Contacts of the helix formed by residues 272 - 290 (chain A) in PDB entry 4KM5
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 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A PHE* 2.8 26.7 + - - +
267A GLU* 4.2 13.8 + - - -
270A ILE* 3.4 6.7 + - - -
271A LEU* 1.3 72.8 - - - +
273A ALA* 1.3 60.9 + - - +
274A SER* 3.3 3.6 + - - -
275A LYS* 3.3 35.5 + - - +
276A MET* 3.5 16.8 + - - +
373A GLU* 3.1 23.7 + - - -
375A TRP* 4.3 2.4 - - - -
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Residues in contact with ALA 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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271A LEU 3.5 3.2 + - - -
272A SER* 1.3 71.8 - - - +
274A SER* 1.3 57.2 + - - +
276A MET* 3.5 1.1 + - - +
277A LEU* 2.9 37.9 + - + +
361A PRO* 3.8 24.9 - - + -
362A LYS 5.5 0.7 - - - +
372A GLU 5.1 4.9 - - - +
373A GLU* 2.5 15.1 + - - +
374A THR 5.1 3.6 - - - +
375A TRP* 3.6 30.3 - - + +
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Residues in contact with SER 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A SER* 3.3 4.2 + - - -
273A ALA* 1.3 79.1 - - - +
275A LYS* 1.3 58.3 + - - +
277A LEU* 3.9 6.0 - - - +
278A SER* 2.9 32.3 + - - -
372A GLU* 4.3 13.7 + - - +
373A GLU* 2.5 25.1 + - - -
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Residues in contact with LYS 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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264A GLN 4.0 10.3 + - - +
265A PHE* 3.7 44.4 - - + +
266A LEU 2.9 25.1 + - - -
267A GLU* 3.5 27.4 + - - +
272A SER* 3.3 10.8 + - - +
274A SER* 1.3 78.4 - - - +
276A MET* 1.3 62.4 + - - +
278A SER* 2.8 22.5 + - - -
279A LYS* 3.3 5.7 + - - +
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Residues in contact with MET 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE* 3.6 6.9 - - + -
232A LEU* 4.6 7.9 - - + -
262A LEU* 4.8 9.0 - - + -
265A PHE* 3.6 39.2 - - + -
271A LEU* 3.7 35.9 - - + -
272A SER 3.5 11.2 + - - +
273A ALA* 3.5 5.3 + - - +
274A SER 3.3 0.2 - - - -
275A LYS* 1.3 79.6 - - - +
277A LEU* 1.3 59.2 + - + +
279A LYS* 3.7 0.7 + - - +
280A PHE* 3.1 27.8 + - - +
322A LEU* 3.6 27.6 - - + -
324A LEU* 3.9 17.5 - - + -
375A TRP* 3.8 18.2 - - + -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 2.9 23.1 + - + +
274A SER* 3.9 4.9 - - - +
276A MET* 1.3 76.3 - - + +
278A SER* 1.3 59.3 + - - +
280A PHE* 3.1 10.3 + - + +
281A ARG* 2.9 62.5 + - - +
304A GLY 4.9 3.4 - - - +
306A PRO* 3.7 43.3 - - + +
322A LEU* 4.4 25.8 - - + -
361A PRO* 4.0 17.9 - - + -
362A LYS 6.0 0.2 - - - +
375A TRP* 6.3 0.4 - - + -
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A SER 2.9 16.8 + - - -
275A LYS* 2.8 17.5 + - - -
277A LEU* 1.3 77.5 - - - +
279A LYS* 1.3 70.4 + - - +
281A ARG* 3.3 11.0 + - - +
282A LYS* 3.1 46.2 + - - +
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Residues in contact with LYS 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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200A ASP* 2.8 41.8 + - - -
201A SER* 4.0 5.5 + - - -
202A ALA* 3.8 3.4 - - - +
203A PHE* 4.1 1.8 - - + -
264A GLN* 3.0 30.6 + - - +
265A PHE* 3.5 27.1 - - + -
275A LYS 3.3 11.3 + - - +
278A SER* 1.3 79.0 + - - +
280A PHE* 1.3 65.0 + - - +
282A LYS* 3.2 14.1 + - + +
283A ILE* 3.0 40.3 + - + +
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.6 29.2 - - + -
203A PHE* 3.9 26.9 - + + -
206A VAL* 5.8 0.7 - - + -
230A PHE* 3.7 22.9 - + + -
276A MET 3.1 20.7 + - - +
277A LEU* 3.1 14.8 + - + +
279A LYS* 1.3 78.1 - - - +
281A ARG* 1.3 61.4 + - - +
283A ILE* 3.7 3.1 + - - +
284A ILE* 3.2 52.5 + - + +
308A VAL* 4.1 19.5 - - + -
320A ILE* 4.2 12.8 - - + -
322A LEU* 4.0 35.2 - - + -
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Residues in contact with ARG 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 LEU* 2.9 56.3 + - - +
278A SER* 3.7 8.6 - - - +
280A PHE* 1.3 76.1 - - + +
282A LYS* 1.3 62.1 + - + +
284A ILE* 3.4 5.5 + - - +
285A LYS* 2.8 34.3 + - - +
298A MET* 3.9 11.8 - - - +
301A LYS* 3.9 37.5 + - - +
304A GLY 3.7 9.7 + - - -
305A SER 3.7 23.4 + - - -
306A PRO* 3.8 6.9 + - - +
307A ALA 4.1 4.4 + - - -
308A VAL* 3.8 30.1 - - + +
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Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 3.1 37.3 + - - +
279A LYS* 3.2 12.2 + - + +
281A ARG* 1.3 78.1 - - + +
283A ILE* 1.3 58.5 + - + +
285A LYS* 3.4 7.3 + - - +
286A GLU* 3.0 29.6 + - - +
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG* 3.7 39.7 - - + +
197A LEU* 3.7 22.7 - - + -
200A ASP* 3.3 36.1 - - + +
203A PHE* 3.7 26.2 - - + -
279A LYS* 3.0 22.0 + - + +
280A PHE 4.1 1.1 - - - +
282A LYS* 1.3 76.8 - - + +
284A ILE* 1.3 63.8 + - - +
286A GLU* 3.4 8.8 + - - +
287A GLU* 3.3 21.9 + - + +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.9 37.7 - - + -
197A LEU* 4.8 11.2 - - + -
230A PHE* 5.3 0.2 - - + -
280A PHE* 3.2 53.9 + - + +
281A ARG* 3.7 4.0 - - - +
282A LYS 3.3 0.6 - - - -
283A ILE* 1.3 75.8 - - - +
285A LYS* 1.3 66.2 + - - +
287A GLU* 3.0 13.4 + - - +
288A ILE* 3.3 14.3 + - + +
298A MET* 3.7 17.5 - - + -
308A VAL* 4.4 13.2 - - + -
310A LEU* 4.1 13.5 - - + -
320A ILE* 4.7 7.0 - - + -
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Residues in contact with LYS 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 ARG* 2.8 23.7 + - - +
282A LYS* 3.8 6.5 - - - +
284A ILE* 1.3 74.0 - - - +
286A GLU* 1.3 59.1 + - - +
287A GLU 3.4 0.3 + - - -
288A ILE* 3.7 8.7 + - + +
289A ASN* 2.8 35.2 + - - +
298A MET* 3.6 37.0 - - + -
300A ARG* 5.5 11.9 - - - +
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Residues in contact with GLU 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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196A ARG* 2.6 33.6 + - - -
282A LYS 3.0 17.9 + - - +
283A ILE* 3.5 6.1 - - - +
284A ILE 3.2 0.2 - - - -
285A LYS* 1.3 76.9 - - - +
287A GLU* 1.3 78.2 + - - +
289A ASN* 3.8 11.9 + - - +
290A ASP* 3.3 21.8 - - - +
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Residues in contact with GLU 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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192A HIS* 3.7 23.0 - - + +
193A LEU* 4.0 19.5 - - + -
195A LEU* 5.8 0.9 - - - +
196A ARG* 3.0 50.9 + - + +
283A ILE* 3.3 14.6 - - + +
284A ILE* 3.0 8.5 + - - +
286A GLU* 1.3 89.8 - - - +
288A ILE* 1.3 60.3 + - - +
289A ASN 3.1 2.2 - - - -
290A ASP* 2.9 29.4 + - - +
291A ILE* 3.3 17.3 + - - +
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Residues in contact with ILE 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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189A VAL* 5.8 1.6 - - + -
193A LEU* 4.7 7.2 - - + -
284A ILE* 3.3 27.1 - - + +
285A LYS* 3.8 9.4 - - + +
287A GLU* 1.3 75.1 - - - +
289A ASN* 1.3 75.4 + - - +
291A ILE* 3.3 25.5 - - + +
296A VAL* 3.7 30.6 - - + +
297A ILE* 3.7 13.7 - - - -
298A MET* 3.5 39.9 - - + +
310A LEU* 4.6 14.4 - - + -
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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 LYS* 2.8 27.9 + - - +
286A GLU* 3.8 9.2 - - - +
287A GLU 3.1 0.2 - - - -
288A ILE* 1.3 83.6 - - - +
290A ASP* 1.3 62.4 + - - +
291A ILE 3.1 7.7 + - - +
292A LYS* 3.6 26.4 - - - +
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A HIS* 5.8 2.3 - - + -
286A GLU* 3.3 23.1 - - - +
287A GLU* 2.9 22.3 + - - +
289A ASN* 1.3 79.6 - - - +
291A ILE* 1.3 59.9 + - - +
292A LYS* 3.9 4.2 + - - -
293A ASP* 4.8 1.2 - - - +
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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
------------------------------------------------------------
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