Contacts of the helix formed by residues 386 - 395 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332D VAL* 3.6 39.4 + - + +
381D GLY 3.9 8.1 + - - -
382D ILE* 3.5 11.9 - - + -
383D HIS* 2.8 62.5 + + - +
385D TRP* 1.3 78.4 + - + +
387D MET* 1.3 64.1 + - - +
388D PRO* 3.4 1.8 - - - -
389D ALA* 3.0 11.5 + - - +
390D LEU* 3.0 34.5 + - + +
465D ILE 4.2 8.2 + - - -
466D LYS* 4.9 13.0 - - + -
467D PHE* 4.7 2.8 - - - -
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Residues in contact with MET 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D LEU* 5.0 0.9 - - + -
383D HIS 3.7 2.8 + - - -
384D VAL* 3.1 21.7 + - - +
386D HIS* 1.3 77.1 - - - +
388D PRO* 1.3 67.0 - - + +
390D LEU* 3.4 4.8 + - - +
391D THR* 2.9 32.4 + - - +
400D LEU* 4.2 11.9 - - - -
402D PHE* 3.4 39.3 - - + -
420D ASN* 3.6 30.5 - - - +
423D ALA* 3.8 15.0 - - + +
424D LEU* 3.7 40.6 - - + +
427D CYS* 3.9 6.3 - - - -
445D ILE* 4.5 0.2 - - + -
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Residues in contact with PRO 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D VAL 4.1 1.6 - - - +
385D TRP 3.6 13.7 - - - +
386D HIS 3.5 4.3 - - - -
387D MET* 1.3 94.3 - - + +
389D ALA* 1.3 56.1 + - - +
391D THR* 3.5 0.4 + - - -
392D GLU* 3.0 29.7 + - - +
427D CYS* 3.6 23.1 - - - -
437D LEU* 3.8 23.2 - - + +
441D GLY* 3.6 42.4 - - - +
444D ILE* 5.4 0.9 - - + -
445D ILE* 3.9 8.1 - - + -
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D VAL* 4.7 20.0 - - + -
339D ARG* 6.1 0.7 - - - +
385D TRP 5.8 0.2 - - - +
386D HIS* 3.0 13.1 + - - +
388D PRO* 1.3 77.6 - - - +
390D LEU* 1.3 60.0 + - - +
392D GLU* 3.3 7.4 + - - +
393D ILE* 2.9 41.9 + - + +
437D LEU 6.3 0.2 - - - -
438D ALA* 6.4 1.3 - - - +
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Residues in contact with LEU 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D THR* 3.9 28.3 - - - +
332D VAL* 4.4 6.7 - - + -
378D ALA* 4.2 12.8 - - + -
382D ILE* 3.8 24.2 - - + -
386D HIS* 3.0 37.5 + - + +
387D MET* 3.8 6.5 - - - +
389D ALA* 1.3 76.0 - - - +
391D THR* 1.3 63.1 + - - +
393D ILE* 4.6 2.2 - - + -
394D PHE* 3.0 47.1 + - + +
400D LEU* 4.3 19.6 - - + +
402D PHE* 4.1 14.8 - - + -
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Residues in contact with THR 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D PRO* 5.0 10.7 - - + +
387D MET* 2.9 23.3 + - - +
388D PRO 3.8 4.3 - - - -
390D LEU* 1.3 75.8 - - - +
392D GLU* 1.3 58.1 + - - +
395D GLY* 2.8 32.2 + - - +
400D LEU* 4.7 2.7 - - - +
424D LEU* 3.7 20.6 - - - +
427D CYS* 4.0 14.7 - - + +
428D VAL* 4.9 11.0 - - + -
431D ARG* 4.3 21.6 + - - +
437D LEU* 3.7 19.5 - - + -
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Residues in contact with GLU 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D ARG* 2.9 41.3 + - - -
388D PRO 3.0 18.9 + - - +
389D ALA* 3.6 7.4 - - - +
391D THR* 1.3 79.6 - - - +
393D ILE* 1.3 62.4 + - - +
395D GLY* 4.3 2.6 + - - -
431D ARG* 6.5 0.7 - - - +
436D ASP* 5.8 0.4 - - - +
437D LEU* 4.0 23.1 - - + +
438D ALA* 4.4 22.8 - - + +
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Residues in contact with ILE 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D THR 4.5 4.9 - - - +
331D VAL* 4.2 33.7 - - + -
332D VAL* 5.1 4.9 - - + -
339D ARG* 3.3 35.9 - - + +
342D THR* 5.3 0.9 - - + -
343D LEU* 3.6 35.9 - - + +
346D VAL* 6.0 0.7 - - - +
350D ARG* 5.4 2.1 + - - -
389D ALA* 2.9 31.3 + - + +
390D LEU* 3.9 4.9 - - + +
392D GLU* 1.3 80.9 - - - +
394D PHE* 1.3 83.6 + - + +
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Residues in contact with PHE 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D SER* 3.5 20.0 - - - -
329D GLY 3.2 22.9 - - - -
330D THR* 4.2 8.3 - - - -
331D VAL* 4.9 0.2 - - + -
342D THR* 4.2 12.1 - - + -
343D LEU* 5.9 0.4 - - + -
346D VAL* 4.1 24.2 - - + -
350D ARG* 2.8 34.2 + - - +
376D PRO* 4.6 11.0 - - + -
378D ALA* 3.8 21.5 - - + -
390D LEU* 3.0 38.6 + - + +
393D ILE* 1.3 95.5 - - + +
395D GLY* 1.3 62.4 + - - +
397D ASP 4.3 0.2 - - - +
398D SER* 3.7 23.1 - - - +
400D LEU* 4.7 2.5 - - + -
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Residues in contact with GLY 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D PRO* 3.3 11.6 - - - +
391D THR* 2.8 26.1 + - - +
392D GLU 4.3 2.1 + - - -
393D ILE 3.7 1.2 - - - -
394D PHE* 1.3 76.9 - - - +
396D ASP* 1.3 66.8 + - - -
398D SER* 3.2 13.5 + - - -
431D ARG* 4.5 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