Contacts of the helix formed by residues 390 - 399 (chain 2) in PDB entry 5IY8
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 GLN 390 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3882 THR* 3.6 11.2 - - + +
3892 ASP* 1.3 77.5 + - + +
3912 ILE* 1.3 58.0 + - - +
3922 ARG 3.2 0.7 - - - -
3932 LEU* 2.9 40.0 + - + +
3942 TRP* 3.1 51.3 + - + -
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Residues in contact with ILE 391 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3882 THR* 3.2 36.5 + - + +
3892 ASP 2.7 7.8 + - - +
3902 GLN* 1.3 73.3 - - - +
3922 ARG* 1.3 69.6 + - + +
3942 TRP* 3.6 20.0 + - + +
3952 GLU* 3.3 21.3 + - - +
511V TRP* 5.2 8.7 - - + -
677V GLN* 4.8 9.4 - - + -
688V LYS* 4.9 2.0 - - - -
689V VAL* 2.9 55.0 - - + +
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Residues in contact with ARG 392 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3882 THR 5.1 4.6 + - - -
3892 ASP* 3.1 16.8 + - - +
3912 ILE* 1.3 84.4 - - + +
3932 LEU* 1.3 64.5 + - + +
3952 GLU* 3.7 22.2 - - - +
3962 LEU* 2.9 28.2 + - + +
674V THR* 2.3 60.2 + - - +
677V GLN* 4.7 11.5 + - - +
678V ARG* 2.8 32.9 - - - +
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Residues in contact with LEU 393 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3892 ASP* 4.0 21.5 - - - +
3902 GLN* 2.9 29.4 + - + +
3922 ARG* 1.3 81.5 - - + +
3942 TRP* 1.3 61.4 + - + +
3962 LEU* 3.4 19.3 + - + +
3972 GLU* 2.9 27.9 + - - +
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Residues in contact with TRP 394 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3882 THR* 5.0 6.1 - - + -
3902 GLN* 3.1 65.8 + - + -
3912 ILE* 3.7 17.7 - - + +
3932 LEU* 1.3 76.7 - - + +
3952 GLU* 1.3 57.0 + - - +
3972 GLU* 3.6 22.5 + - - +
3982 ARG* 3.1 27.2 + - - +
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Residues in contact with GLU 395 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3912 ILE* 3.3 15.1 + - - +
3922 ARG* 3.7 26.6 - - - +
3942 TRP* 1.3 73.5 - - - +
3962 LEU* 1.3 57.5 + - - +
3982 ARG* 3.0 10.9 + - + +
3992 ASP* 2.9 34.1 + - - +
511V TRP* 3.0 46.2 - - + -
670V MET* 3.8 15.4 - - - +
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Residues in contact with LEU 396 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3922 ARG* 2.9 19.6 + - + +
3932 LEU* 3.4 21.7 + - + +
3952 GLU* 1.3 71.7 - - - +
3972 GLU* 1.3 64.5 + - - +
3992 ASP* 3.7 20.7 + - + +
4002 ARG* 3.5 25.4 - - + +
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Residues in contact with GLU 397 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3932 LEU 2.9 16.1 + - - +
3942 TRP* 3.6 24.9 - - - +
3952 GLU 3.3 0.2 - - - -
3962 LEU* 1.3 74.2 - - - +
3982 ARG* 1.3 57.3 + - - +
4002 ARG* 2.9 29.8 + - - +
4012 LEU* 3.1 23.3 - - + +
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Residues in contact with ARG 398 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3942 TRP 3.1 14.2 + - - +
3952 GLU* 3.0 13.9 + - + +
3972 GLU* 1.3 74.7 - - - +
3992 ASP* 1.3 60.8 + - - +
4002 ARG 3.1 1.4 + - - -
4012 LEU* 3.2 27.7 + - + +
4022 ARG* 4.3 4.7 + - - +
511V TRP* 6.5 1.1 - - - -
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Residues in contact with ASP 399 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561 ARG* 5.6 2.1 + - - -
591 GLU* 3.1 6.1 - - - +
3952 GLU* 2.9 18.2 + - - +
3962 LEU* 3.7 23.9 - - + +
3972 GLU 3.2 0.4 + - - -
3982 ARG* 1.3 73.9 - - - +
4002 ARG* 1.3 60.6 + - + +
4012 LEU 3.5 0.4 - - - -
4022 ARG* 2.5 70.4 + - - +
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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