Contacts of the helix formed by residues 315 - 324 (chain D) in PDB entry 3MUP
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 315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283D GLN* 4.7 4.7 - - - +
310D TRP* 4.4 0.7 - - - -
313D GLY 3.4 6.5 + - - +
314D ASP* 1.3 71.8 - - - +
316D PRO* 1.4 75.5 - - - +
317D TRP* 3.2 14.8 + - - +
318D VAL* 3.3 37.1 + - + +
319D GLU* 3.1 26.3 + - - +
338D PHE* 5.1 0.5 - - - -
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Residues in contact with PRO 316 (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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279D VAL* 3.8 10.3 - - + -
283D GLN* 3.4 52.7 - - + +
284D LEU* 3.8 25.1 - - + -
287D ALA* 3.7 11.4 - - + -
289D PHE* 3.6 7.3 - - + -
310D TRP* 3.9 13.4 - - + -
314D ASP 3.8 3.4 - - - +
315D ASP* 1.4 90.3 - - - +
317D TRP* 1.3 55.5 + - - +
319D GLU* 4.0 0.7 - - - +
320D HIS* 3.0 28.1 + - - +
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Residues in contact with TRP 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D GLN 5.6 1.8 - - - -
286D SER* 3.2 26.2 + - - -
287D ALA* 3.7 28.1 - - + +
315D ASP* 3.2 16.2 + - - +
316D PRO* 1.3 74.7 - - + +
318D VAL* 1.3 59.9 + - - +
320D HIS* 3.4 9.0 - - - +
321D ALA* 3.0 27.0 + - - +
329D PHE* 3.5 24.5 - + - -
330D LEU* 3.5 41.9 - - + +
333D MET* 3.6 26.9 - - + -
334D LYS* 3.6 39.5 - - + +
338D PHE* 3.7 7.7 - - + -
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Residues in contact with VAL 318 (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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315D ASP* 3.3 29.9 + - + +
317D TRP* 1.3 72.1 - - - +
319D GLU* 1.4 68.4 + - - +
321D ALA* 3.2 1.4 + - - -
322D LYS* 2.8 31.4 + - + +
338D PHE* 3.8 23.1 - - + -
342D ILE* 3.5 28.2 - - + +
345D ARG* 4.8 6.7 - - - +
346D TYR* 4.5 17.3 - - + +
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Residues in contact with GLU 319 (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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307D LEU* 3.9 20.9 - - + +
310D TRP* 4.1 7.4 - - + -
314D ASP* 3.9 16.4 - - + +
315D ASP 3.1 23.5 + - - +
316D PRO 4.1 2.2 - - - +
318D VAL* 1.4 77.7 - - + +
320D HIS* 1.3 59.5 + - - +
322D LYS* 3.1 36.1 + - - +
323D TRP* 3.1 45.9 + - + +
600D SMK 3.1 35.5 + - + +
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Residues in contact with HIS 320 (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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4D ZN 2.2 37.3 - - - -
287D ALA 2.9 28.7 + - - -
289D PHE* 3.4 21.1 - + + -
300D CYS* 3.3 13.2 - - - +
303D CYS* 3.6 1.4 - - - -
307D LEU* 4.3 0.6 - - - +
316D PRO 3.0 18.2 + - - +
317D TRP* 3.4 15.2 - - - +
319D GLU* 1.3 77.0 - - - +
321D ALA* 1.4 55.1 + - - +
324D PHE* 3.0 49.2 + + + +
327D CYS* 3.7 5.8 - - + -
329D PHE* 4.6 3.8 - + - -
330D LEU* 3.9 13.5 - - + -
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Residues in contact with ALA 321 (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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317D TRP 3.0 16.6 + - - +
318D VAL 3.2 4.9 + - - +
320D HIS* 1.4 73.1 - - - +
322D LYS* 1.3 60.2 + - - +
323D TRP 3.5 0.2 - - - -
325D PRO* 3.5 14.3 - - - +
330D LEU* 3.6 18.4 - - + +
338D PHE* 3.8 22.7 - - + -
339D VAL* 4.3 8.6 - - - +
342D ILE* 4.0 15.0 - - + -
343D GLN* 3.1 20.8 + - - +
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Residues in contact with LYS 322 (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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350B LEU* 4.9 2.4 - - - +
318D VAL* 2.8 19.1 + - + +
319D GLU* 3.1 39.9 + - - +
321D ALA* 1.3 76.3 - - - +
323D TRP* 1.4 82.4 + - + +
325D PRO* 4.4 0.7 - - - +
342D ILE* 3.7 8.3 - - + +
343D GLN* 3.0 21.2 + - - +
346D TYR* 3.9 48.1 - - + -
349D LEU* 3.5 27.7 - - + +
600D SMK 3.7 7.9 + - - -
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Residues in contact with TRP 323 (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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350B LEU* 4.3 15.0 - - + +
351B GLU* 5.6 5.4 - - - +
354B LEU* 3.8 26.6 - - + +
307D LEU* 3.5 19.0 - - + +
319D GLU* 3.1 44.3 + - - +
322D LYS* 1.4 100.3 - - + +
324D PHE* 1.4 86.4 + - + +
325D PRO* 3.3 12.0 - - - +
349D LEU* 4.1 29.2 - - + -
353D LEU* 4.2 23.1 - - + -
600D SMK 3.5 48.9 + - + -
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Residues in contact with PHE 324 (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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351B GLU* 6.5 1.8 - - + -
354B LEU* 4.2 24.5 - - + -
289D PHE* 4.8 0.7 - + - -
303D CYS* 3.8 22.2 - - + -
305D GLY* 3.6 27.1 - - - -
306D GLY 3.3 27.8 - - - -
307D LEU* 3.7 28.9 - - + -
320D HIS* 3.0 37.8 + + + +
323D TRP* 1.4 97.4 - - + +
325D PRO* 1.4 62.1 - - - +
326D ARG 3.3 4.2 + - - -
327D CYS* 3.3 11.5 + - + +
330D LEU* 3.4 7.3 - - - +
600D SMK 4.5 4.9 - + + -
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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