Contacts of the helix formed by residues 369 - 382 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A ARG* 2.9 44.3 + - - -
189B GLN 6.0 0.2 - - - -
364D TYR* 2.8 30.9 + - + +
367D ASP* 3.2 9.1 - - + +
368D ASN* 1.3 70.3 - - - +
370D ALA* 1.3 62.4 + - - +
371D LEU* 3.8 3.1 + - - +
372D MET* 3.3 21.2 + - - +
373D ALA* 3.0 23.0 + - - +
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Residues in contact with ALA 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A VAL* 4.2 9.3 + - + +
333A THR* 4.1 11.8 - - + +
143B TYR* 5.5 0.4 - - + -
186B PHE* 4.0 15.7 - - + +
189B GLN* 3.4 45.2 - - + +
368D ASN 3.2 7.9 + - - +
369D ASP* 1.3 73.4 - - - +
371D LEU* 1.3 58.4 + - - +
373D ALA* 3.3 2.9 + - - +
374D THR* 3.0 31.9 + - - -
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Residues in contact with LEU 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A ASP* 4.5 4.9 - - - +
333A THR* 4.0 15.6 - - + +
337A GLU* 3.6 52.7 - - + +
338A SER* 3.6 18.2 - - - +
341A ASN* 3.7 26.0 - - + +
403A VAL* 4.0 17.5 - - + -
407A ARG* 4.3 1.8 - - - +
186B PHE* 5.7 1.6 - - - -
369D ASP* 3.3 5.7 + - - +
370D ALA* 1.3 78.6 - - - +
372D MET* 1.3 70.2 + - - +
374D THR* 3.3 12.3 - - + +
375D GLU* 3.0 28.1 + - - +
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Residues in contact with MET 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A VAL* 4.7 9.2 - - - -
407A ARG* 3.4 35.7 - - - +
364D TYR* 3.4 48.5 - - + +
369D ASP* 3.3 7.7 + - - +
371D LEU* 1.3 90.4 - - - +
373D ALA* 1.3 56.1 + - - +
375D GLU* 3.7 10.7 - - + +
376D THR* 2.7 39.7 + - - +
379D ARG* 3.8 32.5 - - - +
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Residues in contact with ALA 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B PRO 4.4 1.8 - - - -
188B GLY 3.5 25.6 - - - +
189B GLN* 3.8 6.7 - - - +
361D LEU* 3.6 14.9 - - + +
364D TYR* 3.8 21.6 - - + +
369D ASP 3.0 19.0 + - - +
370D ALA* 3.5 5.4 - - - +
371D LEU 3.2 0.2 - - - -
372D MET* 1.3 77.9 - - - +
374D THR* 1.3 62.6 + - - +
376D THR* 3.1 13.5 + - - -
377D LEU* 3.3 10.9 + - - +
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Residues in contact with THR 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ALA* 4.7 9.1 + - + +
341A ASN* 6.4 0.2 - - - +
186B PHE* 3.7 26.6 - - + +
187B PRO* 2.8 33.9 + - - +
300D TYR* 4.5 3.6 + - - -
370D ALA 3.0 14.5 + - - +
371D LEU* 3.3 16.8 - - + +
373D ALA* 1.3 77.3 - - - +
375D GLU* 1.3 63.2 + - + +
377D LEU* 3.2 5.2 + - - +
378D LYS* 2.9 33.7 + - + +
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Residues in contact with GLU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A ASN* 4.5 19.0 + - - +
345A GLU* 5.6 0.2 - - - +
348A ARG* 5.5 0.3 + - - -
371D LEU 3.0 19.5 + - - +
372D MET* 3.8 14.8 - - + +
374D THR* 1.3 76.6 - - + +
376D THR* 1.3 59.8 + - - +
378D LYS* 4.0 5.4 - - - +
379D ARG* 2.8 68.0 + - - +
382D ARG* 2.9 40.6 + - - -
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Residues in contact with THR 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D VAL* 4.6 5.6 - - + +
357D ASP* 3.8 36.6 + - + +
360D ALA* 4.5 2.9 - - + +
361D LEU* 3.9 19.1 - - + +
364D TYR* 3.3 20.6 - - - -
372D MET* 2.7 22.6 + - - +
373D ALA* 3.1 12.1 + - - -
375D GLU* 1.3 80.2 - - - +
377D LEU* 1.3 62.7 + - - +
379D ARG* 3.5 19.1 + - - +
380D ALA* 3.7 9.5 + - - +
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Residues in contact with LEU 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PRO* 3.6 8.5 - - + +
188B GLY* 3.4 37.7 - - - +
300D TYR* 4.0 7.2 - - - +
303D PHE* 3.6 12.5 - - + -
304D LEU* 4.0 17.0 - - + -
307D ASN* 3.5 38.4 - - - +
356D VAL* 3.8 15.7 - - + -
361D LEU* 4.0 17.7 - - + -
373D ALA 3.3 4.6 + - - +
374D THR 3.2 7.7 + - - +
376D THR* 1.3 81.3 - - - +
378D LYS* 1.3 62.6 + - - +
380D ALA* 3.1 7.3 + - - +
381D TYR* 3.0 18.7 + - - +
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Residues in contact with LYS 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A GLY 2.8 28.8 + - - -
296A ALA* 4.1 7.7 - - - +
299A PRO* 4.3 10.5 - - - +
345A GLU* 3.9 20.5 + - - +
300D TYR* 3.5 44.0 - - + +
374D THR* 2.9 24.4 + - + +
375D GLU* 3.3 9.2 + - - +
377D LEU* 1.3 78.3 - - - +
379D ARG* 1.3 57.8 + - - +
381D TYR* 4.2 10.3 - - + -
382D ARG* 2.7 60.6 + - + +
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Residues in contact with ARG 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ASP* 4.0 19.6 + - - -
36D ARG* 3.2 14.2 + - - +
364D TYR* 5.5 1.4 + - - -
372D MET* 3.8 27.3 - - - +
375D GLU* 2.8 55.2 + - - +
376D THR* 3.7 12.6 + - - +
377D LEU 3.2 0.4 - - - -
378D LYS* 1.3 76.4 - - - +
380D ALA* 1.3 57.4 + - - +
382D ARG* 3.8 14.5 - - - +
383D THR* 2.8 23.2 + - - -
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Residues in contact with ALA 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG* 4.3 2.0 - - - +
303D PHE* 4.3 1.6 - - + -
352D GLN* 3.3 33.7 - - - +
355D LEU* 3.9 10.4 - - - +
356D VAL* 3.6 31.6 - - + +
376D THR 3.7 3.0 + - - +
377D LEU 3.1 8.6 + - - +
379D ARG* 1.3 77.2 - - - +
381D TYR* 1.3 65.5 + - - +
383D THR* 3.1 22.9 + - - -
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Residues in contact with TYR 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A PRO* 3.8 8.5 - - + -
381A TYR* 2.8 36.0 + + - -
299D PRO* 3.2 32.3 - - + +
300D TYR* 3.4 41.6 + + + -
303D PHE* 3.6 26.6 - - + -
352D GLN* 3.1 47.7 + - - -
377D LEU 3.0 15.0 + - - +
378D LYS* 4.0 13.7 - - + +
380D ALA* 1.3 78.2 - - - +
382D ARG* 1.3 63.6 + - + +
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Residues in contact with ARG 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A GLU* 4.4 5.3 + - - -
348A ARG* 3.6 53.2 - - - +
382A ARG 4.3 5.4 - - - +
384A ASP* 3.4 35.5 + - - +
386A GLU* 4.7 14.5 + - - +
375D GLU* 2.9 40.2 + - - -
378D LYS* 2.7 54.1 + - + +
379D ARG* 3.8 17.4 - - - +
381D TYR* 1.3 75.1 - - + +
383D THR* 1.3 63.5 + - - +
384D ASP 3.3 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
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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