Contacts of the helix formed by residues 386 - 395 (chain A) in PDB entry 1IR1
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 HIS 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A VAL* 3.8 40.4 + - + +
381A GLY 3.7 15.3 - - - -
382A ILE* 3.3 7.1 - - + +
383A HIS* 2.8 57.4 + + - +
385A TRP* 1.3 78.3 - - + +
387A MET* 1.3 64.6 + - - +
388A PRO 3.4 2.0 - - - -
389A ALA* 3.2 10.5 + - + +
390A LEU* 3.0 36.8 + - + +
465A ILE 4.3 6.4 + - - -
466A LYS* 4.5 19.2 - - + +
467A PHE* 4.7 4.7 - + - -
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Residues in contact with MET 387 (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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170A LEU* 4.8 1.3 - - + -
383A HIS 3.7 2.6 + - - -
384A VAL* 3.1 21.1 + - - +
386A HIS* 1.3 77.4 - - - +
388A PRO* 1.3 65.3 - - + +
390A LEU* 3.7 4.6 - - - +
391A THR* 2.9 32.5 + - - +
400A LEU* 3.9 21.8 - - - -
402A PHE* 3.4 37.9 - - + -
420A ASN* 3.5 33.2 - - - +
423A ALA* 3.8 15.7 - - + +
424A LEU* 3.7 31.4 - - + +
427A CYS* 4.0 6.1 - - - -
445A ILE* 4.5 0.7 - - + -
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Residues in contact with PRO 388 (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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384A VAL 4.0 3.4 - - - +
385A TRP 3.6 13.0 - - - +
386A HIS 3.5 3.8 - - - -
387A MET* 1.3 94.4 - - + +
389A ALA* 1.3 56.2 + - - +
391A THR* 3.4 2.4 + - - -
392A GLU* 2.9 31.1 + - - +
427A CYS* 3.6 23.1 - - - -
437A LEU* 3.9 20.4 - - + +
441A GLY* 3.6 42.0 - - - +
444A ILE* 5.5 1.1 - - + -
445A ILE* 3.9 7.2 - - + -
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Residues in contact with ALA 389 (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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332A VAL* 4.7 19.5 - - + -
385A TRP 5.3 0.9 + - - +
386A HIS* 3.2 12.6 + - + +
388A PRO* 1.3 79.6 - - - +
390A LEU* 1.3 59.4 + - + +
392A GLU* 3.3 8.9 + - - +
393A ILE* 2.9 41.9 + - + +
437A LEU 6.2 0.2 - - - -
438A ALA* 6.4 1.6 - - - +
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Residues in contact with LEU 390 (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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330A THR* 3.9 30.7 - - - +
332A VAL* 4.2 10.1 - - + -
378A ALA* 4.4 6.7 - - + -
382A ILE* 3.7 25.8 - - + -
386A HIS* 3.0 36.5 + - + +
387A MET* 3.7 6.1 - - - +
389A ALA* 1.3 75.8 - - - +
391A THR* 1.3 58.2 + - - +
393A ILE* 3.4 1.7 + - + -
394A PHE* 3.0 52.7 + - + +
400A LEU* 4.2 20.1 - - + +
402A PHE* 4.2 14.1 - - + -
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Residues in contact with THR 391 (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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168A PRO* 4.9 8.5 - - + -
387A MET* 2.9 19.6 + - - +
388A PRO 3.7 3.4 - - - -
390A LEU* 1.3 74.8 - - - +
392A GLU* 1.3 58.6 + - - +
395A GLY* 3.0 31.0 + - - +
400A LEU* 4.6 5.1 - - - +
424A LEU* 3.8 19.8 - - - +
427A CYS* 4.1 14.5 - - + +
428A VAL* 4.8 10.8 - - + -
431A ARG* 4.1 23.4 + - - +
437A LEU* 3.7 19.7 - - + -
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Residues in contact with GLU 392 (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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339A ARG* 2.5 38.4 + - - -
388A PRO 2.9 18.0 + - - +
389A ALA* 3.5 7.5 - - - +
391A THR* 1.3 80.2 - - - +
393A ILE* 1.3 63.0 + - - +
395A GLY* 4.4 1.9 + - - -
436A ASP* 5.7 1.3 - - - +
437A LEU* 4.1 23.1 - - + +
438A ALA* 4.6 21.7 - - + +
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Residues in contact with ILE 393 (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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330A THR 4.5 5.6 - - - +
331A VAL* 4.3 32.5 - - + -
332A VAL* 5.1 4.9 - - + -
339A ARG* 3.7 33.4 - - + +
342A THR* 5.6 1.8 - - + -
343A LEU* 3.4 37.0 - - + +
346A VAL* 6.1 0.2 - - - +
350A ARG* 5.5 1.9 + - - -
389A ALA* 2.9 30.6 + - + +
390A LEU* 3.9 4.7 - - + +
392A GLU* 1.3 80.4 - - - +
394A PHE* 1.3 85.2 + - + +
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Residues in contact with PHE 394 (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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328A SER* 3.5 19.3 - - - -
329A GLY 3.2 23.6 - - - -
330A THR* 4.3 7.9 - - - -
331A VAL* 5.1 0.4 - - + -
342A THR* 4.3 11.2 - - + -
343A LEU* 6.0 0.7 - - + -
346A VAL* 4.1 24.5 - - + -
350A ARG* 2.8 34.1 + - - +
376A PRO* 4.6 11.4 - - + -
378A ALA* 3.7 22.4 - - + -
390A LEU* 3.0 34.7 + - + +
393A ILE* 1.3 94.9 - - + +
395A GLY* 1.3 62.5 + - - +
397A ASP 4.3 0.2 - - - +
398A SER* 3.6 23.1 - - - +
400A LEU* 4.6 3.1 - - + -
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Residues in contact with GLY 395 (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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168A PRO* 3.4 10.6 - - - +
391A THR* 3.0 21.4 + - - +
392A GLU 4.4 1.7 + - - -
393A ILE 3.7 0.6 - - - -
394A PHE* 1.3 80.9 - - - +
396A ASP* 1.3 67.1 + - - -
398A SER* 3.2 13.2 + - - -
431A ARG* 4.6 7.2 - - - -
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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