Contacts of the helix formed by residues 273 - 296 (chain A) in PDB entry 2LCK
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 PHE 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A VAL* 4.7 15.5 - - + -
240A THR* 4.0 14.4 - - + -
269A PHE 4.8 2.5 - - - +
270A TYR 2.9 28.3 - - - +
271A LYS* 3.7 6.7 - - + +
272A GLY* 1.3 78.2 - - - +
274A MET* 1.3 73.5 + - + +
275A PRO* 3.2 9.2 - - - +
276A SER* 3.6 3.2 + - - -
277A PHE* 3.3 30.2 + + + +
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Residues in contact with MET 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.4 50.5 - - + +
272A GLY* 6.1 0.9 - - - -
273A PHE* 1.3 86.9 - - + +
275A PRO* 1.3 103.0 - - + +
277A PHE* 3.3 7.1 + - - +
278A LEU* 3.1 35.4 + - + +
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Residues in contact with PRO 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 5.4 12.5 - - + +
41A LEU* 6.2 0.2 - - + -
240A THR* 3.4 21.1 - - - +
243A MET* 5.3 13.7 - - + -
272A GLY* 5.0 0.4 - - - -
273A PHE* 3.2 8.1 - - - +
274A MET* 1.3 121.5 - - + +
276A SER* 1.3 56.2 + - - +
278A LEU* 3.2 10.4 + - + +
279A ARG* 2.8 34.9 + - + +
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ASP* 2.7 37.8 + - - +
237A VAL* 4.5 4.9 - - - -
239A LYS* 5.1 0.2 - - - +
240A THR* 2.9 29.5 + - - +
273A PHE* 3.9 5.8 - - - -
274A MET 3.4 0.4 - - - -
275A PRO* 1.3 81.3 - - - +
277A PHE* 1.3 51.8 + - - +
279A ARG* 3.0 13.4 + - - +
280A LEU* 2.7 34.9 + - - +
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PHE* 3.3 24.1 + + + +
274A MET* 3.6 11.4 - - - +
275A PRO 3.2 0.2 - - - -
276A SER* 1.3 77.2 - - - +
278A LEU* 1.3 73.6 + - + +
280A LEU* 3.0 33.1 + - + +
281A GLY* 3.2 6.2 + - - -
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.7 11.9 - - + -
274A MET* 3.1 33.6 + - + +
275A PRO* 3.3 8.7 - - + +
277A PHE* 1.3 86.7 - - + +
279A ARG* 1.3 63.5 + - + +
281A GLY* 3.4 9.4 + - - -
282A SER* 3.5 12.8 + - - -
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 4.8 16.2 - - - +
34A LEU* 5.8 6.5 - - - +
38A LYS* 4.0 34.9 - - + +
236A ASP* 6.2 3.4 - - + -
275A PRO* 2.8 28.6 + - + +
276A SER* 3.0 16.4 + - - +
278A LEU* 1.3 79.3 - - + +
280A LEU* 1.3 50.2 + - - +
282A SER* 3.4 7.5 + - - -
283A TRP* 2.6 47.7 + - + +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 6.2 3.8 - - + -
233A SER* 4.6 20.6 - - - +
236A ASP* 5.3 11.2 - - + +
276A SER 2.7 14.1 + - - +
277A PHE* 3.0 28.2 + - + +
279A ARG* 1.3 71.7 - - - +
281A GLY* 1.3 59.1 + - - +
283A TRP* 4.1 20.4 - - + -
284A ASN* 2.9 32.6 + - + +
287A MET* 5.9 1.1 - - + -
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Residues in contact with GLY 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 PHE 3.2 8.8 + - - -
278A LEU* 3.4 3.3 + - - -
279A ARG 3.3 0.8 - - - -
280A LEU* 1.3 80.8 - - - +
282A SER* 1.3 61.7 + - - +
284A ASN* 3.3 11.2 + - - +
285A VAL* 3.1 17.9 - - - +
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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
----------------------------------------------------------
30A ILE 4.9 0.2 + - - -
31A THR* 4.1 11.1 + - - +
34A LEU* 2.6 41.0 - - - +
278A LEU 3.5 10.1 + - - -
279A ARG* 3.4 9.7 + - - -
281A GLY* 1.3 71.9 - - - +
283A TRP* 1.3 66.0 + - - +
285A VAL* 3.0 33.9 + - - +
286A VAL* 3.5 4.7 - - - +
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Residues in contact with TRP 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 5.3 3.8 - - + -
232A ALA* 4.5 23.6 - - + -
236A ASP* 5.0 22.1 + - - -
279A ARG* 2.6 34.9 + - + +
280A LEU* 3.9 17.5 - - + +
282A SER* 1.3 73.2 + - - +
284A ASN* 1.3 68.9 + - - +
286A VAL* 3.2 39.4 - - + +
287A MET* 3.8 29.4 + - + +
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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
----------------------------------------------------------
229A THR* 5.4 1.0 - - - +
280A LEU* 2.9 27.8 + - + +
281A GLY* 3.3 8.5 + - - +
283A TRP* 1.3 79.6 - - - +
285A VAL* 1.3 63.4 + - - +
287A MET* 2.8 51.1 - - + +
288A PHE* 3.4 12.2 + - - +
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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
----------------------------------------------------------
27A ALA* 6.2 0.4 - - - -
30A ILE* 3.6 31.9 - - + -
31A THR* 5.4 0.9 - - - +
281A GLY 3.1 18.4 - - - +
282A SER* 3.0 20.2 + - - +
284A ASN* 1.3 81.3 - - - +
286A VAL* 1.3 71.8 + - + +
288A PHE* 3.1 21.9 + - + +
289A VAL* 3.3 13.9 + - + +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 4.6 18.6 - - + +
31A THR* 4.7 14.6 - - + +
282A SER* 3.5 12.3 - - - +
283A TRP* 3.2 37.2 - - + +
284A ASN 3.2 0.4 - - - -
285A VAL* 1.3 81.1 - - + +
287A MET* 1.3 66.4 + - + +
289A VAL* 2.7 32.1 - - - +
290A THR* 3.9 4.5 + - - -
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Residues in contact with MET 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 3.8 27.4 - - + -
280A LEU* 5.9 1.1 - - + -
283A TRP* 3.9 24.9 - - + +
284A ASN* 2.8 56.8 - - + +
286A VAL* 1.3 86.5 - - + +
288A PHE* 1.3 62.7 + - + +
290A THR* 3.3 18.0 + - - -
291A TYR* 3.3 33.2 + - + -
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PHE* 5.9 7.9 - + - -
284A ASN* 3.9 14.4 - - - +
285A VAL* 3.1 17.7 + - - +
287A MET* 1.3 80.9 - - + +
289A VAL* 1.3 64.2 + - + +
291A TYR* 3.0 21.0 + + + +
292A GLU* 2.8 36.0 + - + -
295A LYS* 5.1 13.0 - - - -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 4.9 11.2 - - + +
26A ILE* 3.6 41.3 - - + -
27A ALA* 5.2 4.3 - - + -
30A ILE* 5.9 3.1 - - + -
285A VAL* 3.8 11.7 - - + +
286A VAL* 2.7 30.7 - - + +
288A PHE* 1.3 80.6 - - + +
290A THR* 1.3 67.2 + - - +
292A GLU* 2.9 32.8 + - + +
293A GLN* 3.3 3.6 + - - +
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Residues in contact with THR 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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23A ALA* 5.3 9.1 - - + +
286A VAL 3.9 6.6 + - - -
287A MET* 3.3 12.6 + - - -
288A PHE 3.2 0.6 - - - -
289A VAL* 1.3 80.8 - - - +
291A TYR* 1.3 64.6 + - - +
293A GLN* 3.1 20.1 + - + +
294A LEU* 3.2 29.2 - - + +
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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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218A PHE* 5.7 8.7 - + - -
221A ALA* 5.3 15.5 + - + +
222A PHE* 6.3 4.5 - + - -
225A GLY* 5.6 4.9 - - - -
287A MET* 3.3 40.9 + - + -
288A PHE* 3.0 25.9 + + + +
290A THR* 1.3 81.7 - - - +
292A GLU* 1.3 60.5 + - - +
294A LEU* 3.0 24.7 + - + +
295A LYS* 2.9 29.0 + - - +
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Residues in contact with GLU 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 PHE* 2.8 25.7 + - + +
289A VAL* 2.9 21.5 + - + +
291A TYR* 1.3 77.4 - - - +
293A GLN* 1.3 66.6 + - + +
295A LYS* 3.0 13.5 + - - +
296A ARG* 2.8 40.6 + - - +
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Residues in contact with GLN 293 (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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14A THR* 5.6 1.0 + - - -
15A VAL 4.0 8.9 + - - -
16A LYS* 4.3 15.4 + - - +
19A GLY* 3.1 45.2 - - - +
20A ALA* 3.8 1.2 + - - -
22A THR* 6.1 0.2 - - - +
23A ALA* 5.6 0.7 - - - +
289A VAL 3.3 4.0 + - - +
290A THR* 3.1 16.8 + - + +
292A GLU* 1.3 88.7 - - + +
294A LEU* 1.3 65.8 + - + +
296A ARG 2.3 37.3 - - - +
297A ALA* 3.4 10.3 + - + +
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Residues in contact with LEU 294 (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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218A PHE* 4.3 34.4 - - + -
290A THR* 3.2 25.4 - - + +
291A TYR* 3.4 26.9 - - + +
293A GLN* 1.3 85.7 - - + +
295A LYS* 1.3 63.7 + - - +
296A ARG* 4.5 1.0 - - - -
297A ALA* 4.7 5.5 + - - +
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Residues in contact with LYS 295 (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 PHE* 5.1 14.6 - - - -
291A TYR* 2.9 18.2 + - - +
292A GLU* 3.2 13.6 - - - +
294A LEU* 1.3 81.1 - - - +
296A ARG* 1.3 70.5 + - + +
297A ALA 4.3 0.5 + - - -
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU* 2.8 27.9 + - - +
293A GLN* 2.3 29.1 - - - +
295A LYS* 1.3 86.3 - - + +
297A ALA* 1.3 60.6 + - - +
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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
------------------------------------------------------------
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