Contacts of the helix formed by residues 1038 - 1051 (chain R) in PDB entry 3SN6
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 SER1038 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025R TYR* 3.8 7.6 - - - -
1036R SER* 3.1 15.0 + - - +
1037R PRO* 1.3 81.2 - - - +
1039R LEU* 1.3 65.0 + - - +
1040R ASN* 3.5 12.1 + - - +
1041R ALA* 3.6 28.4 + - - +
1042R ALA 4.3 2.1 + - - -
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Residues in contact with LEU1039 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017R ILE* 5.3 3.0 - - + +
1019R LYS* 6.2 0.9 - - - -
1025R TYR* 3.2 45.5 - - + +
1037R PRO 3.6 2.0 + - - -
1038R SER* 1.3 75.2 + - - +
1040R ASN* 1.3 63.7 + - + +
1041R ALA 3.2 1.2 + - - -
1042R ALA 3.9 4.3 + - - -
1043R LYS* 3.8 20.8 + - + +
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Residues in contact with ASN1040 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038R SER* 3.4 6.4 + - - +
1039R LEU* 1.3 79.2 - - + +
1041R ALA* 1.3 62.5 + - - +
1042R ALA 3.4 0.7 - - - -
1043R LYS* 3.1 41.8 + - - +
1044R SER* 3.7 17.3 + - - -
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Residues in contact with ALA1041 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034R THR* 3.9 9.2 - - + +
1036R SER* 3.9 20.4 - - - +
1038R SER* 3.6 30.0 + - - +
1039R LEU 3.2 0.8 - - - -
1040R ASN* 1.3 77.5 - - - +
1042R ALA* 1.3 64.6 + - - +
1044R SER* 3.6 16.9 + - - -
1045R GLU* 3.8 5.2 + - - +
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Residues in contact with ALA1042 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017R ILE* 4.3 3.6 - - + -
1025R TYR* 3.4 43.5 - - + -
1033R LEU* 3.4 26.5 - - + +
1034R THR* 3.4 14.4 - - + +
1038R SER 4.3 0.6 + - - -
1039R LEU 3.9 2.8 + - - +
1040R ASN 3.4 0.2 - - - -
1041R ALA* 1.3 76.0 - - - +
1043R LYS* 1.3 65.7 + - - +
1044R SER 3.1 2.5 - - - -
1045R GLU* 3.1 4.5 + - - -
1046R LEU 2.9 18.5 + - - -
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Residues in contact with LYS1043 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017R ILE* 3.7 20.6 - - + -
1039R LEU* 3.8 17.4 - - + +
1040R ASN* 3.1 44.2 - - - +
1041R ALA 3.4 0.6 - - - -
1042R ALA* 1.3 77.0 - - - +
1044R SER* 1.3 57.4 + - - +
1046R LEU* 3.2 9.2 - - + +
1047R ASP* 2.7 39.7 + - - +
1054R THR 4.7 4.3 - - - +
1055R ASN* 3.5 37.3 + - - +
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Residues in contact with SER1044 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040R ASN* 3.7 9.6 + - - -
1041R ALA* 3.6 13.6 + - - -
1042R ALA 3.1 0.6 - - - -
1043R LYS* 1.3 78.0 - - - +
1045R GLU* 1.3 57.5 + - - +
1047R ASP* 3.0 9.6 + - - +
1048R LYS* 2.9 33.1 + - - +
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Residues in contact with GLU1045 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033R LEU* 3.8 30.3 - - + +
1034R THR* 5.5 0.9 - - - -
1041R ALA 3.8 5.5 + - - +
1042R ALA 3.1 8.3 + - - +
1044R SER* 1.3 79.4 - - - +
1046R LEU* 1.3 56.7 + - - +
1048R LYS* 3.8 7.1 - - - +
1049R ALA* 2.9 32.4 + - - +
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Residues in contact with LEU1046 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017R ILE* 3.9 8.7 - - + -
1027R ILE* 3.8 27.8 - - + -
1033R LEU* 3.4 24.0 - - + +
1042R ALA 2.9 5.7 + - - +
1043R LYS* 3.2 10.8 - - - +
1045R GLU* 1.3 78.9 - - - +
1047R ASP* 1.3 57.0 + - - +
1049R ALA* 4.4 1.1 - - + -
1050R ILE* 2.9 46.4 + - + +
1054R THR* 3.6 18.4 - - + -
1056R GLY* 3.6 31.4 - - - +
1058R ILE* 3.6 22.4 - - + -
1066R LEU* 4.8 3.4 - - + -
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Residues in contact with ASP1047 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043R LYS* 2.7 23.3 + - - +
1044R SER* 3.0 8.7 + - - +
1046R LEU* 1.3 75.8 - - - +
1048R LYS* 1.3 61.1 + - + +
1050R ILE* 4.2 1.1 - - - -
1051R GLY* 2.8 30.1 + - - -
1052R ARG 2.9 25.1 + - - +
1053R ASN* 3.4 22.0 - - - +
1054R THR* 3.2 26.8 - - - +
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Residues in contact with LYS1048 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044R SER* 2.9 18.6 + - - +
1045R GLU* 4.1 7.2 - - - +
1047R ASP* 1.3 77.3 - - + +
1049R ALA* 1.3 63.1 + - - +
1051R GLY* 4.3 3.4 + - - -
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Residues in contact with ALA1049 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031R HIS* 5.3 2.7 - - + -
1033R LEU* 5.0 5.4 - - + -
1045R GLU 2.9 20.5 + - - +
1046R LEU* 3.7 5.4 - - - +
1048R LYS* 1.3 78.4 - - - +
1050R ILE* 1.3 67.7 + - + +
1066R LEU* 4.2 24.2 - - + -
1069R GLN* 5.0 12.0 - - - +
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Residues in contact with ILE1050 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046R LEU* 2.9 38.6 + - + +
1049R ALA* 1.3 77.1 - - + +
1051R GLY* 1.3 62.6 + - - +
1052R ARG* 3.4 41.2 - - + +
1054R THR* 3.3 32.1 - - + -
1058R ILE* 4.3 9.0 - - + -
1062R GLU* 4.1 26.9 - - + +
1066R LEU* 4.6 15.0 - - + -
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Residues in contact with GLY1051 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047R ASP 2.8 19.9 + - - -
1048R LYS* 4.8 3.8 - - - -
1049R ALA 3.3 2.4 - - - -
1050R ILE* 1.3 75.1 - - - +
1052R ARG* 1.3 59.2 + - - +
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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