Contacts of the helix formed by residues 1011 - 1023 (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 SER1011 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A UNX 3.6 3.5 - - - -
929A MSE 3.5 15.0 - - - -
932A GLU* 4.3 10.3 + - - -
1007A ASN* 2.8 24.6 + - - -
1008A CYS 3.5 2.1 + - - +
1010A HIS* 1.3 81.7 - - - +
1012A PRO* 1.4 57.5 - - - +
1013A ARG* 3.2 2.0 + - - +
1014A LEU* 3.1 23.6 + - - +
1015A ALA* 2.7 34.1 + - - +
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Residues in contact with PRO1012 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A UNX 3.3 15.9 - - - -
932A GLU* 6.1 0.2 - - - +
1010A HIS 4.0 5.6 - - - +
1011A SER* 1.4 85.3 - - - +
1013A ARG* 1.3 52.4 + - - +
1015A ALA* 3.3 2.2 + - + +
1016A ALA* 2.8 36.6 + - - +
1019A ARG* 4.5 2.5 + - - +
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Residues in contact with ARG1013 (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 4.4 3.0 + - - -
924A ARG* 4.1 15.0 - - - +
925A ALA* 3.5 41.3 - - + +
928A ASP* 2.8 32.0 + - + +
929A MSE 3.8 17.7 - - + -
932A GLU* 5.5 2.0 - - - +
1011A SER* 3.2 1.9 - - - +
1012A PRO* 1.3 74.6 - - - +
1014A LEU* 1.4 65.0 + - - +
1016A ALA* 3.5 15.0 + - - +
1017A ALA* 3.1 17.2 + - - +
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Residues in contact with LEU1014 (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* 3.7 31.4 - - + -
925A ALA* 4.4 4.3 - - + -
926A LEU* 3.8 11.2 - - + -
929A MSE 3.4 21.6 - - + +
942A LEU* 4.4 7.4 - - + -
1004A LEU* 3.8 28.9 - - + +
1007A ASN* 3.6 32.8 - - + +
1008A CYS* 3.8 7.9 - - - -
1011A SER* 3.0 22.8 + - - +
1013A ARG* 1.4 72.7 - - - +
1015A ALA* 1.4 60.7 + - - +
1017A ALA* 3.1 2.9 + - - +
1018A VAL* 2.9 29.1 + - + +
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Residues in contact with ALA1015 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A UNX 3.5 17.5 - - - -
1008A CYS* 3.6 24.1 - - + +
1011A SER 2.7 20.9 + - - +
1012A PRO* 3.5 4.7 - - + +
1014A LEU* 1.4 71.8 - - - +
1016A ALA* 1.3 52.1 + - - +
1018A VAL* 3.3 1.0 + - - +
1019A ARG* 2.9 53.9 + - + +
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Residues in contact with ALA1016 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012A PRO 2.8 20.9 + - - +
1013A ARG* 3.5 17.7 - - - +
1015A ALA* 1.3 72.0 - - - +
1017A ALA* 1.4 59.5 + - - +
1019A ARG* 3.5 25.1 + - - +
1020A GLU* 3.3 24.4 + - - +
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Residues in contact with ALA1017 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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921A ALA* 3.5 40.2 - - + +
922A VAL* 4.3 10.5 - - + +
925A ALA* 3.9 9.2 - - + -
1013A ARG* 3.1 16.9 + - - +
1014A LEU* 3.1 10.6 + - + +
1016A ALA* 1.4 75.5 - - - +
1018A VAL* 1.3 63.8 + - - +
1020A GLU* 3.5 6.7 - - - +
1021A PHE* 3.3 19.9 + - - +
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Residues in contact with VAL1018 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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918A PHE* 4.9 2.2 - - + -
922A VAL* 4.7 9.9 - - + -
1004A LEU* 3.7 29.8 - - + -
1005A SER* 6.5 0.4 - - - -
1008A CYS* 3.6 23.3 - - - -
1014A LEU* 2.9 19.0 + - + +
1015A ALA 4.0 1.3 - - - +
1017A ALA* 1.3 73.8 - - - +
1019A ARG* 1.4 53.9 + - - +
1021A PHE* 3.1 9.4 + - + +
1022A GLU* 2.8 60.0 + - + +
1032A ALA* 4.6 12.1 - - + -
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Residues in contact with ARG1019 (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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1012A PRO* 4.5 2.8 + - - +
1015A ALA* 2.9 45.5 + - + +
1016A ALA* 3.5 29.8 - - - +
1018A VAL* 1.4 68.8 - - - +
1020A GLU* 1.4 54.7 + - - +
1021A PHE 2.9 1.9 + - - -
1022A GLU* 2.9 34.7 + - - +
1023A GLN* 3.0 13.2 + - - +
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Residues in contact with GLU1020 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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917A ASP* 5.2 3.7 - - - +
921A ALA* 5.6 5.4 - - + -
1016A ALA 3.3 18.1 + - - +
1017A ALA* 3.5 8.1 - - - +
1019A ARG* 1.4 75.4 - - - +
1021A PHE* 1.3 56.6 + - - +
1023A GLN* 3.3 32.8 - - - +
1024A SER 4.4 4.0 + - - +
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Residues in contact with PHE1021 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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913A HIS 5.0 0.4 - - - -
914A LEU* 3.6 30.7 - - + -
917A ASP* 3.4 32.9 + - + +
918A PHE* 3.4 44.9 - + + -
922A VAL* 6.2 0.4 - - + -
1017A ALA 3.3 6.5 + - - +
1018A VAL* 3.1 11.2 + - + +
1020A GLU* 1.3 75.3 - - - +
1022A GLU* 1.4 55.5 + - + +
1023A GLN 2.8 4.4 + - - -
1024A SER* 2.7 33.1 + - - +
1032A ALA* 4.1 25.1 - - + -
1035A ARG* 3.5 39.8 + - + -
1036A LEU* 5.3 1.1 - - + -
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Residues in contact with GLU1022 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1018A VAL* 2.8 43.7 + - + +
1019A ARG* 2.9 13.2 + - - +
1021A PHE* 1.4 74.5 - - + +
1023A GLN* 1.3 56.8 + - - +
1024A SER 3.4 0.2 - - - -
1031A THR* 3.4 15.9 - - - +
1032A ALA* 3.3 28.9 + - - +
1035A ARG* 3.1 28.9 + - - +
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Residues in contact with GLN1023 (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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1019A ARG 3.0 9.4 + - - +
1020A GLU* 3.3 26.7 + - - +
1021A PHE 2.8 0.6 + - - -
1022A GLU* 1.3 75.5 - - - +
1024A SER* 1.4 76.6 + - - +
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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