Contacts of the helix formed by residues 1016 - 1025 (chain W) in PDB entry 5IJO
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 ALA1016 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982W LEU* 5.4 17.0 - - + +
983W VAL* 6.2 2.0 - - - -
1015W GLU* 1.3 78.4 - - - +
1017W GLY* 1.3 62.9 + - - +
1019W HIS* 3.4 16.1 + - - +
1020W PHE* 3.5 11.8 + - - +
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Residues in contact with GLY1017 (chain W).
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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1015W GLU 3.3 1.0 - - - -
1016W ALA* 1.3 77.3 - - - +
1018W HIS* 1.3 66.0 + - - +
1019W HIS 3.1 0.3 + - - -
1020W PHE* 3.2 6.4 + - - +
1021W GLU* 3.0 26.1 + - - +
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Residues in contact with HIS1018 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927W GLU* 4.6 12.1 - - + +
1015W GLU* 3.7 11.7 + - + +
1016W ALA 3.4 0.8 - - - -
1017W GLY* 1.3 76.0 - - - +
1019W HIS* 1.3 63.6 + - - +
1021W GLU* 3.8 3.9 + - - +
1022W GLN* 3.5 18.7 + - - +
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Residues in contact with HIS1019 (chain W).
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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926W TYR* 4.5 22.2 - - + -
927W GLU* 4.5 15.3 - - + +
930W VAL* 5.2 5.4 - - - +
979W LEU* 6.5 0.7 - - - -
982W LEU* 5.0 13.0 - - + -
1015W GLU 4.2 4.6 + - - +
1016W ALA* 3.4 11.8 + - - +
1017W GLY 3.1 0.4 - - - -
1018W HIS* 1.3 79.6 - - - +
1020W PHE* 1.4 62.5 + - - +
1022W GLN* 3.4 17.2 - - - +
1023W MET* 3.6 5.7 + - - +
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Residues in contact with PHE1020 (chain W).
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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1016W ALA 3.5 8.1 + - - +
1017W GLY* 3.2 9.2 + - - +
1019W HIS* 1.4 74.5 - - - +
1021W GLU* 1.3 66.2 + - - +
1022W GLN 3.0 2.2 - - - -
1023W MET* 2.9 20.2 + - - +
1024W LEU* 3.1 12.7 + - - +
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Residues in contact with GLU1021 (chain W).
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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1017W GLY 3.0 16.7 + - - +
1018W HIS* 4.4 3.4 - - - +
1020W PHE* 1.3 77.2 - - - +
1022W GLN* 1.3 53.6 + - - +
1024W LEU* 3.9 6.7 - - - +
1025W LYS* 2.7 40.8 + - + +
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Residues in contact with GLN1022 (chain W).
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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927W GLU* 4.7 17.5 - - + +
930W VAL* 5.4 4.5 - - + -
931W GLU* 5.9 4.0 - - + +
1018W HIS 3.5 11.3 + - - +
1019W HIS* 3.4 13.6 + - - +
1020W PHE 3.0 0.2 - - - -
1021W GLU* 1.3 80.0 - - - +
1023W MET* 1.3 62.2 + - - +
1025W LYS* 3.2 23.0 - - - +
1026W LEU* 3.8 5.2 + - - +
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Residues in contact with MET1023 (chain W).
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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930W VAL* 5.4 11.6 - - + +
1019W HIS 3.6 4.8 + - - +
1020W PHE* 2.9 13.7 + - - +
1022W GLN* 1.3 78.1 - - - +
1024W LEU* 1.3 64.5 + - - +
1026W LEU* 3.4 17.0 - - - +
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Residues in contact with LEU1024 (chain W).
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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1020W PHE 3.1 8.0 + - - +
1021W GLU* 3.9 8.1 - - - +
1023W MET* 1.3 80.1 - - - +
1025W LYS* 1.3 58.4 + - - +
1026W LEU 2.7 15.1 + - - +
1055W VAL* 6.0 5.8 - - + -
1057W SER* 4.7 22.3 - - - +
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Residues in contact with LYS1025 (chain W).
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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1021W GLU* 2.7 25.4 + - + +
1022W GLN* 3.2 12.2 - - - +
1024W LEU* 1.3 72.2 - - - +
1026W LEU* 1.3 54.7 + - - +
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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