Contacts of the helix formed by residues 280 - 292 (chain A) in PDB entry 1M1B
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 ARG 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ARG* 3.1 40.4 - - - +
276A PHE 3.2 0.2 + - - -
277A ARG* 3.1 12.3 + - - +
278A LEU 4.5 0.2 - - - +
279A GLN* 1.3 85.1 - - - +
281A ASP* 1.3 64.3 + - - +
282A ASP* 3.1 15.7 + - - +
283A GLU* 3.2 59.0 + - + +
284A LEU* 3.7 4.0 + - - +
286A GLN* 5.9 0.4 - - - +
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Residues in contact with ASP 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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276A PHE* 3.0 42.5 + - + +
277A ARG* 4.8 0.6 - - - +
279A GLN* 3.4 6.2 - - + +
280A ARG* 1.3 74.4 - - - +
282A ASP* 1.3 66.1 + - - +
284A LEU* 3.2 20.0 + - - +
285A VAL* 3.0 33.8 + - - +
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ARG* 6.0 1.2 - - - +
280A ARG* 3.1 12.5 + - - +
281A ASP* 1.3 80.1 - - - +
283A GLU* 1.3 56.6 + - - +
285A VAL* 3.2 14.1 + - - +
286A GLN* 2.8 57.6 + - - +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ARG* 3.2 47.4 + - + +
282A ASP* 1.3 80.0 - - - +
284A LEU* 1.3 61.8 + - - +
286A GLN* 3.4 11.5 + - + +
287A ALA* 3.0 19.1 + - - +
97B ARG* 2.8 42.6 + - - -
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Residues in contact with LEU 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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280A ARG 3.7 3.7 + - - +
281A ASP* 3.2 24.7 + - - +
283A GLU* 1.3 82.4 + - - +
285A VAL* 1.3 56.8 + - + +
287A ALA* 3.1 2.6 + - - +
288A GLU* 2.6 57.2 + - - +
93B PHE* 4.2 11.2 - - + -
94B ASN* 3.5 44.6 - - + +
97B ARG* 3.9 7.0 - - - +
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Residues in contact with VAL 285 (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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281A ASP* 3.0 32.7 + - - +
282A ASP* 3.2 17.2 + - - +
284A LEU* 1.3 76.8 - - + +
286A GLN* 1.3 65.5 + - + +
288A GLU* 3.2 14.5 + - + +
289A ASP* 2.9 26.3 + - + +
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Residues in contact with GLN 286 (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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280A ARG* 5.9 0.7 - - - +
282A ASP* 2.8 58.7 + - - +
283A GLU* 3.4 11.9 - - + +
285A VAL* 1.3 80.1 - - - +
287A ALA* 1.3 56.7 + - - +
289A ASP* 3.2 8.8 + - - +
290A LYS* 3.1 32.0 + - - +
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Residues in contact with ALA 287 (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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283A GLU* 3.0 15.3 + - - +
284A LEU* 3.5 3.8 - - - +
286A GLN* 1.3 78.8 - - - +
288A GLU* 1.3 59.0 + - - +
290A LYS* 3.2 6.5 + - - +
291A TYR* 2.8 46.7 + - + +
93B PHE* 3.6 12.4 - - + -
97B ARG* 3.6 30.3 - - - +
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Residues in contact with GLU 288 (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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284A LEU* 2.6 43.4 + - - +
285A VAL* 3.5 14.4 - - + +
287A ALA* 1.3 68.7 - - - +
289A ASP* 1.3 66.9 + - - +
292A LEU* 3.0 58.7 + - + +
92B ASN* 5.4 4.5 + - - -
93B PHE* 3.7 14.7 - - + -
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Residues in contact with ASP 289 (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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285A VAL* 2.9 14.6 + - + +
286A GLN* 3.4 11.4 - - - +
288A GLU* 1.3 77.0 - - - +
290A LYS* 1.3 60.1 + - - +
292A LEU 4.3 2.3 - - - +
294A LYS* 3.0 46.1 + - - +
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Residues in contact with LYS 290 (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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286A GLN* 3.1 18.5 + - - +
287A ALA* 3.6 7.0 - - - +
288A GLU 3.1 0.2 - - - -
289A ASP* 1.3 82.1 - - - +
291A TYR* 1.3 98.2 + - + +
292A LEU 3.7 0.9 - - - -
294A LYS* 4.7 7.1 + - - +
140B LEU* 4.3 10.4 - - - +
143B LYS* 5.3 9.8 - - - +
147B ASP* 5.3 0.4 - - - +
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Residues in contact with TYR 291 (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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287A ALA* 2.8 35.3 + - + +
290A LYS* 1.3 110.6 - - + +
292A LEU* 1.3 68.5 + - - +
293A PRO* 4.1 1.6 - - - +
93B PHE* 3.6 32.4 - + + +
97B ARG* 5.4 6.3 - - - -
137B GLU* 4.7 2.1 - - - +
140B LEU* 3.1 46.7 - - + +
141B LYS 4.8 0.2 + - - -
143B LYS* 3.8 13.5 - - + -
144B ALA* 3.5 24.0 - - + -
147B ASP* 2.6 39.2 + - + +
148B SER* 5.9 1.1 - - - -
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Residues in contact with LEU 292 (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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288A GLU* 3.0 50.5 + - + +
289A ASP* 4.3 7.6 - - - +
290A LYS 3.7 0.7 - - - -
291A TYR* 1.3 82.1 - - - +
293A PRO* 1.3 77.3 - - + +
294A LYS* 2.9 9.7 + - - +
92B ASN* 5.1 11.9 - - + +
93B PHE* 3.6 26.9 - - + +
137B GLU* 5.0 12.6 - - + +
140B LEU* 3.9 3.1 - - - +
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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