Contacts of the helix formed by residues 398 - 404 (chain A) in PDB entry 2IO2
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 THR 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A GLN 3.5 8.1 + - - -
386A ASP* 3.8 28.3 - - - +
387A GLU 4.6 0.4 - - - -
388A ILE* 4.1 14.1 - - + +
389A LEU* 4.9 1.1 - - - -
396A ARG* 3.4 15.3 - - + +
397A ILE* 1.3 74.2 - - - +
399A ARG* 1.3 64.6 + - - +
400A GLY* 3.0 13.5 + - - -
401A ASP* 3.2 23.0 + - - +
402A ILE* 2.8 26.8 + - - +
60B ASN* 5.3 9.4 - - - +
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Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A ASN* 2.6 28.6 + - - +
379A ALA* 3.1 21.0 + - - +
381A GLY 3.8 6.2 + - - +
382A HIS 2.6 24.5 + - - -
383A GLY* 3.1 22.0 - - - +
384A PRO* 2.9 47.5 + - - +
385A GLN* 3.7 10.1 - - - +
386A ASP 4.1 1.1 - - - +
387A GLU* 3.5 27.4 + - - +
389A LEU* 3.4 18.4 - - - +
398A THR* 1.3 75.9 + - - +
400A GLY* 1.3 65.9 + - - +
402A ILE* 3.1 3.9 - - - +
403A GLN* 2.7 44.6 + - + +
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Residues in contact with GLY 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A GLN* 3.4 32.1 + - - +
398A THR* 3.0 7.0 + - - -
399A ARG* 1.3 79.5 - - - +
401A ASP* 1.3 65.4 + - - +
403A GLN* 3.1 12.5 - - - +
404A THR* 3.6 7.8 - - - +
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Residues in contact with ASP 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ARG 4.3 1.3 - - - +
397A ILE* 4.2 7.0 - - + -
398A THR* 3.2 38.2 + - - +
399A ARG 3.0 0.8 + - - -
400A GLY* 1.3 74.1 - - - +
402A ILE* 1.3 58.9 + - - +
403A GLN 2.8 2.9 + - - -
404A THR* 2.7 31.9 + - - +
412A ASN* 3.1 17.3 - - - +
414A GLU* 3.2 38.5 - - + +
415A VAL* 3.8 4.1 - - + +
60B ASN* 5.9 2.9 - - - +
63B ARG* 4.0 10.3 + - - -
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Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ALA* 3.8 28.5 - - + +
380A LEU* 3.3 16.3 - - + +
389A LEU* 4.0 8.7 - - + -
397A ILE* 3.9 15.1 - - + +
398A THR 2.8 25.8 + - - +
399A ARG* 3.1 16.2 - - - +
401A ASP* 1.3 72.8 - - - +
403A GLN* 1.3 60.2 + - - +
404A THR 3.2 0.4 - - - -
405A LEU* 3.2 19.5 + - + +
415A VAL* 4.0 11.2 - - + -
580A VAL* 3.6 40.8 - - + +
583A ILE* 5.5 4.7 - - + -
584A LEU* 4.2 9.6 - - + -
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Residues in contact with GLN 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ALA 3.3 13.5 + - - -
380A LEU* 2.9 36.3 + - - +
381A GLY 3.3 10.1 + - - +
385A GLN* 3.2 23.6 + - - +
399A ARG* 2.7 30.4 + - - +
400A GLY* 3.1 11.0 - - - +
401A ASP 2.8 0.4 + - - -
402A ILE* 1.3 72.3 - - - +
404A THR* 1.3 51.6 + - - +
405A LEU 2.8 16.5 + - - -
406A LYS* 2.9 58.3 + - - +
409A HIS* 4.1 4.3 + - - +
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Residues in contact with THR 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLY 3.6 8.1 - - - +
401A ASP 2.7 22.9 + - - +
403A GLN* 1.3 75.5 - - - +
405A LEU* 1.3 58.1 + - - +
406A LYS 3.3 1.1 - - - -
409A HIS* 3.7 16.5 - - - +
410A TRP 3.5 16.6 - - - +
411A LEU* 3.1 31.7 + - - +
412A ASN* 2.9 30.0 + - + +
415A VAL* 3.6 13.3 - - - +
576A ARG* 3.7 3.1 + - - -
93B GLU* 5.3 1.3 - - - +
95B THR* 6.0 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