Contacts of the helix formed by residues 366 - 384 (chain B) in PDB entry 4M83
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 ASP 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B ALA 3.8 14.2 + - - +
363B LEU* 3.3 15.6 + - + +
364B VAL 5.1 1.2 - - - +
365B ASP* 1.3 77.0 - - - +
367B PRO* 1.3 69.0 - - - +
368B GLU* 3.0 21.8 + - - +
369B VAL* 3.4 26.4 + - + +
370B ALA* 3.3 19.6 + - - +
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Residues in contact with PRO 367 (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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365B ASP 3.3 10.5 - - - +
366B ASP* 1.3 91.4 - - - +
368B GLU* 1.3 57.9 + - + +
370B ALA* 3.2 8.8 + - + +
371B ARG* 2.8 28.9 + - - +
374B ARG* 5.4 1.0 + - - -
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ASP* 3.0 9.7 + - - +
367B PRO* 1.3 78.8 - - + +
369B VAL* 1.3 65.8 + - + +
371B ARG* 3.9 22.3 - - - +
372B ARG* 2.9 79.8 + - - +
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PRO* 4.1 19.1 - - + -
341B GLY 3.5 20.2 - - - +
342B VAL* 4.1 12.5 - - - +
363B LEU* 4.2 21.5 - - + +
366B ASP* 3.4 34.2 + - + +
368B GLU* 1.3 76.5 - - + +
370B ALA* 1.3 57.4 + - - +
372B ARG* 3.4 3.8 + - - +
373B LEU* 2.9 48.4 + - + +
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Residues in contact with ALA 370 (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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320B PRO* 6.3 0.7 - - - -
366B ASP 3.3 9.2 + - - +
367B PRO* 3.2 12.9 + - + +
368B GLU 3.2 0.6 - - - -
369B VAL* 1.3 78.6 - - - +
371B ARG* 1.3 67.2 + - - +
373B LEU* 3.2 8.6 + - - +
374B ARG* 2.9 53.2 + - - +
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Residues in contact with ARG 371 (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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367B PRO 2.8 19.5 + - - +
368B GLU* 3.8 24.2 + - - +
370B ALA* 1.3 73.2 - - - +
372B ARG* 1.3 63.0 + - + +
374B ARG* 3.6 15.1 + - - +
375B ARG* 3.2 23.0 + - + +
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Residues in contact with ARG 372 (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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175A THR* 6.3 0.8 - - - -
340B LEU 3.2 23.4 + - - -
341B GLY* 3.6 21.7 + - - -
342B VAL* 3.8 11.2 - - + -
368B GLU* 2.9 68.7 + - - +
369B VAL* 3.7 5.2 - - - +
371B ARG* 1.3 74.9 - - + +
373B LEU* 1.3 60.1 + - - +
375B ARG* 2.6 37.5 + - - +
376B ILE* 3.0 19.3 + - - +
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Residues in contact with LEU 373 (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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315B LEU* 3.8 24.4 - - + +
318B ALA* 3.8 21.9 - - + +
319B THR 3.7 21.1 - - - +
320B PRO* 3.4 38.8 - - + -
342B VAL* 3.7 24.2 - - + -
369B VAL* 2.9 33.6 + - + +
370B ALA* 3.2 7.2 + - - +
372B ARG* 1.3 73.4 - - - +
374B ARG* 1.3 61.2 + - - +
376B ILE* 3.4 4.5 + - - +
377B GLN* 2.9 30.1 + - - +
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Residues in contact with ARG 374 (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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318B ALA* 4.6 9.9 - - + -
367B PRO 5.4 0.8 + - - -
370B ALA* 2.9 43.3 + - - +
371B ARG* 4.0 13.5 - - - +
373B LEU* 1.3 75.6 - - - +
375B ARG* 1.3 58.6 + - - +
377B GLN* 3.6 13.7 - - - +
378B ALA* 2.8 31.6 + - - +
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Residues in contact with ARG 375 (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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170A LYS* 5.5 3.8 - - - +
195B ALA* 6.0 0.4 - - - +
340B LEU* 4.4 12.5 + - - +
371B ARG* 3.2 14.2 + - + +
372B ARG* 2.6 55.8 + - - +
374B ARG* 1.3 79.8 - - - +
376B ILE* 1.3 80.2 + - - +
378B ALA* 3.4 7.3 + - - +
379B GLU* 3.0 34.9 + - - +
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Residues in contact with ILE 376 (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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195B ALA* 4.0 16.8 - - + -
315B LEU* 3.6 31.4 - - + +
340B LEU* 4.1 24.9 - - + +
342B VAL* 4.0 22.4 - - + -
372B ARG* 3.0 21.2 + - + +
373B LEU* 3.8 4.0 - - - +
375B ARG* 1.3 97.1 - - - +
377B GLN* 1.3 61.0 + - - +
379B GLU* 3.1 12.1 + - + +
380B MET* 2.9 42.3 + - + +
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Residues in contact with GLN 377 (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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315B LEU 3.8 14.1 - - - +
316B ALA* 3.3 24.7 + - - +
317B THR* 3.3 22.0 + - - +
318B ALA* 3.6 11.7 - - + +
373B LEU 2.9 18.6 + - - +
374B ARG* 3.6 12.6 - - - +
376B ILE* 1.3 76.3 - - - +
378B ALA* 1.3 56.6 + - - +
380B MET* 3.4 5.9 + - - +
381B ALA* 2.9 31.5 + - + +
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Residues in contact with ALA 378 (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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374B ARG 2.8 18.1 + - - +
375B ARG* 3.6 7.6 - - - +
376B ILE 3.2 0.2 - - - -
377B GLN* 1.3 80.0 - - - +
379B GLU* 1.3 60.1 + - - +
381B ALA* 3.5 10.4 + - - +
382B GLN* 3.5 22.3 + - - +
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Residues in contact with GLU 379 (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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194B LYS* 4.0 33.2 + - - +
195B ALA* 5.1 9.4 + - - +
375B ARG* 3.0 23.3 + - - +
376B ILE* 3.1 18.0 + - + +
378B ALA* 1.3 75.4 - - - +
380B MET* 1.3 65.9 + - + +
382B GLN* 3.1 15.4 + - - +
383B GLU* 3.3 24.5 + - + +
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Residues in contact with MET 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PRO* 3.6 36.3 - - + -
195B ALA* 5.7 0.9 - - + -
212B GLY* 6.2 1.6 - - - -
312B GLN* 3.2 38.1 - - - +
315B LEU* 3.6 26.7 - - - -
316B ALA* 3.7 19.1 - - + -
376B ILE* 2.9 27.5 + - + +
377B GLN* 3.8 4.3 - - - +
379B GLU* 1.3 71.1 - - + +
381B ALA* 1.3 58.6 + - - +
382B GLN 3.0 10.1 + - - -
383B GLU* 3.1 27.6 + - - +
384B GLY 4.0 3.6 + - - -
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Residues in contact with ALA 381 (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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377B GLN* 2.9 20.7 + - + +
378B ALA* 3.8 9.4 - - - +
379B GLU 3.2 0.6 - - - -
380B MET* 1.3 75.0 - - - +
382B GLN* 1.3 72.5 + - - +
384B GLY* 5.0 2.9 + - - -
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Residues in contact with GLN 382 (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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378B ALA 3.5 14.1 + - - +
379B GLU* 3.1 8.8 + - - +
380B MET 3.0 0.4 - - - -
381B ALA* 1.3 93.8 + - - +
383B GLU* 1.3 65.4 + - - +
384B GLY* 3.2 5.0 + - - -
388B ARG* 3.9 11.6 + - - -
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Residues in contact with GLU 383 (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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193B PRO* 3.3 25.9 - - - +
194B LYS* 2.9 33.4 + - - +
195B ALA 4.7 0.5 + - - -
210B PHE* 3.5 22.8 - - + +
211B VAL* 3.7 17.4 - - - +
212B GLY* 4.0 8.7 - - - -
379B GLU* 3.3 21.3 + - + +
380B MET* 3.1 26.2 + - - +
382B GLN* 1.3 75.2 - - - +
384B GLY* 1.3 59.4 + - - +
385B GLY 3.5 1.1 - - - -
388B ARG* 2.6 29.6 + - - +
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Residues in contact with GLY 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 MET 4.0 4.8 + - - -
381B ALA 5.0 2.2 - - - -
382B GLN* 3.2 5.5 - - - +
383B GLU* 1.3 78.2 - - - +
385B GLY* 1.3 66.4 + - - +
386B THR* 3.6 0.9 + - - +
387B ARG* 3.7 15.9 + - - +
388B ARG* 3.4 24.7 + - - -
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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