Contacts of the helix formed by residues 273 - 292 (chain A) in PDB entry 2JM1
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 LEU 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.7 11.4 - - + +
194A VAL* 3.4 28.5 - - + -
222A TRP* 3.6 8.3 - - + -
247A ASN* 4.1 4.9 - - - +
266A TYR* 3.4 44.0 - - + +
269A HIS 3.9 3.4 - - - +
270A PRO* 3.5 28.3 - - + -
271A GLU 3.3 5.1 - - - +
272A PRO* 1.3 84.7 - - + +
274A LEU* 1.3 67.4 + - - +
275A ASP* 3.3 3.8 - - - +
276A LEU* 3.2 15.3 + - + +
277A VAL* 3.0 23.3 + - + +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PRO* 3.2 41.3 - - + +
271A GLU* 4.2 17.0 + - - +
272A PRO 3.9 0.6 - - - -
273A LEU* 1.3 77.7 - - - +
275A ASP* 1.3 51.5 + - - +
277A VAL* 3.1 10.5 + - + +
278A THR* 2.6 44.4 + - + +
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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
----------------------------------------------------------
273A LEU* 3.3 1.3 - - - +
274A LEU* 1.3 75.0 - - - +
276A LEU* 1.3 58.3 + - - +
278A THR* 2.4 25.7 + - - -
279A ALA* 2.9 19.8 + - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A THR* 2.7 43.1 - - + +
194A VAL* 3.8 13.3 - - + +
195A LEU* 4.6 2.5 + - - +
222A TRP* 3.2 29.6 - - + -
246A ARG 5.7 0.7 - - - +
247A ASN* 3.7 22.0 - - + +
273A LEU* 3.2 18.1 + - + +
275A ASP* 1.3 79.2 - - - +
277A VAL* 1.3 63.1 + - - +
279A ALA* 3.3 15.7 + - + +
280A CYS* 3.3 10.6 + - - +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU 3.5 7.6 - - - +
193A GLN* 2.7 34.8 - - + +
194A VAL* 3.2 23.8 - - + +
270A PRO* 5.0 9.0 - - + -
273A LEU* 3.0 21.2 + - + +
274A LEU* 3.1 13.2 + - + +
276A LEU* 1.3 75.7 - - - +
278A THR* 1.3 66.7 + - + +
280A CYS* 3.0 19.3 + - + +
281A ASN* 3.2 14.6 - - - +
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Residues in contact with THR 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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274A LEU* 2.6 23.2 + - + +
275A ASP* 2.4 36.8 + - - -
277A VAL* 1.3 73.0 - - + +
279A ALA* 1.3 60.3 + - - -
281A ASN* 3.1 20.3 + - - +
282A SER* 3.3 13.9 + - - -
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 5.3 0.4 - - + -
275A ASP* 2.9 16.2 + - - +
276A LEU* 3.5 13.7 - - + +
277A VAL 3.2 0.2 - - - -
278A THR* 1.3 76.8 - - - +
280A CYS* 1.3 57.5 + - - +
282A SER* 3.1 9.6 + - - -
283A VAL* 2.8 42.6 + - + +
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Residues in contact with CYS 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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188A ARG* 3.9 16.2 - - - -
193A GLN 4.5 3.6 - - - +
194A VAL* 3.8 8.5 - - - -
195A LEU* 3.5 49.2 - - - +
276A LEU 3.3 3.0 + - - +
277A VAL* 3.0 16.7 + - - +
279A ALA* 1.3 79.1 - - - +
281A ASN* 1.3 58.6 + - - +
284A PHE* 2.8 51.2 + - - +
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Residues in contact with ASN 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 VAL* 3.2 20.8 - - - +
278A THR* 3.1 11.2 + - - +
280A CYS* 1.3 78.0 - - - +
282A SER* 1.3 59.3 + - - +
284A PHE* 4.7 3.1 - - - -
285A GLU* 2.8 31.7 + - - +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A THR 3.3 12.5 + - - -
279A ALA* 3.1 10.2 + - - -
281A ASN* 1.3 77.8 - - - +
283A VAL* 1.3 64.8 + - - +
285A GLU* 3.7 11.8 - - - +
286A ASN* 3.2 26.5 + - - -
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE 4.3 13.7 - - - +
169A VAL* 3.5 44.0 - - + -
170A SER 5.0 3.1 - - - +
181A PHE* 4.4 2.4 - - - -
186A ILE* 4.1 7.0 - - + +
195A LEU* 3.5 22.2 - - + -
279A ALA* 2.8 34.3 + - + +
280A CYS* 4.7 0.2 - - - -
282A SER* 1.3 75.2 - - - +
284A PHE* 1.3 63.8 + - - +
286A ASN* 3.4 22.2 + - - +
287A LEU 3.8 2.6 + - - -
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Residues in contact with PHE 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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183A LYS 5.4 2.2 - - - -
184A ASP* 6.4 0.2 - - - -
186A ILE* 3.4 44.2 - - + -
187A TYR* 3.6 14.6 - - - -
188A ARG* 3.0 42.6 - - + -
195A LEU* 3.3 21.3 - - + -
280A CYS* 2.8 24.0 + - - +
281A ASN* 4.3 3.4 - - - +
283A VAL* 1.3 70.5 - - - +
285A GLU* 1.3 66.1 + - - +
287A LEU* 2.8 35.0 + - + +
288A GLU* 3.4 10.9 - - - +
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Residues in contact with GLU 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 ASN 2.8 21.6 + - - +
282A SER* 3.7 11.6 - - - +
283A VAL 3.3 0.2 - - - -
284A PHE* 1.3 76.4 - - - +
286A ASN* 1.3 66.3 + - - +
288A GLU* 3.0 30.8 + - + +
289A GLN* 3.6 9.5 + - + +
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Residues in contact with ASN 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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167A GLY* 4.9 17.8 + - - -
169A VAL* 6.0 3.9 - - + +
181A PHE* 3.5 20.1 - - + -
282A SER 3.2 19.3 + - - -
283A VAL* 3.4 13.6 + - - +
284A PHE 3.1 0.2 - - - -
285A GLU* 1.3 81.9 - - - +
287A LEU* 1.3 63.8 + - - +
289A GLN* 3.0 25.0 + - - +
290A LEU* 3.0 10.0 + - - +
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Residues in contact with LEU 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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181A PHE* 3.4 24.2 - - + -
182A GLN 3.1 28.3 - - - +
183A LYS* 3.0 38.6 - - + +
186A ILE* 4.4 10.8 - - + -
283A VAL 3.8 0.4 + - - -
284A PHE* 2.8 34.6 + - + +
286A ASN* 1.3 79.1 - - - +
288A GLU* 1.3 68.6 + - - +
290A LEU* 3.2 10.3 + - + +
291A LEU* 3.3 12.6 + - + +
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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 PHE* 3.4 19.9 - - - +
285A GLU* 3.0 19.9 + - + +
287A LEU* 1.3 88.3 - - - +
289A GLN* 1.3 68.8 + - + +
291A LEU* 3.1 22.3 + - + +
292A GLN* 3.6 15.0 + - - +
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Residues in contact with GLN 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 GLU* 3.6 14.3 + - + +
286A ASN* 3.0 19.2 + - - +
288A GLU* 1.3 80.2 - - + +
290A LEU* 1.3 61.8 + - - +
292A GLN* 3.0 19.4 + - - +
293A GLN* 3.0 29.2 + - + +
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Residues in contact with LEU 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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181A PHE* 3.6 54.3 - - + +
182A GLN* 4.2 0.9 - - - -
183A LYS* 3.8 26.2 - - + +
286A ASN 3.0 6.3 + - - -
287A LEU* 3.4 10.5 - - + +
289A GLN* 1.3 75.3 - - - +
291A LEU* 1.3 64.8 + - - +
292A GLN 3.1 0.7 + - - -
293A GLN* 3.2 20.9 + - + -
294A ASN* 3.7 17.1 + - + +
295A LYS* 3.7 14.7 + - - +
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Residues in contact with LEU 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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183A LYS* 5.8 4.9 - - + +
287A LEU* 3.3 11.5 + - + +
288A GLU* 3.1 14.8 + - - +
290A LEU* 1.3 78.6 - - - +
292A GLN* 1.3 78.5 + - + +
295A LYS* 3.1 40.4 - - - +
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Residues in contact with GLN 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* 3.6 13.3 + - - +
289A GLN* 3.0 13.5 + - - +
291A LEU* 1.3 99.8 - - + +
293A GLN* 1.3 59.6 + - - +
295A LYS* 5.2 1.6 - - - -
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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