Contacts of the helix formed by residues 386 - 395 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332C VAL* 3.8 42.0 + - + +
381C GLY 3.7 18.6 - - - -
382C ILE* 3.3 7.1 - - + +
383C HIS* 2.9 54.6 + + - +
385C TRP* 1.3 80.2 - - + +
387C MET* 1.3 65.5 + - - +
388C PRO* 3.3 2.2 - - - -
389C ALA* 3.1 10.0 + - + +
390C LEU* 2.9 36.0 + - + +
465C ILE 4.3 7.1 + - - -
466C LYS* 5.1 6.7 - - - +
467C PHE* 4.8 3.4 - + - -
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Residues in contact with MET 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LEU* 4.8 1.1 - - + -
383C HIS 3.7 2.4 + - - -
384C VAL* 3.1 18.7 + - - +
386C HIS* 1.3 76.7 - - - +
388C PRO* 1.3 65.7 - - + +
390C LEU* 3.3 4.0 + - - +
391C THR* 2.8 32.7 + - - +
400C LEU* 4.0 21.3 - - - -
402C PHE* 3.5 37.7 - - + -
420C ASN* 3.4 34.5 - - - +
423C ALA* 3.8 14.6 - - + +
424C LEU* 3.7 32.1 - - + +
427C CYS* 4.0 7.2 - - - -
445C ILE* 4.5 0.7 - - + -
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Residues in contact with PRO 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C VAL 4.0 3.8 - - - +
385C TRP 3.5 12.8 - - - +
386C HIS 3.4 4.3 - - - -
387C MET* 1.3 94.9 - - + +
389C ALA* 1.3 55.3 + - - +
391C THR* 3.4 3.6 + - - +
392C GLU* 3.0 30.4 + - - +
427C CYS* 3.7 22.0 - - - -
437C LEU* 4.0 20.5 - - + +
441C GLY* 3.6 42.2 - - - +
442C ASN* 5.9 0.7 - - - +
444C ILE* 5.6 0.2 - - + -
445C ILE* 3.8 8.1 - - + -
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Residues in contact with ALA 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C VAL* 4.6 20.4 - - + -
339C ARG* 6.2 0.4 - - - +
385C TRP 5.7 0.2 - - - +
386C HIS* 3.1 12.8 + - + +
388C PRO* 1.3 79.9 - - - +
390C LEU* 1.3 60.1 + - + +
392C GLU* 3.2 8.6 + - - +
393C ILE* 2.9 41.4 + - + +
437C LEU 5.3 0.6 + - - -
438C ALA* 6.4 0.9 - - - +
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Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C THR* 3.9 26.2 - - - +
332C VAL* 4.3 9.9 - - + -
378C ALA* 4.3 9.6 - - + -
382C ILE* 3.7 25.4 - - + -
386C HIS* 2.9 36.2 + - + +
387C MET* 3.8 4.9 - - - +
389C ALA* 1.3 77.4 - - - +
391C THR* 1.3 62.5 + - - +
393C ILE* 4.7 2.5 - - + -
394C PHE* 3.0 48.1 + - + +
400C LEU* 4.3 20.9 - - + +
402C PHE* 4.2 15.3 - - + -
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Residues in contact with THR 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C PRO* 4.8 14.8 - - + -
387C MET* 2.8 22.8 + - - +
388C PRO 3.7 3.8 - - - -
390C LEU* 1.3 76.5 - - - +
392C GLU* 1.3 59.5 + - - +
395C GLY* 3.0 29.2 + - - +
400C LEU* 4.7 2.6 - - - +
424C LEU* 3.9 19.1 - - - +
427C CYS* 4.0 15.4 - - + +
428C VAL* 4.8 9.4 - - + -
431C ARG* 4.3 21.2 + - - +
437C LEU* 3.8 18.8 - - + +
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Residues in contact with GLU 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C ARG* 2.9 40.0 + - - -
388C PRO 3.0 17.4 + - - +
389C ALA* 3.2 8.0 + - - +
391C THR* 1.3 80.1 - - - +
393C ILE* 1.3 62.2 + - - +
395C GLY* 4.6 1.2 + - - -
436C ASP* 5.9 0.4 - - - +
437C LEU* 4.2 22.9 - - + +
438C ALA* 4.6 20.3 - - + +
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Residues in contact with ILE 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C THR 4.5 5.8 - - - +
331C VAL* 4.3 33.0 - - + -
332C VAL* 5.0 5.2 - - + -
339C ARG* 3.3 36.3 - - + +
342C THR* 5.4 2.5 - - + -
343C LEU* 3.5 35.2 - - + +
346C VAL* 6.1 0.7 - - - +
350C ARG* 5.4 2.4 + - - -
389C ALA* 2.9 30.2 + - + +
390C LEU* 4.0 4.5 - - + +
392C GLU* 1.3 81.0 - - - +
394C PHE* 1.3 84.6 - - + +
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Residues in contact with PHE 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C SER* 3.6 18.8 - - - -
329C GLY 3.4 21.8 - - - -
330C THR* 4.4 7.9 - - - -
331C VAL* 5.0 0.2 - - + -
342C THR* 4.2 12.3 - - + -
343C LEU* 6.3 0.4 - - + -
346C VAL* 4.0 24.9 - - + -
350C ARG* 2.8 35.0 + - - +
376C PRO* 4.5 11.4 - - + -
378C ALA* 3.8 22.7 - - + -
390C LEU* 3.0 33.2 + - + +
393C ILE* 1.3 96.9 - - + +
395C GLY* 1.3 59.4 + - - +
398C SER* 3.6 23.8 - - - +
400C LEU* 4.6 2.7 - - + -
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Residues in contact with GLY 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C PRO* 3.4 10.3 - - - +
391C THR* 3.0 22.7 + - - +
392C GLU 4.6 1.5 + - - -
393C ILE 3.7 0.6 - - - -
394C PHE* 1.3 77.9 - - - +
396C ASP* 1.3 67.2 + - - -
397C ASP 3.4 0.2 - - - -
398C SER* 3.1 16.6 + - - -
431C ARG* 4.6 7.4 - - - -
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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