Contacts of the helix formed by residues 918 - 930 (chain A) in PDB entry 3MPX
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 PHE 918 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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914A LEU* 2.7 27.3 + - + +
917A ASP* 1.3 74.5 - - - +
919A HIS* 1.3 66.2 + - - -
921A ALA 3.4 0.9 + - - -
922A VAL* 2.9 40.0 + - + +
946A LEU* 3.4 26.0 - - + -
949A LEU* 3.6 19.3 - - + -
1000A TYR* 4.6 3.8 - + - -
1001A LEU* 4.4 1.8 - - + -
1004A LEU* 3.5 33.2 - - + -
1018A VAL* 4.9 4.3 - - + -
1021A PHE* 3.4 42.6 - + + -
1032A ALA* 4.1 11.9 - - + -
1036A LEU* 3.6 24.2 - - + -
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Residues in contact with HIS 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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914A LEU 3.0 5.5 + - - -
915A ASN* 3.6 31.6 - - + +
918A PHE* 1.3 77.5 - - - +
920A GLY* 1.3 59.2 + - - +
922A VAL* 3.6 1.2 - - - +
923A MSE 2.7 68.3 + - + +
946A LEU* 3.0 39.5 + - + +
947A SER* 4.7 4.0 - - - -
949A LEU* 4.1 12.6 - - + -
950A PRO* 3.5 23.7 - - + +
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Residues in contact with GLY 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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915A ASN 2.8 21.7 + - - -
916A LEU* 3.8 6.7 + - - -
918A PHE 3.4 0.4 - - - -
919A HIS* 1.3 79.4 - - - +
921A ALA* 1.4 54.6 + - - +
923A MSE 3.4 4.6 + - - +
924A ARG* 2.9 43.0 + - - +
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Residues in contact with ALA 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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916A LEU 3.8 2.6 + - - -
917A ASP* 3.4 24.0 - - - +
918A PHE 3.4 1.4 + - - +
919A HIS 3.4 0.4 - - - -
920A GLY* 1.4 74.5 - - - +
922A VAL* 1.3 57.8 + - + +
924A ARG* 3.6 29.4 + - - +
925A ALA* 3.1 20.8 + - - +
1013A ARG* 4.4 3.1 + - - -
1017A ALA* 3.5 28.4 - - + +
1020A GLU* 5.6 4.7 - - + -
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Residues in contact with VAL 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 PHE* 2.9 44.0 + - + +
919A HIS 3.8 2.2 - - - +
921A ALA* 1.3 74.4 - - + +
923A MSE 1.4 56.2 + - - +
925A ALA* 3.2 1.6 + - - +
926A LEU* 2.8 41.6 + - + +
942A LEU* 5.3 0.2 - - + -
946A LEU* 3.7 26.9 - - + -
1004A LEU* 4.5 7.0 - - + -
1014A LEU* 3.7 23.3 - - + -
1017A ALA* 4.3 16.6 - - + -
1018A VAL* 4.7 9.6 - - + -
1021A PHE* 6.2 0.2 - - + -
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Residues in contact with MSE 923 (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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919A HIS* 2.7 56.6 + - + +
920A GLY* 3.7 5.8 - - - +
922A VAL* 1.4 71.2 - - - +
924A ARG* 1.4 52.3 + - - +
926A LEU* 3.8 7.5 - - - +
927A ASP* 2.9 50.6 + - - +
943A ARG* 4.1 44.0 - - + +
946A LEU* 4.6 15.3 - - - -
947A SER* 6.6 0.2 - - - -
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Residues in contact with ARG 924 (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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916A LEU* 3.8 15.2 + - - +
917A ASP* 5.5 0.6 - - - +
920A GLY* 2.9 18.0 + - - +
921A ALA* 3.6 39.0 + - - +
922A VAL 3.3 0.2 - - - -
923A MSE 1.4 76.6 - - - +
925A ALA* 1.3 63.5 + - - +
927A ASP* 3.5 10.5 + - - +
928A ASP* 3.3 21.5 + - - +
1013A ARG* 4.1 14.2 - - - +
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Residues in contact with ALA 925 (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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921A ALA 3.1 16.7 + - - +
922A VAL* 3.6 4.7 - - - +
924A ARG* 1.3 75.1 - - - +
926A LEU* 1.4 53.1 + - - +
928A ASP* 2.8 26.7 + - - +
929A MSE 3.0 33.5 + - + +
1013A ARG* 3.5 38.2 - - - +
1014A LEU* 4.4 1.6 - - + -
1017A ALA* 3.9 7.9 - - + -
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Residues in contact with LEU 926 (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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922A VAL* 2.8 38.3 + - + +
923A MSE 3.9 4.7 - - - +
925A ALA* 1.4 71.1 - - - +
927A ASP* 1.4 61.0 + - - +
929A MSE 3.1 23.2 + - - +
930A ASP* 3.1 10.7 + - - -
939A ARG* 3.8 27.6 - - + +
942A LEU* 3.8 33.9 - - + -
943A ARG* 3.3 40.5 + - + +
946A LEU* 4.3 5.8 - - + -
1014A LEU* 3.8 21.1 - - + -
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Residues in contact with ASP 927 (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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923A MSE 2.9 35.7 + - - +
924A ARG* 3.6 8.8 - - - +
926A LEU* 1.4 74.3 - - - +
928A ASP* 1.4 62.8 + - - +
930A ASP* 3.3 23.9 - - - +
931A HIS* 3.6 14.5 - - - -
943A ARG* 3.2 18.0 + - - -
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Residues in contact with ASP 928 (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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924A ARG 3.5 11.8 - - - +
925A ALA 2.8 14.0 + - - +
927A ASP* 1.4 71.3 - - - +
929A MSE 1.3 59.8 + - - +
930A ASP 3.2 6.2 + - - -
931A HIS* 3.3 24.0 + - - +
932A GLU* 3.9 2.8 + - - +
1013A ARG* 2.8 38.3 + - + +
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Residues in contact with MSE 929 (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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925A ALA* 3.0 43.8 + - + +
926A LEU* 3.1 25.3 + - - +
928A ASP* 1.3 72.0 - - - +
930A ASP* 1.3 64.4 + - - +
931A HIS 3.2 2.5 - - - -
932A GLU* 3.1 44.5 + - + +
939A ARG* 3.2 26.4 + - - -
1007A ASN* 6.3 1.1 - - - -
1011A SER* 3.5 16.8 - - - -
1013A ARG* 3.8 12.1 - - + -
1014A LEU* 3.4 32.8 - - + +
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Residues in contact with ASP 930 (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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926A LEU 3.1 1.9 + - - -
927A ASP* 3.3 19.9 - - - +
928A ASP 3.2 0.8 - - - -
929A MSE 1.3 78.7 - - - +
931A HIS* 1.4 67.3 + - + +
932A GLU* 3.7 1.7 + - - +
939A ARG* 3.1 35.3 + - - +
940A GLU* 4.7 1.6 - - - +
943A ARG* 2.7 35.0 + - - -
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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