Contacts of the helix formed by residues 386 - 395 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332B VAL* 3.8 40.8 + - + -
381B GLY 3.7 15.0 - - - -
382B ILE* 3.3 6.0 - - + +
383B HIS* 2.8 57.9 + + - +
385B TRP* 1.3 79.5 - - + +
387B MET* 1.3 65.0 + - - +
388B PRO* 3.4 2.0 - - - -
389B ALA* 3.2 9.7 + - + +
390B LEU* 3.0 36.2 + - + +
465B ILE 4.2 7.1 + - - -
466B LYS* 4.9 6.1 - - - +
467B PHE* 4.8 3.6 - + - -
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Residues in contact with MET 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 4.7 1.6 - - + -
383B HIS 3.7 2.8 + - - -
384B VAL* 3.2 19.8 + - - +
386B HIS* 1.3 77.4 - - - +
388B PRO* 1.3 68.0 - - + +
390B LEU* 3.4 4.6 + - - +
391B THR* 2.8 31.9 + - - +
400B LEU* 4.0 21.5 - - - -
402B PHE* 3.6 36.3 - - + -
420B ASN* 3.3 35.9 - - - +
423B ALA* 3.8 15.0 - - + +
424B LEU* 3.7 30.3 - - + +
427B CYS* 4.1 6.3 - - - -
445B ILE* 4.5 0.2 - - + -
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Residues in contact with PRO 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B VAL 4.1 2.0 - - - +
385B TRP 3.5 17.3 - - - +
386B HIS 3.5 1.1 - - - -
387B MET* 1.3 95.2 - - + +
389B ALA* 1.3 56.6 + - - +
391B THR* 3.4 2.9 + - - +
392B GLU* 3.0 29.3 + - - +
427B CYS* 3.7 21.8 - - - -
437B LEU* 3.8 20.2 - - + +
441B GLY* 3.6 42.6 - - - +
444B ILE* 5.5 0.4 - - + -
445B ILE* 3.9 9.2 - - + -
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B VAL* 4.7 20.0 - - + -
385B TRP 5.7 0.4 - - - +
386B HIS* 3.2 13.1 + - + +
388B PRO* 1.3 75.8 - - - +
390B LEU* 1.3 61.5 + - - +
392B GLU* 3.4 7.3 + - - +
393B ILE* 2.9 41.2 + - + +
437B LEU 5.3 0.6 + - - -
438B ALA* 6.4 1.1 - - - +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B THR* 3.9 20.2 - - - +
332B VAL* 4.2 10.1 - - + -
378B ALA* 4.3 11.0 - - + -
382B ILE* 3.8 24.0 - - + -
386B HIS* 3.0 37.0 + - + +
387B MET* 3.8 5.6 - - - +
389B ALA* 1.3 76.1 - - - +
391B THR* 1.3 56.8 + - - +
393B ILE* 3.4 1.5 + - + -
394B PHE* 3.0 59.0 + - + +
400B LEU* 4.1 22.1 - - + +
402B PHE* 4.1 15.0 - - + -
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Residues in contact with THR 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B PRO* 4.9 12.1 - - + -
387B MET* 2.8 22.4 + - - +
388B PRO 3.7 4.3 - - - -
390B LEU* 1.3 76.2 - - - +
392B GLU* 1.3 57.5 + - - +
395B GLY* 3.0 30.2 + - - +
400B LEU* 4.8 2.8 - - - +
424B LEU* 3.9 19.2 - - - +
427B CYS* 4.0 14.7 - - + +
428B VAL* 4.9 10.8 - - + -
431B ARG* 4.2 22.7 + - - +
437B LEU* 3.7 18.6 - - + -
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Residues in contact with GLU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B ARG* 3.1 38.0 + - - -
388B PRO 3.0 17.8 + - - +
389B ALA* 3.7 7.1 - - - +
391B THR* 1.3 79.4 - - - +
393B ILE* 1.3 63.4 + - - +
395B GLY* 4.4 2.3 + - - -
431B ARG* 6.5 0.2 - - - +
436B ASP* 5.7 0.4 - - - +
437B LEU* 4.1 23.1 - - + +
438B ALA* 4.5 21.0 - - + +
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Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B THR 4.5 5.6 - - - +
331B VAL* 4.3 33.4 - - + -
332B VAL* 5.0 4.7 - - + -
339B ARG* 3.3 36.8 - - + +
342B THR* 5.5 2.0 - - + -
343B LEU* 3.5 36.3 - - + +
346B VAL* 6.1 0.5 - - - +
350B ARG* 5.4 2.3 + - - -
389B ALA* 2.9 30.5 + - + +
390B LEU* 3.9 3.4 - - + +
392B GLU* 1.3 81.4 - - - +
394B PHE* 1.3 85.0 + - + +
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Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B SER* 3.6 20.2 - - - -
329B GLY 3.4 20.9 - - - -
330B THR* 4.2 10.3 - - - -
331B VAL* 4.9 0.7 - - + -
342B THR* 4.2 11.7 - - + -
343B LEU* 6.1 0.2 - - + -
346B VAL* 4.2 24.0 - - + -
350B ARG* 2.8 35.6 + - - +
376B PRO* 4.6 11.2 - - + -
378B ALA* 3.9 21.1 - - + -
390B LEU* 3.0 39.9 + - + +
393B ILE* 1.3 95.0 - - + +
395B GLY* 1.3 62.9 + - - +
397B ASP 4.2 0.2 - - - +
398B SER* 3.7 23.6 - - - +
400B LEU* 4.6 2.7 - - + -
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Residues in contact with GLY 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B PRO* 3.4 9.8 - - - +
391B THR* 3.0 21.7 + - - +
392B GLU 4.4 1.5 + - - -
393B ILE 3.7 1.6 - - - -
394B PHE* 1.3 81.0 - - - +
396B ASP* 1.3 66.9 + - - -
397B ASP 3.4 0.4 - - - -
398B SER* 3.2 13.9 + - - -
431B ARG* 4.6 7.0 - - - -
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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