Contacts of the helix formed by residues 371 - 390 (chain B) in PDB entry 3IOT
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 MET 371 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A ALA* 5.5 2.2 - - - +
383A SER* 6.0 2.0 - - - -
384A LEU* 4.4 17.3 - - + -
338B ALA* 3.2 41.7 - - + +
341B TYR* 4.2 30.5 - - + -
342B ALA* 5.8 0.7 - - + -
367B ASN* 3.2 23.1 - - - +
368B ALA* 3.4 3.6 - - - +
369B ALA 2.8 1.8 + - - -
370B ALA* 1.3 86.3 - - - +
372B ALA* 1.3 57.7 + - - +
373B THR 3.0 0.9 - - - +
374B LEU* 3.2 48.3 + - + +
375B GLU* 2.7 25.7 - - - +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 5.4 6.5 - - + -
368B ALA 4.2 0.4 + - - -
369B ALA* 2.8 16.0 + - - +
371B MET* 1.3 77.0 - - - +
373B THR* 1.3 61.3 + - - +
375B GLU* 3.3 11.3 + - - +
376B LYS* 3.2 33.2 + - + +
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Residues in contact with THR 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 3.0 45.6 - - + +
380A ALA* 3.7 11.1 - - + +
381A PHE* 5.2 9.6 - - + +
384A LEU* 5.9 3.4 - - + -
370B ALA 3.5 15.7 + - - -
372B ALA* 1.3 76.3 - - - +
374B LEU* 1.3 70.9 + - + +
376B LYS* 4.4 6.1 - - - -
377B LEU* 2.9 44.9 + - + +
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LEU* 4.3 17.7 - - + -
337B SER* 5.0 16.4 - - - -
338B ALA* 5.1 4.0 - - + +
370B ALA 5.2 0.7 - - - +
371B MET* 3.2 52.2 + - + +
372B ALA 3.2 0.8 - - - -
373B THR* 1.3 82.1 - - + +
375B GLU* 1.3 66.2 + - - +
377B LEU* 3.6 0.6 - - - -
378B MET* 2.7 45.8 + - + +
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Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PRO* 5.0 25.8 - - + +
335B GLN* 5.0 19.5 + - - +
337B SER* 6.0 1.0 - - - -
338B ALA* 5.8 1.0 - - - +
371B MET 2.7 23.2 - - - +
372B ALA* 3.3 8.7 + - - +
374B LEU* 1.3 87.9 - - - +
376B LYS* 1.3 82.4 + - - +
378B MET* 4.7 1.5 - - - +
379B LYS* 2.8 43.8 + - + +
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Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 5.6 9.4 - - + -
372B ALA* 3.2 19.2 + - + +
373B THR* 3.7 10.8 - - - +
375B GLU* 1.3 106.4 - - - +
377B LEU* 1.3 64.6 + - + +
379B LYS* 3.1 10.2 + - - +
380B ALA* 3.0 22.5 + - - +
369C ALA* 4.5 7.5 - - - +
370C ALA* 4.4 17.7 - - - +
373C THR* 3.6 45.5 - - + +
374C LEU* 5.2 6.0 - - + +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 6.1 3.6 - - + -
381A PHE* 4.3 24.5 - - + -
373B THR* 2.9 36.1 + - + +
374B LEU* 3.6 1.1 - - - -
376B LYS* 1.3 75.5 - - + +
378B MET* 1.3 61.7 + - - +
380B ALA* 3.6 29.7 - - + +
381B PHE* 3.9 21.3 - - - -
374C LEU* 4.6 10.5 - - + -
377C LEU* 6.3 0.4 - - + -
407C PRO* 5.7 6.1 - - + -
408C PRO* 4.3 20.4 - - + -
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Residues in contact with MET 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 2.7 25.0 + - + +
375B GLU* 4.7 0.7 - - - -
377B LEU* 1.3 75.4 - - - +
379B LYS* 1.3 83.4 + - - +
380B ALA 3.2 1.1 - - - -
381B PHE* 3.3 43.1 + - + +
382B GLU* 3.4 22.7 + - - +
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Residues in contact with LYS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLU* 2.8 35.8 + - - +
376B LYS* 3.3 12.6 - - - +
378B MET* 1.3 96.6 + - - +
380B ALA* 1.3 48.6 + - - +
381B PHE 3.1 4.9 - - - -
382B GLU* 4.0 11.0 + - + +
383B SER* 2.8 41.4 + - - -
366C THR* 4.7 14.4 - - - +
367C ASN* 4.5 15.0 - - - +
370C ALA* 3.5 31.0 - - + +
374C LEU* 6.1 0.7 - - - -
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LYS 3.0 7.7 + - - +
377B LEU* 3.6 38.8 - - + +
378B MET 3.2 0.2 - - - -
379B LYS* 1.3 77.4 - - - +
381B PHE* 1.3 64.1 + - + +
383B SER* 3.5 7.3 + - - -
384B LEU* 3.4 23.2 + - - +
374C LEU* 4.8 12.8 - - + +
408C PRO* 4.4 17.5 - - + +
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Residues in contact with PHE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU 3.9 15.3 - - - -
378B MET* 3.3 38.0 + - + +
379B LYS 3.1 0.6 - - - -
380B ALA* 1.3 83.5 - - + +
382B GLU* 1.3 64.4 + - - +
383B SER 3.2 0.2 - - - -
384B LEU* 3.6 1.7 + - - +
385B LYS* 3.1 57.5 + - - +
407C PRO* 6.2 4.7 - - + -
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B MET* 3.4 20.7 + - - +
379B LYS* 3.2 15.2 + - + +
381B PHE* 1.3 86.7 - - - +
383B SER* 1.3 57.4 + - - +
385B LYS* 4.3 19.7 + - - +
386B SER* 3.4 23.9 + - - -
367C ASN* 5.5 7.2 - - - +
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LYS* 2.8 24.2 + - - -
380B ALA* 3.5 11.6 + - - -
382B GLU* 1.3 76.1 - - - +
384B LEU* 1.3 61.3 + - - +
385B LYS 3.3 1.6 - - - -
386B SER* 3.2 5.0 + - - -
387B PHE* 3.0 27.4 + - - +
341C TYR* 3.2 12.4 + - - -
367C ASN* 5.9 6.7 - - - -
370C ALA* 6.1 1.3 - - - -
371C MET* 3.8 32.1 - - - +
374C LEU* 4.8 3.8 - - - +
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Residues in contact with LEU 384 (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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380B ALA 3.4 17.2 + - - +
381B PHE* 3.6 2.5 + - - +
383B SER* 1.3 82.0 + - - +
385B LYS* 1.3 62.0 + - + +
387B PHE* 3.9 5.2 + - + +
388B GLN* 3.2 59.8 + - - +
408C PRO* 5.6 3.4 - - + -
409C PRO* 3.4 41.7 - - + +
411C PRO* 3.9 20.4 - - + -
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Residues in contact with LYS 385 (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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381B PHE* 3.1 47.3 + - - +
382B GLU* 4.4 21.1 + - - +
384B LEU* 1.3 78.9 - - + +
386B SER* 1.3 51.2 + - - +
388B GLN* 3.4 6.2 - - - +
389B GLN* 2.7 48.8 + - - +
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Residues in contact with SER 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU 3.4 16.4 + - - -
383B SER* 3.2 7.0 + - - -
385B LYS* 1.3 76.0 - - - +
387B PHE* 1.3 63.2 + - - +
388B GLN 3.0 1.3 - - - -
389B GLN* 3.5 13.3 + - - +
390B GLN* 2.9 30.7 + - - +
341C TYR* 2.9 21.0 + - - -
345C THR* 4.3 21.4 + - - +
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Residues in contact with PHE 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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383B SER 3.0 9.1 + - - +
384B LEU* 4.1 8.5 - - + +
386B SER* 1.3 79.7 + - - +
388B GLN* 1.3 63.6 + - + +
390B GLN* 3.9 7.8 + - - +
391B GLN* 3.4 56.2 + - + +
341C TYR* 3.5 36.6 - + + +
411C PRO* 3.4 53.8 - - + -
412C PRO 3.5 15.7 - - - -
413C PRO* 5.4 4.0 - - + -
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Residues in contact with GLN 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 LEU* 3.2 44.1 + - + +
385B LYS* 3.4 6.4 + - - +
386B SER 3.0 0.6 - - - -
387B PHE* 1.3 88.2 - - + +
389B GLN* 1.3 60.5 + - - +
390B GLN 3.3 1.5 + - - -
391B GLN* 3.7 25.8 + - - +
392B GLN* 3.9 2.4 + - - -
411C PRO* 5.4 5.1 - - - +
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Residues in contact with GLN 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU 5.5 0.2 - - - +
385B LYS* 2.7 37.0 + - + +
386B SER* 3.0 13.5 + - - +
388B GLN* 1.3 73.1 - - - +
390B GLN* 1.3 61.1 + - + +
392B GLN* 3.4 21.7 - - - +
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Residues in contact with GLN 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B SER* 2.9 20.3 + - - +
387B PHE* 4.2 8.9 - - - +
389B GLN* 1.3 75.2 - - + +
391B GLN* 1.3 60.0 + - + +
392B GLN* 3.0 9.2 + - - +
393B GLN* 4.2 9.7 + - - +
396B GLN* 5.5 0.7 - - - +
341C TYR* 4.4 8.1 - - - -
344C ARG* 4.5 8.8 - - - +
345C THR* 3.2 52.9 + - + +
348C ILE* 4.4 22.0 - - + +
349C ASN* 5.0 2.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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