Contacts of the helix formed by residues 923 - 939 (chain A) in PDB entry 3MP1
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 ASN 923 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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903A GLY 3.0 23.2 + - - +
905A TYR* 3.6 17.6 - - - -
920A GLY* 3.3 18.3 + - - -
921A VAL 3.6 0.2 - - - -
922A ASP* 1.3 81.3 - - - +
924A ALA* 1.3 62.0 + - - +
925A GLY* 2.9 7.2 + - - +
926A ALA* 2.6 35.3 + - - +
927A LYS* 2.9 20.6 + - - +
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Residues in contact with ALA 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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902A ASP* 4.8 0.6 - - - +
923A ASN* 1.3 74.4 - - - +
925A GLY* 1.3 64.0 + - - +
927A LYS* 3.9 15.3 - - - +
928A ALA* 3.0 27.5 + - - +
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Residues in contact with GLY 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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899A ILE 3.9 4.5 - - - +
902A ASP* 3.3 45.5 + - - +
903A GLY* 3.8 4.0 - - - -
904A GLY 3.7 6.3 - - - -
923A ASN* 2.9 9.9 + - - +
924A ALA* 1.3 81.7 - - - +
926A ALA* 1.3 61.2 + - - +
928A ALA* 3.7 4.2 + - - +
929A GLY* 3.8 4.5 + - - -
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Residues in contact with ALA 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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899A ILE* 3.5 28.7 - - + +
904A GLY* 3.7 14.5 - - - +
920A GLY 3.8 6.5 - - - +
921A VAL* 3.7 21.5 - - - +
923A ASN* 2.6 21.7 + - - +
925A GLY* 1.3 71.9 - - - +
927A LYS* 1.3 64.8 + - - +
929A GLY* 3.0 12.0 + - - -
930A LEU* 3.3 12.5 + - - +
1099A LEU* 4.3 3.5 - - + +
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Residues in contact with LYS 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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922A ASP* 2.9 39.8 + - - +
923A ASN 2.9 19.0 + - - +
924A ALA* 3.9 10.7 - - - +
926A ALA* 1.3 76.6 - - - +
928A ALA* 1.3 55.8 + - - +
930A LEU 4.8 0.2 - - - +
931A THR* 2.7 38.8 + - - +
1095A VAL* 3.9 10.1 - - + +
1096A ASP* 3.4 25.9 + - - +
1099A LEU* 3.5 27.1 - - + +
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Residues in contact with ALA 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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902A ASP* 4.1 14.4 - - - +
924A ALA 3.0 19.2 + - - +
925A GLY 4.0 4.7 - - - +
926A ALA 3.1 0.2 - - - -
927A LYS* 1.3 74.2 - - - +
929A GLY* 1.3 63.3 + - - +
931A THR* 4.1 5.3 - - - +
932A PHE* 3.5 12.1 + - - +
988A PHE* 3.3 22.8 - - + -
989A LYS* 4.5 11.2 - - - -
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Residues in contact with GLY 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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898A LEU* 3.7 41.2 - - - +
899A ILE* 4.5 2.9 - - - -
925A GLY 3.8 4.7 + - - -
926A ALA 3.0 7.4 + - - -
928A ALA* 1.3 78.5 - - - +
930A LEU* 1.3 65.0 + - - +
932A PHE* 3.0 6.9 + - - +
933A LEU 3.0 16.1 + - - -
988A PHE* 4.0 6.7 - - - -
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Residues in contact with LEU 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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899A ILE* 4.4 18.9 - - + +
926A ALA 3.3 12.2 + - - +
927A LYS 4.3 2.2 - - - +
929A GLY* 1.3 72.5 - - - +
931A THR* 1.3 56.7 + - - +
933A LEU* 2.9 26.7 + - + +
934A VAL* 2.7 44.3 + - + +
1084A ALA 4.5 6.5 - - - +
1085A VAL* 4.4 25.1 - - + +
1088A ALA* 3.6 24.0 - - + -
1089A ALA* 5.8 0.9 - - + +
1095A VAL* 4.0 15.0 - - + +
1098A ALA* 5.3 0.4 - - + -
1099A LEU* 4.1 31.2 - - + -
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Residues in contact with THR 931 (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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927A LYS* 2.7 24.9 + - - +
928A ALA* 4.2 6.7 - - - +
930A LEU* 1.3 77.0 - - - +
932A PHE* 1.3 59.3 + - - +
934A VAL* 3.4 2.9 + - + +
935A ASP* 2.7 46.4 + - - +
1095A VAL* 3.6 26.2 - - + +
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Residues in contact with PHE 932 (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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867A TRP* 3.7 48.9 - + + -
868A GLU* 4.0 20.0 - - + -
871A PRO* 4.2 16.2 - - + -
898A LEU* 4.7 5.8 - - + -
928A ALA 3.5 13.4 + - - +
929A GLY* 3.0 10.1 + - - +
931A THR* 1.3 77.6 - - - +
933A LEU* 1.3 64.7 + - - +
935A ASP* 3.4 10.6 + - + +
936A LEU* 3.2 42.7 + - + +
988A PHE* 3.7 23.8 - + + -
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Residues in contact with LEU 933 (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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867A TRP* 5.0 1.1 - - + -
887A PHE* 3.9 17.9 - - + -
889A LEU* 4.1 14.6 - - + -
895A THR* 3.1 27.4 - - + +
898A LEU* 3.9 19.5 - - + +
929A GLY 3.0 11.3 + - - +
930A LEU* 2.9 22.4 + - + +
932A PHE* 1.3 76.3 - - - +
934A VAL* 1.3 65.8 + - + +
936A LEU* 3.2 20.4 + - + +
937A ILE* 3.4 19.2 + - + +
942A MET* 3.4 27.8 - - + -
1085A VAL* 4.6 7.0 - - + -
1089A ALA* 5.5 3.1 - - + -
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Residues in contact with VAL 934 (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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930A LEU* 2.7 27.7 + - + +
931A THR* 3.7 7.4 - - + +
933A LEU* 1.3 73.8 - - + +
935A ASP* 1.3 63.5 + - - +
937A ILE* 3.1 14.0 + - - +
938A LYS* 3.0 44.1 + - + +
1088A ALA* 3.7 35.4 - - + +
1089A ALA* 4.3 5.6 - - + +
1095A VAL* 3.7 23.3 - - + -
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Residues in contact with ASP 935 (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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931A THR* 2.7 39.0 + - - +
932A PHE* 3.7 10.9 - - + +
933A LEU 3.2 0.2 - - - -
934A VAL* 1.3 73.8 - - - +
936A LEU* 1.3 60.5 + - - +
938A LYS* 3.0 20.7 + - - +
939A ASN* 2.8 46.4 + - - +
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Residues in contact with LEU 936 (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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867A TRP* 4.3 17.5 - - + -
870A ILE* 4.4 15.5 - - + -
871A PRO* 3.8 28.5 - - + -
885A LEU* 5.5 0.7 - - + -
932A PHE* 3.2 39.7 + - + +
933A LEU* 3.2 11.6 + - + +
935A ASP* 1.3 78.7 - - + +
937A ILE* 1.3 55.3 + - - +
940A LYS 3.6 1.7 + - - -
941A HIS* 2.7 59.9 + - + +
942A MET* 3.7 28.5 - - + -
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Residues in contact with ILE 937 (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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889A LEU* 4.1 16.8 - - + -
933A LEU* 3.5 21.1 - - + +
934A VAL* 3.4 8.3 - - - +
935A ASP 3.0 0.2 - - - -
936A LEU* 1.3 77.1 - - - +
938A LYS* 1.3 65.6 + - + +
939A ASN 3.2 0.2 - - - -
940A LYS* 3.0 20.4 + - - +
942A MET* 3.4 34.3 - - + +
943A ASN* 4.6 0.7 - - - -
944A ALA* 4.0 15.0 - - + +
1089A ALA* 3.4 49.8 - - + +
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Residues in contact with LYS 938 (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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934A VAL* 3.0 36.3 + - + +
935A ASP* 3.0 25.2 + - - +
937A ILE* 1.3 77.1 - - + +
939A ASN* 1.3 64.3 + - - +
940A LYS* 3.1 21.6 + - - +
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Residues in contact with ASN 939 (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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935A ASP* 2.8 32.3 + - - +
937A ILE 3.2 0.2 - - - -
938A LYS* 1.3 79.8 - - - +
940A LYS* 1.3 70.6 + - - +
941A HIS* 3.3 37.2 + - + +
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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