Contacts of the helix formed by residues 271 - 289 (chain A) in PDB entry 2AJA
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 THR 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LEU 4.6 0.2 - - - +
270A VAL* 1.3 92.1 - - + +
272A LYS* 1.3 97.6 + - + +
273A SER* 3.0 4.2 + - - -
274A GLU* 2.8 40.9 + - - +
275A CYS* 3.4 13.7 + - - -
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Residues in contact with LYS 272 (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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270A VAL 4.2 0.4 + - - -
271A THR* 1.3 105.9 + - + +
273A SER* 1.3 74.5 + - - +
275A CYS* 3.3 11.1 + - - +
276A LEU* 3.1 36.2 + - + +
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Residues in contact with SER 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP 4.6 5.0 + - - -
222A PRO* 3.7 24.8 - - - +
271A THR* 3.0 3.5 + - - -
272A LYS* 1.3 92.5 - - - +
274A GLU* 1.3 67.4 + - - +
275A CYS 3.1 1.7 + - - -
276A LEU* 3.5 6.9 + - - -
277A GLN* 3.4 17.7 + - - +
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Residues in contact with GLU 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 ARG* 5.2 6.8 + - - -
254A MSE 5.9 2.6 - - - +
269A LEU* 3.2 38.1 - - + +
270A VAL* 3.8 13.8 + - - +
271A THR* 2.8 40.6 + - - +
273A SER* 1.3 77.7 - - - +
275A CYS* 1.3 61.9 + - - +
277A GLN* 3.5 18.5 + - - +
278A GLY* 3.3 16.3 + - - -
306A ILE* 5.5 0.5 - - - +
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Residues in contact with CYS 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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269A LEU* 3.7 24.5 - - - -
270A VAL 5.4 0.2 - - - -
271A THR 3.6 15.5 - - - -
272A LYS* 3.3 13.0 + - - +
273A SER 3.1 0.4 - - - -
274A GLU* 1.3 78.6 - - - +
276A LEU* 1.3 65.2 + - + +
278A GLY* 3.2 11.4 + - - -
279A PHE 3.3 8.1 + - - -
305A GLY* 2.8 43.4 - - - +
306A ILE* 4.1 4.8 - - - +
309A LEU* 3.7 14.1 - - + +
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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
----------------------------------------------------------
222A PRO* 3.8 26.7 - - + -
272A LYS* 3.1 25.1 + - + +
273A SER* 3.5 3.1 + - - +
275A CYS* 1.3 78.0 - - + +
277A GLN* 1.3 62.5 + - - +
279A PHE* 3.1 19.8 + - - +
280A TYR* 3.3 20.3 + - + -
309A LEU* 3.5 28.7 - - + -
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Residues in contact with GLN 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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219A LEU 3.8 4.8 - - - +
220A ASP* 3.8 17.4 + - - +
222A PRO* 4.1 11.8 - - + +
225A LEU* 3.8 16.9 - - + +
243A PHE* 3.6 19.8 - - - -
247A HIS* 3.8 15.2 + - - -
273A SER 3.4 10.0 + - - +
274A GLU* 3.5 21.4 + - - +
276A LEU* 1.3 79.4 - - - +
278A GLY* 1.3 56.6 + - - +
280A TYR* 3.4 0.8 + - - -
281A MSE 2.8 59.3 + - + +
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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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251A LEU* 6.0 2.0 - - - -
274A GLU 3.3 6.0 + - - -
275A CYS 3.2 9.0 + - - -
277A GLN* 1.3 79.0 - - - +
279A PHE* 1.3 52.4 + - - +
281A MSE 3.3 11.6 - - - +
282A LEU* 2.7 35.5 + - - +
300A LEU* 4.2 6.3 - - - +
306A ILE* 3.8 25.6 - - - +
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Residues in contact with PHE 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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275A CYS 3.3 8.2 + - - +
276A LEU* 3.1 13.4 + - - +
278A GLY* 1.3 74.8 - - - +
280A TYR* 1.3 81.4 + + - +
282A LEU* 2.9 11.5 + - + +
283A ARG* 2.8 32.2 + - - +
306A ILE* 4.4 8.0 - - + +
309A LEU* 3.2 44.0 - - + -
310A ALA* 4.5 3.1 - - - -
312A THR* 4.0 18.4 - - - -
313A ALA 5.2 0.4 - - - -
314A THR* 4.1 5.8 - - - -
321A GLU* 3.6 26.2 - - + -
322A LEU* 3.5 39.8 - - + +
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Residues in contact with TYR 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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222A PRO* 3.6 30.5 - - + -
223A VAL* 5.3 5.8 - - + +
225A LEU* 4.0 21.1 - - + -
226A ALA* 3.6 19.1 - - + -
229A GLU* 4.2 5.1 - - + +
276A LEU* 3.3 30.9 + - + -
277A GLN 4.1 0.9 - - - +
279A PHE* 1.3 93.5 - + - +
281A MSE 1.3 60.9 + - - +
283A ARG* 3.0 51.0 - - - +
284A ASN* 3.0 29.1 + - - +
314A THR* 3.1 32.5 + - + +
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Residues in contact with MSE 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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225A LEU* 3.8 8.5 - - + +
243A PHE* 3.7 21.3 - - + -
244A ILE* 3.4 39.1 - - + +
247A HIS* 3.7 28.0 - - + -
248A VAL* 4.7 7.6 - - + -
251A LEU* 5.4 8.7 - - - -
277A GLN* 2.8 61.2 + - + +
278A GLY* 3.3 11.2 - - - +
280A TYR* 1.3 77.3 - - - +
282A LEU* 1.3 61.4 + - - +
284A ASN* 3.5 3.1 + - - +
285A LEU* 3.3 25.6 + - - +
300A LEU* 4.4 9.0 - - + -
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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
----------------------------------------------------------
278A GLY 2.7 12.0 + - - +
279A PHE* 2.9 10.1 + - - +
281A MSE 1.3 76.2 - - - +
283A ARG* 1.3 62.4 + - - +
285A LEU* 3.3 3.5 + - - +
286A ILE* 3.0 37.9 + - + +
297A ILE* 3.4 44.4 - - + +
300A LEU* 3.9 14.6 - - + -
301A LEU* 3.5 30.3 - - + -
306A ILE* 4.2 15.3 - - + -
310A ALA* 5.8 0.2 - - + -
322A LEU* 3.6 25.8 - - + -
338A LEU* 5.4 0.7 - - + -
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Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 2.8 29.3 + - - +
229A GLU* 2.6 26.6 + - - -
230A ILE* 5.0 2.9 - - - +
279A PHE* 2.8 13.5 + - + +
280A TYR* 3.0 49.2 + - - +
282A LEU* 1.3 77.9 - - - +
284A ASN* 1.3 50.8 + - - +
286A ILE* 3.3 3.9 + - - +
287A ARG* 2.7 47.5 + - - +
314A THR* 3.7 6.1 + - - +
321A GLU* 3.6 30.3 + - - -
322A LEU* 3.8 17.7 - - + -
325A LEU* 3.3 22.4 - - + +
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Residues in contact with ASN 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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229A GLU* 2.8 52.1 + - + +
232A GLU* 5.1 2.3 - - - +
240A VAL* 4.0 7.3 - - - +
241A ASN* 3.9 7.1 + - - +
244A ILE* 4.0 13.2 - - + +
280A TYR 3.0 14.7 + - - +
281A MSE 3.7 6.5 - - - +
283A ARG* 1.3 74.7 - - - +
285A LEU* 1.3 65.6 + - - +
287A ARG* 3.0 5.7 + - - +
288A ARG* 2.9 68.6 + - - +
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Residues in contact with LEU 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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244A ILE* 4.2 9.0 - - + -
248A VAL* 4.7 5.8 - - + -
281A MSE 3.3 10.9 + - - +
282A LEU* 3.3 7.2 + - - +
284A ASN* 1.3 79.9 - - - +
286A ILE* 1.3 63.0 + - - +
288A ARG* 3.5 20.1 + - - +
289A ASN* 3.5 5.9 + - - -
290A ASP 4.6 1.0 + - - -
293A LEU* 3.5 48.6 - - + +
296A ASP* 3.7 32.8 - - + +
297A ILE* 3.9 18.7 - - + +
300A LEU* 3.5 32.3 - - + -
331A ASN* 4.8 0.2 - - - +
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Residues in contact with ILE 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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282A LEU* 3.0 40.0 + - + +
283A ARG 3.6 4.3 - - - +
285A LEU* 1.3 72.9 - - - +
287A ARG* 1.3 56.9 + - - +
288A ARG 3.0 2.2 - - - -
289A ASN* 2.8 27.9 + - - +
297A ILE* 4.3 10.5 - - + -
322A LEU* 4.2 28.3 - - + +
325A LEU* 4.6 7.0 - - + -
326A ALA* 4.1 19.3 - - - +
329A LEU* 3.9 4.5 - - + +
331A ASN* 3.0 33.2 - - + +
334A ALA* 4.1 7.9 - - + -
338A LEU* 4.4 13.0 - - + -
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Residues in contact with ARG 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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229A GLU* 2.8 45.0 + - - +
230A ILE* 3.4 40.6 - - - +
232A GLU* 3.6 30.7 - - + +
283A ARG* 2.7 39.3 + - - +
284A ASN* 3.0 7.8 + - - +
286A ILE* 1.3 72.5 - - - +
288A ARG* 1.3 61.7 + - + +
289A ASN* 4.4 1.6 - - - +
325A LEU* 4.1 21.2 - - + +
329A LEU* 3.8 29.1 - - - +
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Residues in contact with ARG 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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232A GLU* 4.4 15.9 - - + +
241A ASN* 3.4 41.6 + - - +
244A ILE* 4.1 14.8 - - - +
245A ALA* 5.5 0.8 - - - +
284A ASN* 2.9 43.5 + - - +
285A LEU* 3.6 25.4 - - - +
286A ILE 3.0 0.4 - - - -
287A ARG* 1.3 75.6 - - + +
289A ASN* 1.3 74.0 + - - +
290A ASP* 4.4 3.2 - - + +
293A LEU* 3.7 29.3 - - + +
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Residues in contact with ASN 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 LEU 3.5 3.2 + - - -
286A ILE 2.8 16.7 + - - +
287A ARG 4.4 3.6 - - - +
288A ARG* 1.3 86.9 - - - +
290A ASP* 1.3 59.5 + - - +
329A LEU* 4.8 17.0 + - + -
330A GLY 3.9 5.7 + - - +
331A ASN* 2.6 48.7 + - + +
332A GLN* 5.0 2.4 + - - +
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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
------------------------------------------------------------
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