Contacts of the helix formed by residues 272 - 284 (chain D) in PDB entry 3MA2
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 PRO 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D ASP* 5.9 0.4 - - - +
254D SER* 3.8 21.8 - - - +
255D ALA* 4.1 9.4 - - - -
256D ILE* 4.0 7.4 - - + +
264D MET* 4.8 8.5 - - - -
269D PHE* 4.3 8.7 - - + -
270D VAL* 3.4 10.8 - - + +
271D LEU* 1.3 89.8 - - + +
273D ASP* 1.3 68.8 + - - +
274D ASP* 4.5 2.2 - - + +
275D ASP* 3.0 39.0 + - - +
276D ARG 3.0 10.2 + - - -
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Residues in contact with ASP 273 (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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271D LEU 3.5 1.9 + - - -
272D PRO* 1.3 74.9 - - - +
274D ASP* 1.3 62.1 + - - +
276D ARG* 2.8 39.9 + - - +
277D ARG* 3.0 55.4 + - - +
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Residues in contact with ASP 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLY* 3.3 12.8 - - - -
326B THR* 2.7 60.4 + - - +
379B ARG* 4.5 1.4 + - - -
250D SER* 2.8 28.1 + - - -
251D SER* 4.9 0.7 + - - -
252D ASP* 4.0 23.3 - - - +
255D ALA* 4.1 8.7 - - + -
272D PRO* 3.1 2.4 + - + +
273D ASP* 1.3 79.8 - - - +
275D ASP* 1.3 57.5 + - - +
277D ARG* 4.6 3.0 - - - +
278D GLY* 3.0 14.4 + - - -
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Residues in contact with ASP 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D TRP* 4.1 7.8 - - + -
247D LEU* 4.5 2.5 - - - +
250D SER* 4.6 1.0 - - - -
255D ALA* 3.3 13.5 - - - +
256D ILE* 2.8 33.1 + - + -
257D MET* 3.1 34.7 + - + +
271D LEU* 3.8 16.4 - - + -
272D PRO* 3.0 23.5 + - - +
274D ASP* 1.3 76.2 - - - +
276D ARG* 1.3 64.9 + - - +
278D GLY* 3.2 1.9 + - - -
279D ILE* 3.1 27.2 + - - +
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Residues in contact with ARG 276 (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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328B GLU* 5.6 3.6 - - - +
154D ALA* 4.8 7.0 - - + -
271D LEU* 3.9 23.2 - - + +
272D PRO 3.0 12.2 + - - +
273D ASP* 2.8 37.1 + - - +
275D ASP* 1.3 74.0 - - - +
277D ARG* 1.3 92.7 + - - +
279D ILE* 3.2 9.3 - - - +
280D GLN* 3.0 64.1 + - - +
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Residues in contact with ARG 277 (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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324B VAL 5.5 2.6 + - - -
326B THR* 3.1 34.4 + - - +
327B PRO* 3.4 24.4 - - - +
328B GLU* 3.3 37.9 - - - +
329B VAL* 5.5 0.7 - - - +
337B ARG 4.9 1.6 + - - -
339B GLU* 5.6 8.5 + - - +
273D ASP* 3.0 37.6 + - - +
274D ASP* 4.9 1.6 - - - +
276D ARG* 1.3 96.4 - - - +
278D GLY* 1.3 61.5 + - - +
280D GLN* 3.7 2.6 - - - +
281D GLN* 2.8 30.5 + - - +
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Residues in contact with GLY 278 (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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326B THR* 3.8 17.0 - - - -
247D LEU* 3.4 21.0 - - - +
274D ASP 3.0 16.3 + - - -
275D ASP* 3.2 4.0 + - - -
277D ARG* 1.3 79.4 - - - +
279D ILE* 1.3 61.0 + - - +
281D GLN* 3.4 18.9 + - - +
282D LEU* 3.6 7.3 + - - +
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Residues in contact with ILE 279 (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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151D TRP* 3.3 31.0 - - + -
154D ALA* 3.6 30.5 - - + -
155D THR* 3.6 16.8 - - + -
245D LEU* 4.5 13.9 - - + -
247D LEU* 3.6 17.8 - - + +
275D ASP 3.1 15.0 + - - +
276D ARG* 3.2 20.6 - - - +
278D GLY* 1.3 74.1 - - - +
280D GLN* 1.3 68.1 + - + +
282D LEU* 3.1 5.8 + - + +
283D TYR* 2.8 50.3 + - + +
284D GLY 4.4 0.2 - - - +
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Residues in contact with GLN 280 (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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329B VAL* 5.0 4.8 - - + +
331B GLN* 4.5 8.3 + - - +
154D ALA* 2.9 30.1 - - - +
276D ARG* 3.0 55.5 + - - +
277D ARG* 4.0 3.3 - - - +
279D ILE* 1.3 77.4 - - + +
281D GLN* 1.3 64.8 + - - +
284D GLY* 2.8 38.5 + - - +
285D GLY* 3.8 13.4 - - - +
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Residues in contact with GLN 281 (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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326B THR* 5.7 2.6 - - - +
327B PRO* 3.5 17.4 - - + +
329B VAL* 4.2 14.7 - - + +
336B GLN* 2.8 34.1 + - - +
338B TYR* 3.1 15.2 + - - -
365B ALA 5.2 2.1 - - - +
373B PHE* 3.4 37.1 - - + +
374B HIS 4.6 7.6 + - - -
118D LYS* 5.2 1.0 + - - -
277D ARG 2.8 19.4 + - - +
278D GLY* 3.4 11.6 + - - +
279D ILE 3.2 0.2 - - - -
280D GLN* 1.3 77.6 - - - +
282D LEU* 1.4 69.0 + - + +
284D GLY 4.9 0.3 + - - -
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Residues in contact with LEU 282 (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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373B PHE* 5.5 6.5 - - + -
115D GLN 5.7 1.6 - - - +
116D GLY* 4.9 12.1 - - - +
117D LEU 5.6 0.7 - - - +
118D LYS* 2.9 50.3 + - + +
245D LEU 3.8 12.8 - - - +
246D GLY* 3.7 34.5 - - - +
247D LEU* 4.0 20.0 - - + +
278D GLY 3.6 4.2 + - - +
279D ILE* 3.1 8.8 + - + +
281D GLN* 1.4 95.1 - - + +
283D TYR* 1.3 73.3 + - + +
284D GLY 3.7 0.2 - - - -
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Residues in contact with TYR 283 (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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118D LYS* 3.6 18.5 - - + -
119D TRP* 3.0 49.2 + + + -
122D ASN* 5.9 0.9 - - - +
155D THR* 4.3 12.1 - - + -
156D PRO* 3.2 20.8 - - + +
157D LEU* 3.9 41.5 - - + -
245D LEU* 2.6 35.9 + - + -
279D ILE* 2.8 27.5 + - + +
282D LEU* 1.3 92.6 - - + +
284D GLY* 1.3 63.3 + - - +
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Residues in contact with GLY 284 (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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331B GLN* 3.8 17.7 - - - -
155D THR* 3.6 6.8 - - - +
156D PRO* 3.4 7.8 - - - +
280D GLN* 2.8 40.4 + - - +
281D GLN 4.9 0.2 + - - -
282D LEU 3.7 0.6 - - - -
283D TYR* 1.3 76.6 - - - +
285D GLY* 1.3 59.7 + - - -
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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