 17.1 - - - +
883B ASN* 2.4 76.8 + - - +
913B GLN* 3.4 20.3 + - - +
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Residues in contact with LEU 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846B LEU* 6.0 2.7 - - + +
847B ARG* 3.9 48.5 - - + +
853B ILE* 4.5 2.8 - - - +
876B ALA* 3.0 21.4 + - + +
877B GLU* 3.1 11.4 + - - +
879B GLN* 1.3 76.8 - - + +
881B VAL* 1.3 64.4 + - + +
883B ASN* 3.7 19.4 + - - +
884B GLU* 3.8 18.4 + - - +
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Residues in contact with VAL 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846B LEU* 4.0 27.1 - - + -
853B ILE* 3.9 30.2 - - + +
866B ILE* 4.2 12.8 - - + -
870B LEU* 4.0 20.0 - - + -
877B GLU 3.6 11.7 - - - +
878B ARG 3.1 7.5 + - - +
880B LEU* 1.3 75.2 - - + +
882B PHE* 1.3 67.9 + - - +
884B GLU* 3.2 11.1 + - - -
885B ILE* 3.4 13.1 + - + +
901B VAL* 4.6 4.0 - - + -
905B PHE* 3.8 22.7 - - + -
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Residues in contact with PHE 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878B ARG 2.9 13.8 + - - +
879B GLN* 3.2 26.9 + - - +
881B VAL* 1.3 77.5 - - - +
883B ASN* 1.3 64.8 + - - +
885B ILE* 3.0 20.3 + - + +
886B LEU* 3.0 43.1 + - + +
905B PHE* 3.7 22.0 - + + -
912B GLU* 6.4 1.3 - - + -
913B GLN* 3.6 45.1 - - + +
916B ALA* 3.7 27.6 - - + -
917B LEU* 3.9 20.4 - - + -
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Residues in contact with ASN 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879B GLN* 2.4 60.1 + - - +
880B LEU* 3.8 16.5 - - - +
882B PHE* 1.3 73.7 - - - +
884B GLU* 1.3 63.9 + - + +
886B LEU* 4.2 9.5 + - - +
887B GLN* 5.1 2.1 + - - +
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Residues in contact with GLU 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850B ALA* 3.5 6.8 - - - +
851B GLY* 2.6 36.7 + - - -
853B ILE* 2.9 55.6 + - + +
854B MET* 3.4 26.3 + - + +
880B LEU 3.8 7.3 + - - +
881B VAL 3.2 2.6 + - - +
882B PHE 3.1 1.2 - - - -
883B ASN* 1.3 80.2 - - + +
885B ILE* 1.3 60.5 + - - +
886B LEU 3.7 0.2 - - - -
887B GLN* 5.4 1.9 + - - +
888B ALA 5.6 0.9 + - - -
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Residues in contact with ILE 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853B ILE* 3.5 26.5 - - + -
854B MET* 4.0 7.6 - - - -
857B SER* 4.2 4.3 - - - +
881B VAL* 3.4 14.6 - - + +
882B PHE* 3.0 16.1 + - + +
884B GLU* 1.3 83.3 - - - +
886B LEU* 1.3 73.6 + - - +
887B GLN 3.4 2.0 + - - -
888B ALA 3.4 3.0 - - - -
889B ALA* 2.8 24.9 + - - -
892B LEU* 3.4 28.7 - - + -
901B VAL* 4.9 2.7 - - + -
902B ILE* 3.8 21.1 - - + -
905B PHE* 4.0 24.9 - - + -
917B LEU* 4.4 7.2 - - + -
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Residues in contact with LEU 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882B PHE* 3.0 49.4 + - + +
883B ASN* 4.2 7.5 + - - +
884B GLU 3.7 0.6 - - - -
885B ILE* 1.3 85.5 - - - +
887B GLN* 1.3 66.3 + - - +
889B ALA* 3.2 15.4 + - - +
916B ALA* 4.0 11.7 - - + +
917B LEU* 4.8 3.1 - - + -
920B ARG* 3.2 56.2 + - + +
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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