Contacts of the helix formed by residues 269 - 284 (chain A) in PDB entry 1MKP
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 SER 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A ASN* 2.7 29.6 + - - -
268A LEU* 1.3 76.6 - - - +
270A GLN* 1.3 60.7 + - - +
271A PHE 3.1 0.4 - - - -
272A PHE* 3.1 50.3 + - - +
273A PRO* 3.8 2.9 - - - +
339A GLN* 3.0 24.6 + - - +
342A ASP* 5.6 1.9 + - - -
343A PHE* 5.3 3.3 - - - -
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Residues in contact with GLN 270 (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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266A GLN* 3.3 14.0 + - - -
267A ASN* 2.7 43.1 + - - +
268A LEU 3.0 0.6 + - - -
269A SER* 1.3 73.6 - - - +
271A PHE* 1.3 83.5 + - + +
272A PHE 3.3 0.9 - - - -
273A PRO* 3.4 20.5 - - - +
274A GLU* 5.0 2.1 - - - +
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Residues in contact with PHE 271 (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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258A ILE* 3.8 31.2 - - + -
259A PRO* 3.4 45.5 - - + -
260A ILE* 4.2 10.8 - - + -
266A GLN* 4.0 8.7 - - - -
267A ASN 3.9 14.8 - - - -
268A LEU* 2.9 22.9 + - + +
270A GLN* 1.3 101.2 - - + +
272A PHE* 1.3 66.6 + - + +
273A PRO* 3.4 1.8 - - - -
274A GLU* 3.4 31.4 + - + +
275A ALA* 2.9 24.9 + - + +
303A VAL* 6.4 0.7 - - + -
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Residues in contact with PHE 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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268A LEU* 3.9 14.4 - - + -
269A SER* 3.1 45.0 + - - +
271A PHE* 1.3 78.2 - - + +
273A PRO* 1.4 68.8 - - + +
275A ALA* 3.1 3.0 + - - +
276A ILE* 2.8 35.8 + - + +
302A THR* 3.8 32.1 - - + -
303A VAL* 4.4 14.4 - - + -
306A ALA* 3.8 26.9 - - + -
339A GLN* 4.4 5.6 - - + -
340A LEU* 4.0 9.6 - - + -
343A PHE* 3.7 41.1 - + + -
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Residues in contact with PRO 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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269A SER 3.8 4.3 - - - +
270A GLN* 3.4 20.0 - - - +
272A PHE* 1.4 92.1 - - + +
274A GLU* 1.3 57.4 + - + +
276A ILE* 3.8 6.6 - - + +
277A SER* 3.0 29.3 + - - -
310A GLN* 5.9 2.0 - - - +
343A PHE* 5.8 2.5 - - + -
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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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245A ASN* 4.6 5.9 + - - -
256A LYS* 2.7 35.9 + - - +
258A ILE* 3.6 11.5 - - + +
259A PRO* 6.1 0.2 - - - -
270A GLN 5.0 1.4 - - - +
271A PHE* 3.4 39.3 - - + +
273A PRO* 1.3 77.9 - - + +
275A ALA* 1.3 66.4 + - - +
277A SER* 3.7 7.4 + - - -
278A PHE* 3.2 22.3 + - - +
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Residues in contact with ALA 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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237A LEU* 4.0 18.3 - - + +
256A LYS* 5.5 1.1 - - - +
258A ILE* 5.5 4.5 - - + -
271A PHE* 2.9 22.1 + - + +
272A PHE* 3.6 5.6 - - - +
274A GLU* 1.3 76.6 - - + +
276A ILE* 1.3 62.8 + - + +
278A PHE* 3.3 4.7 + - - +
279A ILE* 2.9 34.6 + - - +
303A VAL* 3.8 29.2 - - + -
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Residues in contact with ILE 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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272A PHE* 2.8 26.2 + - + +
273A PRO* 3.8 5.6 - - + +
275A ALA* 1.3 75.8 - - + +
277A SER* 1.3 59.7 + - - +
279A ILE* 3.4 1.9 + - + +
280A ASP* 2.8 38.0 + - + +
303A VAL* 5.3 1.8 - - + +
306A ALA* 3.9 21.5 - - + +
307A TYR* 3.7 37.6 - - + +
310A GLN* 3.8 43.3 - - + +
311A LYS* 5.9 1.1 - - + +
343A PHE* 4.1 9.4 - - + -
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Residues in contact with SER 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 PRO 3.0 17.4 + - - -
274A GLU* 3.9 8.5 - - - -
276A ILE* 1.3 77.7 - - - +
278A PHE* 1.3 57.8 + - - +
280A ASP* 3.9 4.9 - - - +
281A GLU* 3.0 30.3 + - - +
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Residues in contact with PHE 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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235A TYR* 3.4 29.0 - + + -
236A ILE 3.6 33.0 - - - -
237A LEU* 3.8 20.2 - - + -
247A PHE* 3.7 29.2 - + - -
254A LYS 3.6 10.1 - - - -
256A LYS* 3.6 29.6 - - + -
274A GLU 3.2 16.6 + - - +
275A ALA* 3.5 4.5 - - - +
277A SER* 1.3 77.5 - - - +
279A ILE* 1.3 65.3 + - - +
281A GLU* 3.3 10.0 + - - +
282A ALA* 3.2 22.3 + - - +
289A VAL* 3.9 19.1 - - + -
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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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214A LEU* 3.6 25.1 - - + -
237A LEU* 4.7 5.6 - - + -
275A ALA 2.9 21.9 + - - +
276A ILE 3.8 3.6 - - - +
278A PHE* 1.3 75.0 - - - +
280A ASP* 1.3 58.5 + - - +
282A ALA* 3.3 4.3 + - - +
283A ARG* 3.0 35.2 + - - +
289A VAL* 3.7 22.7 - - + -
291A VAL* 3.9 26.0 - - + -
303A VAL* 4.4 15.0 - - + +
304A THR* 5.2 0.7 - - - -
307A TYR* 3.6 43.5 - - + -
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Residues in contact with ASP 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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276A ILE* 2.8 23.6 + - + +
277A SER* 3.9 5.6 - - - +
279A ILE* 1.3 75.3 - - - +
281A GLU* 1.3 59.2 + - - +
283A ARG* 3.7 2.9 + - - +
284A GLY* 2.8 29.3 + - - -
307A TYR* 2.7 33.3 + - + -
311A LYS* 3.6 25.5 + - - +
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Residues in contact with GLU 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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235A TYR* 2.8 29.8 + - - -
247A PHE* 5.2 8.3 - - - -
254A LYS* 5.5 0.2 - - - +
277A SER 3.0 20.3 + - - +
278A PHE* 3.3 8.3 + - - +
280A ASP* 1.3 74.7 - - - +
282A ALA* 1.3 60.7 + - - +
284A GLY* 3.7 1.6 + - - -
285A LYS* 2.7 56.6 + - - +
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Residues in contact with ALA 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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235A TYR* 3.6 32.7 - - + -
278A PHE 3.2 8.0 + - - +
279A ILE 3.4 8.7 - - - +
280A ASP 3.1 0.6 - - - -
281A GLU* 1.3 76.1 - - - +
283A ARG* 1.3 63.3 + - - +
285A LYS* 3.2 7.3 + - - -
287A CYS* 2.9 35.3 + - - +
289A VAL* 3.6 26.2 - - + -
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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
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211A LEU* 3.5 28.9 - - - +
212A PRO* 2.7 35.5 + - - +
213A PHE* 3.9 27.5 - - + +
214A LEU* 3.8 12.4 - - - +
279A ILE* 3.0 29.0 + - + +
280A ASP* 3.9 5.8 + - - +
282A ALA* 1.3 73.3 - - - +
284A GLY* 1.3 65.9 + - - +
286A ASN* 3.1 18.4 + - - -
287A CYS 4.0 3.8 - - - -
289A VAL* 4.3 0.9 - - + -
307A TYR* 2.9 35.4 + - - +
311A LYS* 4.3 13.1 - - - +
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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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280A ASP 2.8 17.5 + - - -
281A GLU* 4.1 2.0 - - - -
282A ALA 3.2 0.2 - - - -
283A ARG* 1.3 78.2 - - - +
285A LYS* 1.3 58.0 + - - +
286A ASN* 3.1 13.2 + - - -
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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