Contacts of the helix formed by residues 1018 - 1027 (chain B) in PDB entry 2IUI
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 SER1018 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017B ILE* 1.3 76.5 - - - +
1019B ARG* 1.3 65.6 + - - +
1020B GLU* 3.5 10.2 + - - +
1021B GLU* 3.0 42.1 + - - +
1022B VAL* 3.1 16.2 + - - +
1037B ARG* 4.6 1.1 - - - -
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Residues in contact with ARG1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018B SER* 1.3 74.2 - - - +
1020B GLU* 1.3 58.0 + - - +
1022B VAL* 3.5 4.6 + - - +
1023B ASN* 3.1 43.0 + - - +
1037B ARG* 3.6 24.7 - - - +
1040B SER* 5.2 5.3 - - - -
1059B LEU* 4.4 19.5 - - + +
1203D ASP* 2.9 39.4 + - - -
1204D PTR 2.8 35.3 + - - -
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Residues in contact with GLU1020 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018B SER* 3.1 9.4 + - - +
1019B ARG* 1.3 76.8 - - - +
1021B GLU* 1.3 66.0 + - - +
1023B ASN* 3.4 13.9 + - + +
1024B GLU* 3.3 25.1 + - + +
1027B ARG* 5.4 0.3 + - - -
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Residues in contact with GLU1021 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016B ASP 5.1 0.3 - - - +
1017B ILE* 3.7 27.3 - - + +
1018B SER* 3.0 39.4 + - - +
1020B GLU* 1.3 74.2 - - + +
1022B VAL* 1.3 65.0 + - - +
1024B GLU* 3.0 20.6 + - - +
1025B LYS* 3.2 24.0 + - - +
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Residues in contact with VAL1022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017B ILE* 3.4 27.3 - - + +
1018B SER 3.1 9.3 + - - +
1019B ARG* 3.6 9.2 - - + +
1021B GLU* 1.3 75.3 - - - +
1023B ASN* 1.3 60.5 + - - +
1025B LYS* 3.0 10.2 + - - +
1026B LEU* 2.9 33.8 + - + +
1035B LEU* 3.8 19.5 - - + -
1037B ARG* 3.8 19.3 - - - +
1050B THR* 3.8 35.4 - - + +
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Residues in contact with ASN1023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019B ARG* 3.1 32.9 + - - +
1020B GLU* 3.5 14.4 - - + +
1021B GLU 3.2 0.4 - - - -
1022B VAL* 1.3 78.3 - - - +
1024B GLU* 1.3 57.8 + - - +
1026B LEU 3.7 0.5 - - - -
1027B ARG* 2.9 42.4 + - - +
1057B ASN* 2.8 33.9 + - - +
1059B LEU* 6.1 0.9 - - - +
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Residues in contact with GLU1024 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020B GLU* 3.3 13.2 + - + +
1021B GLU* 3.0 14.4 + - - +
1023B ASN* 1.3 81.8 - - - +
1025B LYS* 1.3 62.5 + - + +
1027B ARG* 2.7 51.3 + - - +
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Residues in contact with LYS1025 (chain B).
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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1014B TRP* 3.2 48.5 - - + -
1017B ILE* 3.9 18.4 - - + -
1021B GLU* 3.7 18.3 + - - +
1022B VAL* 3.0 7.9 + - - +
1024B GLU* 1.3 79.2 - - + +
1026B LEU* 1.3 63.9 + - - +
1027B ARG 3.6 1.2 + - - +
1029B THR* 3.5 13.9 - - - +
1035B LEU* 3.8 23.6 - - + -
1107B VAL* 4.2 17.6 - - + +
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Residues in contact with LEU1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022B VAL* 2.9 21.0 + - + +
1025B LYS* 1.3 76.5 - - - +
1027B ARG* 1.3 63.9 + - - +
1028B ASP 3.1 2.6 + - - -
1029B THR* 2.7 24.0 + - - +
1033B THR* 3.7 18.4 - - + -
1034B PHE* 4.5 1.3 - - - +
1035B LEU* 4.5 6.1 - - + +
1050B THR* 3.4 44.9 - - + +
1051B LEU 4.4 1.6 - - - +
1052B ARG* 3.3 20.6 + - + +
1057B ASN* 3.6 25.6 - - + +
1107B VAL* 3.6 30.5 - - + -
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Residues in contact with ARG1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020B GLU 5.4 0.4 + - - -
1023B ASN* 2.9 23.7 + - - +
1024B GLU* 2.7 62.2 + - - +
1025B LYS 3.3 3.3 - - - +
1026B LEU* 1.3 76.7 - - - +
1028B ASP* 1.3 89.0 + - + +
1029B THR* 3.3 7.6 + - - +
1052B ARG* 4.7 4.9 - - - +
1057B ASN* 6.2 0.2 - - - +
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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