Contacts of the helix formed by residues 910 - 922 (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 SER 910 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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878B ARG* 4.9 3.3 - - - +
909B GLY* 1.3 74.7 - - - -
911B LEU* 1.3 66.2 + - - +
912B GLU* 3.7 8.8 + - - +
913B GLN* 2.8 47.5 + - - +
914B LYS* 2.9 11.7 + - - +
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Residues in contact with LEU 911 (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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909B GLY 3.9 1.0 + - - -
910B SER* 1.3 73.1 - - - +
912B GLU* 1.3 58.6 + - - +
914B LYS* 4.3 18.7 - - + +
915B LEU* 2.9 53.1 + - + +
946B PRO* 4.0 33.4 - - + -
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Residues in contact with GLU 912 (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* 6.4 1.3 - - + -
910B SER* 3.1 9.2 - - - +
911B LEU* 1.3 80.1 - - - +
913B GLN* 1.3 58.4 + - + +
915B LEU* 3.2 11.8 + - + +
916B ALA* 2.9 29.4 + - + +
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Residues in contact with GLN 913 (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 5.1 1.2 + - - -
878B ARG* 3.6 12.9 - - - +
879B GLN* 3.4 31.0 + - - +
882B PHE* 3.6 43.1 - - + +
905B PHE* 3.5 20.4 - - + +
909B GLY* 3.5 10.3 - - - -
910B SER* 2.8 42.6 + - - +
912B GLU* 1.3 74.4 - - + +
914B LYS* 1.3 64.9 + - - +
916B ALA* 3.1 2.9 + - - +
917B LEU* 2.9 29.7 + - + +
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Residues in contact with LYS 914 (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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905B PHE 3.8 14.3 + - - +
906B PHE* 3.1 44.6 + - + +
907B GLU 5.0 3.0 + - - -
909B GLY 3.4 20.4 - - - +
910B SER 2.9 14.7 + - - +
911B LEU* 3.8 22.4 - - + +
913B GLN* 1.3 76.1 - - - +
915B LEU* 1.3 58.0 + - + +
917B LEU* 3.3 6.1 + - - +
918B ALA* 2.8 29.9 + - - +
944B PHE* 3.1 36.1 + - - +
945B ILE* 4.3 8.3 - - + -
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Residues in contact with LEU 915 (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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911B LEU* 2.9 49.4 + - + +
912B GLU* 3.3 9.9 - - + +
914B LYS* 1.3 78.2 - - + +
916B ALA* 1.3 61.7 + - - +
918B ALA* 3.3 5.8 + - + +
919B GLU* 3.1 21.5 + - - +
945B ILE* 6.1 0.9 - - + -
946B PRO* 5.0 1.3 - - + -
949B GLN* 3.7 39.9 - - + +
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Residues in contact with ALA 916 (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* 3.7 22.0 - - + -
886B LEU* 4.0 12.6 - - + -
912B GLU* 2.9 15.7 + - + +
913B GLN 3.1 7.2 + - - +
915B LEU* 1.3 75.4 - - - +
917B LEU* 1.3 62.5 + - - +
919B GLU* 3.1 17.7 + - - +
920B ARG* 3.1 22.9 + - - +
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Residues in contact with LEU 917 (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* 3.9 20.2 - - + -
885B ILE* 4.4 10.1 - - + -
886B LEU* 4.8 4.3 - - + -
889B ALA* 4.0 26.2 - - + -
893B MET* 4.6 2.1 - - + +
902B ILE* 4.4 13.0 - - + +
905B PHE* 3.4 33.4 - - + -
906B PHE* 3.6 31.0 - - + -
913B GLN 2.9 22.0 + - - +
914B LYS* 3.6 3.8 - - - +
916B ALA* 1.3 72.5 - - - +
918B ALA* 1.3 65.8 + - - +
920B ARG* 2.9 17.3 + - - +
921B ILE* 3.0 16.5 + - + +
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Residues in contact with ALA 918 (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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906B PHE* 4.2 4.6 - - + -
914B LYS 2.8 17.6 + - - +
915B LEU* 3.4 10.8 - - + +
916B ALA 3.2 0.2 - - - -
917B LEU* 1.3 76.2 - - - +
919B GLU* 1.3 62.8 + - - +
921B ILE* 3.1 9.7 + - - +
922B ARG* 3.1 24.8 + - - +
945B ILE* 5.0 4.9 - - + -
949B GLN* 4.9 15.7 - - + -
953B MET* 4.3 20.9 - - + +
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Residues in contact with GLU 919 (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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915B LEU 3.1 12.9 + - - +
916B ALA* 3.1 15.4 + - - +
918B ALA* 1.3 78.7 - - - +
920B ARG* 1.3 70.1 + - - +
921B ILE 3.4 0.3 + - - -
922B ARG* 3.6 36.1 + - - +
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Residues in contact with ARG 920 (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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886B LEU* 3.2 62.4 + - + +
887B GLN* 4.7 13.1 + - - +
889B ALA* 4.2 5.8 - - + -
890B TYR* 4.6 10.4 - - + +
893B MET* 4.1 19.8 - - + +
916B ALA* 3.4 22.6 + - - +
917B LEU* 2.9 12.4 + - - +
919B GLU* 1.3 93.2 - - - +
921B ILE* 1.3 59.4 + - - +
922B ARG 4.6 1.0 - - - +
924B HIS* 4.2 14.7 - - - -
928B LEU* 5.7 0.2 - - - +
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Residues in contact with ILE 921 (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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893B MET* 3.6 28.7 - - + -
906B PHE* 3.9 28.0 - - + -
917B LEU 3.0 9.7 + - - +
918B ALA* 3.1 8.7 + - - +
920B ARG* 1.3 78.9 - - - +
922B ARG* 1.3 66.4 + - - +
923B GLY 3.3 0.2 + - - -
924B HIS* 2.9 23.1 + - - +
925B VAL* 3.6 16.1 + - + -
928B LEU* 4.0 8.3 - - + -
937B VAL* 4.2 8.7 - - + -
938B ILE* 3.7 32.3 - - + -
941B ALA* 4.4 1.8 - - + -
953B MET* 4.0 20.4 - - + -
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Residues in contact with ARG 922 (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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918B ALA 3.1 12.6 + - - +
919B GLU* 3.7 38.0 + - - +
920B ARG 3.6 1.3 - - - +
921B ILE* 1.3 78.0 - - - +
923B GLY* 1.3 64.0 + - - +
924B HIS* 3.5 9.0 + - - -
925B VAL* 4.9 0.7 - - - -
952B GLU* 2.7 61.7 + - - +
953B MET* 5.0 4.4 - - - +
955B ARG* 3.7 19.2 - - - +
956B GLU* 3.8 11.4 + - - +
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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