Contacts of the helix formed by residues 910 - 922 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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909A GLY* 1.3 73.3 - - - -
911A LEU* 1.3 65.8 + - - +
912A GLU* 3.6 14.8 + - - +
913A GLN* 2.7 43.7 + - - +
914A LYS* 3.0 24.5 + - - +
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Residues in contact with LEU 911 (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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910A SER* 1.3 70.9 - - - +
912A GLU* 1.3 75.0 + - - +
914A LYS* 3.1 15.2 + - + +
915A LEU* 3.0 66.6 + - + +
946A PRO* 5.1 9.9 - - + -
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Residues in contact with GLU 912 (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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882A PHE* 5.8 0.2 - - - -
910A SER* 3.7 14.5 + - - +
911A LEU* 1.3 98.2 + - - +
913A GLN* 1.3 60.3 + - + +
915A LEU* 3.4 12.6 + - + +
916A ALA* 3.0 27.9 + - - +
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Residues in contact with GLN 913 (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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875A PRO 4.9 1.8 + - - -
878A ARG* 4.2 7.5 + - - +
879A GLN* 3.1 43.9 + - - +
882A PHE* 3.7 35.9 - - + +
905A PHE* 3.5 18.4 - - + -
909A GLY* 3.2 11.3 - - - -
910A SER* 2.7 47.8 + - - +
912A GLU* 1.3 75.2 - - + +
914A LYS* 1.3 68.1 + - - +
916A ALA 3.1 1.0 + - - -
917A LEU* 2.9 28.8 + - - +
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Residues in contact with LYS 914 (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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905A PHE 3.6 14.6 - - - +
906A PHE* 2.6 49.8 + - + +
907A GLU 3.7 11.3 + - - -
909A GLY 3.0 24.7 + - - +
910A SER 3.0 13.8 + - - +
911A LEU* 3.4 11.0 - - + +
913A GLN* 1.3 76.1 - - - +
915A LEU* 1.3 59.4 + - + +
917A LEU* 3.4 5.9 + - - +
918A ALA* 3.0 29.2 + - - +
944A PHE* 3.9 30.4 + - + +
945A ILE* 4.8 8.3 - - + -
946A PRO* 6.4 0.7 - - + -
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Residues in contact with LEU 915 (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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911A LEU* 3.0 43.6 + - + +
912A GLU* 3.7 13.0 - - + +
913A GLN 3.2 0.2 - - - -
914A LYS* 1.3 79.6 - - + +
916A ALA* 1.3 61.1 + - - +
918A ALA* 3.3 7.6 + - - +
919A GLU* 3.1 19.9 + - - +
945A ILE* 5.7 0.9 - - + -
946A PRO* 4.1 18.6 - - + -
949A GLN* 3.9 32.5 - - + +
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Residues in contact with ALA 916 (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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882A PHE* 3.7 20.2 - - + -
886A LEU* 3.8 11.9 - - + -
912A GLU 3.0 17.8 + - - +
913A GLN 3.7 3.6 - - - +
915A LEU* 1.3 74.1 - - - +
917A LEU* 1.3 64.5 + - - +
919A GLU* 3.2 11.7 + - + +
920A ARG* 3.1 26.4 + - - +
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Residues in contact with LEU 917 (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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882A PHE* 3.7 20.2 - - + -
885A ILE* 5.2 1.8 - - + -
886A LEU* 4.9 3.8 - - + -
889A ALA* 3.8 27.6 - - + -
893A MET* 5.4 1.7 - - - +
902A ILE* 4.1 30.5 - - + -
905A PHE* 3.6 32.3 - - + -
906A PHE* 3.7 22.0 - - + -
913A GLN 2.9 21.3 + - - +
914A LYS* 3.6 4.7 - - - +
916A ALA* 1.3 74.0 - - - +
918A ALA* 1.3 62.6 + - - +
920A ARG* 2.9 22.3 + - + +
921A ILE* 3.1 16.2 + - + +
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Residues in contact with ALA 918 (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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906A PHE* 4.3 1.7 - - + -
914A LYS 3.0 17.5 + - - +
915A LEU* 3.4 10.1 - - - +
916A ALA 3.3 0.2 - - - -
917A LEU* 1.3 77.1 - - - +
919A GLU* 1.3 59.7 + - - +
921A ILE* 3.4 16.0 + - - +
922A ARG* 3.3 18.2 + - - +
945A ILE* 4.4 16.8 - - + -
949A GLN* 4.4 16.8 - - + -
952A GLU* 5.3 1.9 - - - +
953A MET* 4.4 12.5 - - + +
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Residues in contact with GLU 919 (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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915A LEU 3.1 11.7 + - - +
916A ALA* 3.3 17.0 - - + +
917A LEU 3.1 0.6 - - - -
918A ALA* 1.3 74.1 - - - +
920A ARG* 1.3 102.0 + - - +
921A ILE 3.1 1.9 + - - -
922A ARG* 2.5 61.9 + - - +
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Residues in contact with ARG 920 (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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886A LEU* 3.3 41.6 + - + +
887A GLN* 3.2 39.4 + - - +
889A ALA* 4.1 16.6 - - + +
890A TYR* 4.8 12.2 - - - +
893A MET* 5.4 1.8 - - - -
916A ALA 3.1 16.6 + - - +
917A LEU* 2.9 11.3 + - - +
919A GLU* 1.3 112.9 + - - +
921A ILE* 1.3 58.3 + - + +
922A ARG 3.4 0.8 - - - +
924A HIS* 3.4 22.2 + - - -
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Residues in contact with ILE 921 (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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893A MET* 3.2 36.1 - - + -
906A PHE* 3.9 24.0 - - + -
917A LEU* 3.1 13.7 + - + +
918A ALA* 3.5 8.7 - - - +
919A GLU 3.1 0.4 - - - -
920A ARG* 1.3 77.9 - - - +
922A ARG* 1.3 58.8 + - - +
923A GLY 3.2 0.5 + - - -
924A HIS* 2.8 28.6 + - - +
925A VAL* 3.7 22.8 + - + +
928A LEU* 4.2 6.3 - - + -
937A VAL* 4.3 5.8 - - + -
938A ILE* 3.9 16.8 - - + -
941A ALA* 4.4 2.9 - - + -
953A MET* 3.9 22.0 - - + -
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Residues in contact with ARG 922 (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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918A ALA 3.3 8.3 + - - +
919A GLU* 2.5 58.4 + - - +
920A ARG 4.4 0.3 - - - +
921A ILE* 1.3 79.0 - - - +
923A GLY* 1.3 64.1 + - - +
924A HIS* 3.4 11.4 + - - -
952A GLU* 3.2 31.2 + - + +
956A GLU* 3.7 8.7 - - - +
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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