Contacts of the helix formed by residues 1013 - 1018 (chain B) in PDB entry 4QMI
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 PRO1013 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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978B LEU* 4.1 17.5 - - + -
1009B LEU* 3.5 26.2 - - + -
1011B SER 3.3 6.9 - - - +
1012B THR* 1.3 85.4 - - - +
1014B THR* 1.3 64.1 + - - +
1015B ASP 3.2 3.1 - - - -
1016B LEU* 2.9 31.9 + - + +
1017B ILE 4.7 0.2 + - - -
1048B HIS* 3.5 38.8 - - + +
1049B LEU* 4.9 4.5 - - - +
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Residues in contact with THR1014 (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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1012B THR* 2.9 24.5 + - - +
1013B PRO* 1.3 72.7 - - - +
1015B ASP* 1.3 66.1 + - - +
1016B LEU 3.2 1.3 + - - -
1017B ILE* 3.7 16.8 + - - +
1049B LEU* 5.1 3.8 - - - +
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Residues in contact with ASP1015 (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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978B LEU 3.5 22.2 + - - +
979B GLU* 3.7 15.1 - - - +
980B GLY* 2.7 35.2 + - - +
1013B PRO 3.2 1.0 - - - -
1014B THR* 1.3 83.5 - - - +
1016B LEU* 1.3 64.7 + - - +
1017B ILE* 3.0 7.0 - - - +
1018B LEU* 3.0 33.2 + - + +
1019B CYS* 4.2 2.4 + - - -
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Residues in contact with LEU1016 (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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978B LEU* 4.5 20.7 + - + -
1002B LEU* 5.4 1.8 - - + -
1006B LEU* 4.1 24.5 - - + -
1013B PRO* 2.9 38.7 + - + +
1015B ASP* 1.3 77.6 - - - +
1017B ILE* 1.3 62.1 + - - +
1019B CYS* 3.0 27.9 + - - +
1020B VAL* 3.8 2.9 + - - +
1045B PHE* 3.6 55.4 - - + -
1048B HIS* 4.2 10.5 - - + -
1049B LEU* 4.3 10.8 - - + -
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Residues in contact with ILE1017 (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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1014B THR 3.7 16.4 + - - +
1015B ASP* 4.3 3.4 - - - +
1016B LEU* 1.3 79.8 - - - +
1018B LEU* 1.3 73.0 + - + +
1020B VAL* 3.1 36.4 + - + +
1021B PRO* 3.5 5.9 - - - +
1049B LEU* 4.0 24.1 - - + +
1053B LYS* 4.2 35.0 - - + +
1057B ALA* 5.0 4.7 - - + -
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Residues in contact with LEU1018 (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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980B GLY 3.8 25.4 - - - +
981B GLU* 3.9 17.3 - - + -
984B SER* 3.5 23.0 - - - +
1015B ASP* 3.0 30.2 + - + +
1017B ILE* 1.3 87.3 - - + +
1019B CYS* 1.3 58.3 - - - +
1020B VAL 3.3 0.4 + - - -
1021B PRO* 3.7 8.0 - - - +
1022B HIS* 3.6 12.6 + - - -
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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