Contacts of the helix formed by residues 1038 - 1051 (chain C) in PDB entry 4DAJ
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1036C SER* 3.1 19.1 + - - +
1037C PRO* 1.3 81.2 - - - +
1039C LEU* 1.3 64.9 + - - +
1040C ASN* 2.5 26.8 + - - -
1041C ALA* 3.3 14.9 + - - +
1042C ALA* 3.3 11.4 + - - +
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Residues in contact with LEU1039 (chain C).
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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1017C ILE* 5.7 1.2 - - - +
1037C PRO 3.4 5.4 + - - +
1038C SER* 1.3 69.1 + - - +
1040C ASN* 1.3 62.0 + - - +
1041C ALA 3.1 1.8 - - - -
1042C ALA* 3.3 6.9 + - - +
1043C LYS* 2.9 28.9 + - - +
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Residues in contact with ASN1040 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038C SER* 2.5 29.4 + - - -
1039C LEU* 1.3 76.1 - - - +
1041C ALA* 1.3 62.7 + - - +
1043C LYS* 3.6 8.9 - - - +
1044C SER* 2.9 26.9 + - - -
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Residues in contact with ALA1041 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034C THR* 4.5 4.2 - - + +
1036C SER* 3.7 24.0 - - - +
1038C SER* 3.3 17.0 - - - +
1039C LEU 3.1 0.4 - - - -
1040C ASN* 1.3 81.1 + - - +
1042C ALA* 1.3 64.7 - - - +
1044C SER* 3.0 8.5 + - - -
1045C GLU* 2.9 22.9 + - - +
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Residues in contact with ALA1042 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017C ILE* 5.0 7.4 - - + -
1025C TYR* 3.9 28.9 - - + -
1033C LEU* 3.8 14.3 - - + +
1034C THR* 3.9 18.7 - - + +
1036C SER 5.2 0.7 - - - +
1038C SER 3.3 8.1 + - - +
1039C LEU* 3.8 8.1 - - - +
1041C ALA* 1.3 78.4 - - - +
1043C LYS* 1.3 58.0 + - - +
1045C GLU* 3.3 4.4 + - - +
1046C LEU* 2.9 30.5 + - - +
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Residues in contact with LYS1043 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017C ILE* 5.0 10.6 - - + +
1039C LEU 2.9 17.7 + - - +
1040C ASN* 3.6 11.0 - - - +
1042C ALA* 1.3 77.6 - - - +
1044C SER* 1.3 57.4 + - - +
1046C LEU* 4.5 5.4 - - - -
1047C ASP* 2.9 44.3 + - - +
1054C THR* 5.9 0.2 - - - -
1055C ASN* 6.2 2.2 - - - -
1056C GLY* 5.8 5.4 - - - +
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Residues in contact with SER1044 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040C ASN 2.9 16.2 + - - -
1041C ALA* 3.0 11.8 + - - -
1043C LYS* 1.3 76.3 - - - +
1045C GLU* 1.3 56.9 + - - +
1047C ASP* 3.9 6.3 - - - +
1048C LYS* 2.9 29.1 + - - +
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Residues in contact with GLU1045 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033C LEU* 4.1 30.7 - - + +
1034C THR* 5.1 3.4 - - - -
1041C ALA 2.9 12.1 + - - +
1042C ALA* 3.7 7.4 - - - +
1044C SER* 1.3 74.5 - - - +
1046C LEU* 1.3 60.7 + - - +
1048C LYS* 3.2 8.1 + - - +
1049C ALA* 2.9 28.6 + - - +
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Residues in contact with LEU1046 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017C ILE* 4.0 20.4 - - + -
1027C ILE* 3.7 38.1 - - + -
1033C LEU* 4.0 15.7 - - + +
1042C ALA 2.9 17.4 + - - +
1043C LYS* 3.8 4.3 - - - +
1045C GLU* 1.3 73.9 - - - +
1047C ASP* 1.3 67.2 + - - +
1049C ALA* 2.9 5.5 + - + -
1050C ILE* 2.9 41.2 + - + +
1054C THR* 3.2 28.5 - - + +
1056C GLY* 4.3 3.1 - - - -
1058C ILE* 3.9 8.3 - - + -
1066C LEU* 4.8 7.0 - - + -
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Residues in contact with ASP1047 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043C LYS* 2.9 33.9 + - - +
1044C SER* 4.0 5.3 - - - +
1046C LEU* 1.3 74.5 - - - +
1048C LYS* 1.3 61.7 + - - +
1051C GLY* 3.1 21.1 + - - -
1052C ARG 3.2 19.5 + - - +
1053C ASN* 3.9 20.0 + - - +
1054C THR* 2.9 37.8 + - - -
1055C ASN* 3.7 5.2 + - - -
1056C GLY 4.9 0.2 + - - -
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Residues in contact with LYS1048 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044C SER 2.9 21.0 + - - +
1045C GLU* 3.3 9.9 - - - +
1046C LEU 3.1 0.2 - - - -
1047C ASP* 1.3 79.0 - - - +
1049C ALA* 1.3 61.2 + - - +
1051C GLY* 3.8 7.3 + - - -
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Residues in contact with ALA1049 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031C HIS* 4.8 10.3 - - + +
1033C LEU* 5.8 1.6 - - + -
1045C GLU 2.9 15.9 + - - +
1046C LEU* 2.9 9.6 + - + +
1048C LYS* 1.3 76.5 - - - +
1050C ILE* 1.3 65.0 + - - +
1051C GLY* 3.5 0.5 + - - -
1066C LEU* 4.6 20.7 - - + +
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Residues in contact with ILE1050 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046C LEU* 2.9 19.7 + - + +
1047C ASP 4.4 0.7 - - - +
1049C ALA* 1.3 76.5 - - - +
1051C GLY* 1.3 58.4 + - - +
1052C ARG* 3.7 23.7 - - + +
1054C THR* 3.8 22.4 - - + -
1058C ILE* 3.9 8.1 - - + -
1062C GLU* 3.1 51.8 - - + +
1066C LEU* 3.8 24.7 - - + -
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Residues in contact with GLY1051 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047C ASP 3.1 13.2 + - - -
1048C LYS 4.2 7.0 - - - -
1049C ALA 3.3 2.4 - - - -
1050C ILE* 1.3 77.9 - - - +
1052C ARG* 1.3 59.8 + - - +
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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