Contacts of the helix formed by residues 369 - 382 (chain B) in PDB entry 3M0V
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 369 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B TYR* 2.8 35.2 + - + +
367B ASP* 3.2 8.9 - - + +
368B ASN* 1.3 70.6 - - - +
370B ALA* 1.3 57.0 + - - +
371B LEU* 3.8 3.6 + - - +
372B MET* 3.2 22.2 + - - +
373B ALA* 2.9 27.8 + - - +
407C ARG* 2.8 43.6 + - - -
189D GLN 6.1 0.2 - - - -
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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
----------------------------------------------------------
368B ASN 3.3 7.1 + - - +
369B ASP* 1.3 73.6 + - - +
371B LEU* 1.3 63.0 + - - +
373B ALA* 3.7 3.1 - - - +
374B THR* 3.1 26.7 + - - +
332C VAL* 4.1 8.6 + - + +
333C THR* 4.1 11.4 - - + +
143D TYR* 5.5 0.2 - - + -
186D PHE* 4.0 15.1 - - + +
189D GLN* 3.4 46.7 - - + +
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ASP* 3.3 5.5 + - - +
370B ALA* 1.3 79.4 - - - +
372B MET* 1.3 65.5 + - - +
374B THR* 3.3 12.1 - - + +
375B GLU* 3.1 27.4 + - - +
293C ASP* 4.4 5.4 - - - +
333C THR* 4.0 16.7 - - + +
337C GLU* 3.6 28.5 - - + +
338C SER* 3.6 42.4 - - - +
341C ASN* 3.6 25.6 - - + +
403C VAL* 4.0 19.1 - - + -
407C ARG* 4.2 3.4 - - - +
186D PHE* 5.6 1.3 - - - -
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Residues in contact with MET 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B TYR* 3.5 37.4 - - + +
369B ASP* 3.2 18.2 + - - +
371B LEU* 1.3 90.4 - - - +
373B ALA* 1.3 55.8 + - - +
375B GLU* 3.7 11.4 - - + +
376B THR* 2.7 39.8 + - - +
379B ARG* 3.8 33.0 - - - +
341C ASN* 5.9 0.2 - - - -
403C VAL* 4.6 11.2 - - - -
407C ARG* 3.4 32.3 - - - +
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 3.4 15.9 - - + +
364B TYR* 3.8 21.9 - - + +
365B GLN* 4.6 0.2 - - + -
369B ASP 2.9 18.7 + - - +
370B ALA* 3.7 4.5 - - - +
371B LEU 3.3 0.2 - - - -
372B MET* 1.3 77.2 - - - +
374B THR* 1.3 62.5 + - - +
376B THR* 3.2 17.5 + - - -
377B LEU* 3.3 6.8 + - - +
187D PRO 4.4 1.6 - - - -
188D GLY 3.3 25.4 - - - +
189D GLN* 3.9 6.7 - - - -
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Residues in contact with THR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 4.4 4.2 + - - -
370B ALA 3.1 14.9 + - - +
371B LEU* 3.3 15.7 - - + +
373B ALA* 1.3 74.2 - - - +
375B GLU* 1.3 65.1 + - + +
377B LEU* 3.2 5.6 + - - +
378B LYS* 2.9 33.2 + - + +
296C ALA* 4.6 8.9 + - + +
186D PHE* 3.8 20.8 - - + +
187D PRO* 2.8 42.8 + - - +
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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
----------------------------------------------------------
371B LEU 3.1 14.0 + - - +
372B MET* 3.8 16.4 - - + +
374B THR* 1.3 81.1 - - + +
376B THR* 1.3 60.4 + - - +
378B LYS* 4.0 5.3 - - - +
379B ARG* 2.8 67.7 + - - +
382B ARG* 2.9 41.7 + - - -
341C ASN* 4.8 18.5 + - - +
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Residues in contact with THR 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B VAL* 4.6 6.7 - - + +
357B ASP* 3.8 36.5 + - + +
360B ALA* 4.5 2.8 - - + +
361B LEU* 4.0 17.7 - - + +
364B TYR* 3.3 21.3 - - - -
372B MET* 2.7 22.7 + - - +
373B ALA 3.3 11.2 - - - -
374B THR 3.1 0.4 - - - -
375B GLU* 1.3 79.3 - - - +
377B LEU* 1.3 62.1 + - - +
379B ARG* 3.6 18.1 + - - +
380B ALA* 3.8 10.0 + - - +
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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
----------------------------------------------------------
300B TYR* 4.0 8.5 - - - +
303B PHE* 3.6 13.8 - - + -
304B LEU* 4.0 21.5 - - + -
307B ASN* 3.6 33.7 - - - +
356B VAL* 3.8 17.5 - - + -
361B LEU* 4.0 15.7 - - + -
373B ALA 3.3 8.7 + - - +
374B THR 3.2 8.1 + - - +
376B THR* 1.3 79.8 - - - +
378B LYS* 1.3 57.8 + - - +
380B ALA* 3.1 7.3 + - - +
381B TYR* 3.0 22.9 + - - +
187D PRO* 3.6 7.4 - - + +
188D GLY* 3.4 34.3 - - - +
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Residues in contact with LYS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 3.4 42.8 - - + +
374B THR* 2.9 24.9 + - + +
375B GLU* 3.2 9.2 + - - +
377B LEU* 1.3 74.9 - - - +
379B ARG* 1.3 58.1 + - - +
381B TYR* 4.2 11.2 - - + +
382B ARG* 2.7 62.3 + - + +
295C GLY 2.9 30.1 + - - -
296C ALA* 4.2 7.2 - - - +
299C PRO* 4.2 10.7 - - - +
345C GLU* 3.8 22.0 + - - +
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Residues in contact with ARG 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 3.3 14.4 + - - +
364B TYR* 5.7 0.6 + - - -
372B MET* 3.8 27.2 - - - +
375B GLU* 2.8 59.4 + - - +
376B THR* 3.8 12.0 + - - +
377B LEU 3.3 0.4 - - - -
378B LYS* 1.3 73.3 - - - +
380B ALA* 1.3 58.9 + - - +
382B ARG* 3.9 13.8 - - - +
383B THR* 2.8 23.0 + - - -
401C ASP* 4.0 19.0 + - - -
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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
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36B ARG* 4.2 6.1 - - - +
303B PHE* 4.4 0.7 - - + -
352B GLN* 3.3 36.8 - - - +
355B LEU* 3.9 5.5 - - + +
356B VAL* 3.6 30.7 - - + +
376B THR 3.8 3.0 + - - +
377B LEU 3.1 8.9 + - - +
378B LYS 3.1 0.2 - - - -
379B ARG* 1.3 77.9 - - - +
381B TYR* 1.3 64.7 + - - +
383B THR* 3.2 20.8 + - - -
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Residues in contact with TYR 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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299B PRO* 3.2 34.1 - - + +
300B TYR* 3.4 47.0 + + + -
303B PHE* 3.6 19.9 - - + -
352B GLN* 3.1 43.8 + - - -
377B LEU 3.0 16.3 + - - +
378B LYS* 3.9 12.6 - - + +
380B ALA* 1.3 77.2 - - - +
382B ARG* 1.3 66.6 + - + +
299C PRO* 3.8 7.9 - - + -
381C TYR* 2.8 36.1 + + - -
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Residues in contact with ARG 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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375B GLU* 2.9 40.6 + - - -
378B LYS* 2.7 46.2 + - + +
379B ARG* 3.9 15.8 - - - +
381B TYR* 1.3 79.0 - - + +
383B THR* 1.3 62.9 + - - +
384B ASP 3.4 2.6 + - - -
345C GLU* 4.2 6.7 + - - -
348C ARG* 3.5 53.9 - - - +
382C ARG 4.2 5.7 - - - +
384C ASP* 3.5 35.3 + - - +
386C GLU* 4.7 14.5 + - - +
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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