Contacts of the helix formed by residues 272 - 284 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ASP* 6.1 0.2 - - - +
254A SER* 3.6 28.0 - - - +
255A ALA* 4.2 4.9 - - - -
256A ILE* 3.9 6.1 - - + +
264A MET* 4.9 7.9 - - + -
269A PHE* 4.2 9.2 - - + -
270A VAL* 3.2 10.5 - - + +
271A LEU* 1.4 90.7 - - + +
273A ASP* 1.4 66.0 + - - +
274A ASP* 3.2 3.2 + - + +
275A ASP* 3.3 27.4 + - - +
276A ARG* 3.1 18.4 + - - +
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Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU 4.6 3.0 - - - +
272A PRO* 1.4 72.3 - - - +
274A ASP* 1.3 57.1 + - - +
276A ARG* 3.3 27.0 + - - +
277A ARG* 2.9 61.8 + - - +
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Residues in contact with ASP 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A SER* 2.7 34.8 + - - -
252A ASP* 3.9 24.4 + - - +
255A ALA* 4.0 9.8 - - + +
272A PRO* 3.3 1.7 - - + +
273A ASP* 1.3 78.6 - - - +
275A ASP* 1.3 59.3 + - - +
277A ARG* 3.4 15.2 + - - +
278A GLY* 2.9 24.1 + - - -
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Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TRP* 4.1 9.9 - - + -
247A LEU* 4.6 2.8 - - - +
255A ALA* 3.4 7.8 - - - +
256A ILE* 2.6 39.4 + - + +
257A MET* 3.2 34.8 + - + +
271A LEU* 3.6 20.6 - - + -
272A PRO* 3.3 21.3 + - - +
274A ASP* 1.3 72.7 - - - +
276A ARG* 1.3 66.9 + - - +
278A GLY* 3.0 2.2 + - - +
279A ILE* 3.0 26.0 + - - +
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ALA* 4.6 11.0 - - + +
271A LEU* 4.0 21.5 + - + +
272A PRO 3.1 14.1 + - - +
273A ASP* 3.3 39.2 + - - +
275A ASP* 1.3 76.1 - - - +
277A ARG* 1.3 85.1 + - - +
279A ILE* 3.5 2.5 - - - +
280A GLN* 3.0 63.4 + - + +
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ASP* 2.9 50.9 + - - +
274A ASP* 3.8 11.9 + - - +
276A ARG* 1.3 98.5 - - - +
278A GLY* 1.3 62.1 + - - +
280A GLN* 4.3 4.6 - - - +
281A GLN* 3.1 26.0 + - - +
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Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 3.6 21.7 - - - +
274A ASP 2.9 15.8 + - - -
275A ASP* 3.0 5.2 + - - -
277A ARG* 1.3 79.0 - - - +
279A ILE* 1.3 61.8 + - - +
281A GLN* 3.4 15.0 + - - +
282A LEU* 3.4 12.0 + - - +
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TRP* 3.7 26.7 - - + -
154A ALA* 3.9 16.4 - - + -
155A THR* 3.8 26.9 - - + -
157A LEU* 4.9 0.7 - - + -
245A LEU* 3.8 37.5 - - + -
247A LEU* 3.9 23.5 - - + +
275A ASP 3.0 9.7 + - - +
276A ARG* 3.5 10.5 - - - +
278A GLY* 1.3 76.1 - - - +
280A GLN* 1.3 56.6 + - + +
282A LEU* 3.1 6.9 + - + +
283A TYR* 2.8 46.9 + - + +
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ALA* 2.8 30.9 - - - +
276A ARG* 3.0 55.1 + - + +
277A ARG* 4.3 3.8 - - - +
279A ILE* 1.3 76.2 - - + +
281A GLN* 1.3 63.8 + - - +
283A TYR 3.7 0.3 - - - -
284A GLY* 2.7 42.3 + - - +
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ARG 3.1 19.6 + - - +
278A GLY* 3.5 8.1 - - - +
279A ILE 3.2 0.2 - - - -
280A GLN* 1.3 79.6 - - - +
282A LEU* 1.4 68.0 + - + +
120D GLN* 5.7 5.0 - - - +
207D PRO* 6.1 3.0 - - - +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 6.1 5.4 - - + +
118A LYS* 3.9 30.3 - - + +
245A LEU 4.0 11.4 - - - +
246A GLY* 3.8 32.8 - - - +
247A LEU* 3.9 22.0 - - + -
278A GLY 3.4 7.3 + - - +
279A ILE* 3.1 8.2 + - + +
281A GLN* 1.4 89.3 - - + +
283A TYR* 1.3 78.4 + - + +
120D GLN* 5.5 11.7 - - + -
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Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LYS* 3.5 22.4 - - + +
119A TRP* 3.3 41.0 + + + -
122A ASN* 4.4 9.1 + - - +
155A THR* 4.2 12.6 - - + -
156A PRO* 3.5 18.0 - - + +
157A LEU* 3.6 42.6 - - + -
245A LEU* 2.6 32.1 + - + -
279A ILE* 2.8 31.9 + - + +
280A GLN 3.7 0.2 - - - -
282A LEU* 1.3 91.1 - - + +
284A GLY* 1.3 56.2 + - - +
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Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ALA 4.2 7.4 - - - +
155A THR* 4.3 5.0 - - - -
156A PRO* 3.7 21.8 - - - +
280A GLN* 2.7 49.8 + - - +
283A TYR* 1.3 75.2 - - - +
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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