Contacts of the helix formed by residues 326 - 341 (chain D) in PDB entry 1MVW
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 326 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325D ILE* 1.3 73.3 - - - +
327D ASP* 1.3 65.7 + - - +
328D GLN* 3.0 21.2 + - - +
329D GLU* 2.9 48.7 + - + +
330D GLU* 2.9 19.8 + - + +
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Residues in contact with ASP 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D ARG* 3.2 33.0 + - - -
286D HIS* 5.0 2.1 - - - +
289D TYR* 3.7 29.8 - - - +
290D GLN* 3.3 16.3 + - - +
293D SER* 3.9 9.8 + - - -
320D ILE 4.7 1.9 - - - +
321D THR* 4.5 10.6 + - - -
322D VAL 5.3 1.6 + - - +
325D ILE* 3.8 13.1 + - - +
326D ASP* 1.3 72.3 + - - +
328D GLN* 1.3 63.2 + - + +
330D GLU* 4.0 7.1 - - - +
331D LEU* 3.1 21.5 + - - +
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Residues in contact with GLN 328 (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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293D SER* 3.8 31.9 + - - +
294D ASN 4.5 1.2 - - - +
295D MLY 3.7 48.5 + - + +
326D ASP* 2.9 19.3 + - - +
327D ASP* 1.3 81.1 - - + +
329D GLU* 1.3 59.1 + - - +
331D LEU* 3.7 7.7 + - - +
332D MET* 3.4 17.0 - - - +
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Residues in contact with GLU 329 (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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295D MLY 5.7 0.2 - - - -
326D ASP* 2.9 36.3 + - + +
328D GLN* 1.3 76.8 - - - +
330D GLU* 1.3 73.8 + - + +
332D MET* 3.2 12.3 + - - +
333D ALA* 3.0 18.5 + - - +
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Residues in contact with GLU 330 (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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290D GLN* 3.5 20.4 - - + +
325D ILE* 4.4 17.0 - - + +
326D ASP* 2.9 25.8 + - - +
327D ASP* 3.9 4.7 - - - +
329D GLU* 1.3 83.2 - - - +
331D LEU* 1.3 52.6 - - - +
333D ALA* 2.7 16.4 + - - +
334D THR* 2.6 41.0 + - - +
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Residues in contact with LEU 331 (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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290D GLN* 2.8 51.1 - - + +
291D ILE* 3.1 18.2 - - + +
293D SER* 3.8 7.0 - - - +
295D MLY 4.9 8.1 - - + +
296D MLY 3.8 30.7 - - + +
299D LEU* 4.2 9.4 - - + -
327D ASP 3.1 15.3 + - - +
328D GLN* 3.7 8.1 - - - +
329D GLU 3.3 0.2 - - - -
330D GLU* 1.3 74.0 - - - +
332D MET* 1.3 60.0 + - + +
334D THR* 3.3 3.3 - - + +
335D ASP* 2.8 28.1 + - - +
352D TYR* 4.0 17.7 + - + +
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Residues in contact with MET 332 (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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295D MLY 3.0 55.6 - - + -
296D MLY 4.8 23.8 - - - -
328D GLN 3.4 11.9 - - - +
329D GLU* 3.4 9.0 - - - +
330D GLU 3.0 0.2 - - - -
331D LEU* 1.3 76.4 - - - +
333D ALA* 1.3 56.7 + - - +
335D ASP* 3.8 6.1 - - - -
336D SER* 2.3 46.4 + - - +
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Residues in contact with ALA 333 (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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227D PRO* 4.9 14.6 - - + +
329D GLU 3.0 9.0 + - - +
330D GLU* 2.7 27.5 + - + +
332D MET* 1.3 76.2 - - - +
334D THR* 1.3 65.1 + - - +
336D SER* 3.8 4.6 - - - -
337D ALA* 2.8 26.3 + - - +
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Residues in contact with THR 334 (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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227D PRO 3.8 18.3 + - - +
228D LEU* 4.2 18.5 - - + +
231D ALA* 3.8 9.3 - - + +
287D ILE* 4.5 11.2 - - + -
290D GLN* 2.4 34.0 + - - +
330D GLU* 2.6 16.4 + - - +
331D LEU* 3.3 6.1 - - + +
333D ALA* 1.3 74.3 - - - +
335D ASP* 1.3 68.1 + - - +
337D ALA* 3.0 15.5 + - - +
338D ILE* 3.0 18.2 + - + +
352D TYR* 4.9 4.9 - - + +
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Residues in contact with ASP 335 (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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296D MLY 2.8 45.8 + - - +
331D LEU* 2.8 14.4 + - + +
332D MET* 3.3 5.8 - - - +
334D THR* 1.3 80.3 - - - +
336D SER* 1.3 58.1 + - - +
338D ILE* 2.9 31.6 + - - +
339D ASP* 3.2 6.5 - - - +
348D MLY 2.5 35.7 + - - -
352D TYR* 2.7 25.6 + - - +
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Residues in contact with SER 336 (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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214D MET* 4.7 18.7 - - - +
215D GLN* 2.2 36.7 + - - +
296D MLY 5.2 3.3 - - - -
332D MET* 2.3 35.7 + - - +
333D ALA* 3.9 4.2 - - - -
335D ASP* 1.3 73.5 + - - +
337D ALA* 1.3 52.2 + - - +
339D ASP* 3.4 8.5 - - - +
340D ILE* 3.1 6.3 + - - +
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Residues in contact with ALA 337 (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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224D SER* 3.7 35.4 - - - +
227D PRO* 4.8 4.3 - - + -
228D LEU* 4.6 11.0 - - + +
333D ALA 2.8 20.2 + - - +
334D THR* 3.1 7.9 - - - +
336D SER* 1.3 74.2 - - - +
338D ILE* 1.3 55.8 + - - +
340D ILE* 3.2 2.8 + - - +
341D LEU* 2.7 44.7 + - + +
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Residues in contact with ILE 338 (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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228D LEU* 3.5 26.5 - - + -
232D PHE* 5.5 1.1 - - + -
287D ILE* 6.4 0.2 - - + -
334D THR* 3.0 20.5 + - + +
335D ASP* 2.9 17.7 + - - +
337D ALA* 1.3 75.8 - - - +
339D ASP* 1.3 65.4 + - - +
341D LEU* 3.0 12.7 + - - -
342D GLY 3.3 6.6 + - - -
343D PHE* 3.3 38.4 + - + +
348D MLY 3.6 35.0 - - + -
351D ILE* 4.7 23.3 - - + -
352D TYR* 4.7 9.9 - - + +
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Residues in contact with ASP 339 (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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215D GLN* 1.4 64.9 - - - +
296D MLY 5.5 0.5 - - - -
335D ASP* 3.2 14.4 - - - +
336D SER* 3.4 5.8 - - - +
338D ILE* 1.3 76.3 - - - +
340D ILE* 1.3 47.9 + - - -
342D GLY* 2.5 29.1 + - - -
343D PHE 4.0 10.1 + - - +
345D ALA* 6.0 0.3 - - - -
348D MLY 2.8 48.2 + - - +
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Residues in contact with ILE 340 (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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213D LYS 3.3 9.4 - - - +
214D MET* 2.8 32.3 - - + +
215D GLN* 1.0 199.5 - - + +
216D GLY 3.9 5.2 + - - +
217D THR 4.1 11.2 - - - +
221D GLN* 3.6 22.5 - - - +
224D SER* 3.8 20.4 - - - +
336D SER* 3.5 13.2 - - - +
337D ALA* 3.6 6.7 - - - +
339D ASP 1.3 26.2 - - - -
341D LEU* 1.3 59.5 - - - +
342D GLY* 3.0 5.5 + - - -
448D GLN* 5.1 0.2 - - - +
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Residues in contact with LEU 341 (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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221D GLN* 3.4 35.2 - - + +
224D SER* 3.4 35.7 - - - +
225D ALA* 3.6 6.1 - - - +
228D LEU* 4.5 11.9 - - + -
337D ALA* 2.7 26.7 + - + +
338D ILE 3.3 4.7 - - - +
339D ASP 2.9 0.4 - - - -
340D ILE* 1.3 80.9 - - - +
342D GLY* 1.3 50.2 + - - +
343D PHE* 3.4 21.2 + - + -
444D ARG 5.0 1.0 - - - +
445D ILE* 3.9 27.9 - - + +
448D GLN* 2.6 37.3 + - + +
449D LEU* 4.5 5.4 - - + -
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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