Contacts of the helix formed by residues 271 - 285 (chain A) in PDB entry 1K4S
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 LYS 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A HIS* 4.8 3.0 - - - -
267A GLU* 2.9 55.0 + - + +
268A TYR* 2.6 59.0 + - + +
269A THR 3.2 0.2 - - - -
270A THR* 1.3 70.7 - - - +
272A GLU* 1.3 66.0 + - - +
273A ILE* 3.5 4.9 - - + -
274A PHE* 3.0 11.5 - - + +
275A ARG* 2.9 24.2 + - - -
363A GLY 5.5 0.6 + - - -
365A GLY 5.5 4.8 + - - +
370A MET* 3.9 18.5 - - + +
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A THR 3.5 11.1 + - - +
271A LYS* 1.3 68.3 - - - +
273A ILE* 1.3 65.0 + - + +
275A ARG* 2.7 69.5 + - - +
276A LYS* 3.2 6.9 + - - +
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Residues in contact with ILE 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 LYS* 4.6 4.0 - - + -
272A GLU* 1.3 86.9 - - + +
274A PHE* 1.3 63.4 + - - +
276A LYS* 3.5 6.6 + - + +
277A ASN* 3.1 36.6 + - - +
366A ASN* 6.2 3.1 - - + -
367A HIS 5.0 1.1 - - - +
368A PRO* 4.8 20.2 - - + +
370A MET* 4.1 25.4 - - + -
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Residues in contact with PHE 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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260A PHE* 5.3 4.5 - + - -
263A MET* 3.9 22.0 - - + -
268A TYR* 3.4 57.9 - + + +
269A THR* 4.5 12.8 - - + -
271A LYS* 3.0 14.5 + - + +
272A GLU 3.1 0.4 - - - -
273A ILE* 1.3 80.1 - - - +
275A ARG* 1.3 65.7 + - + +
277A ASN* 3.2 8.0 - - - +
278A PHE* 3.1 23.9 + - + -
360A LEU* 4.7 15.7 - - + -
361A PHE 4.3 7.6 - - - -
362A ARG* 5.3 0.2 - - - -
370A MET* 3.2 27.4 - - + +
371A GLY* 3.4 32.7 - - - -
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Residues in contact with ARG 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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260A PHE* 4.7 15.4 - - + -
269A THR* 2.9 29.3 + - - +
270A THR* 4.1 1.3 - - - -
271A LYS 2.9 25.5 + - - +
272A GLU* 2.7 54.9 + - - +
274A PHE* 1.3 73.2 - - + +
276A LYS* 1.3 66.7 + - - +
278A PHE* 2.7 17.7 + - - +
279A PHE* 3.0 16.0 + - - +
297A LEU* 5.2 19.2 - - + +
298A SER* 6.3 0.6 - - - -
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Residues in contact with LYS 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 GLU 3.2 6.1 + - - +
273A ILE* 3.8 11.9 - - + +
274A PHE 3.4 0.2 - - - -
275A ARG* 1.3 77.6 - - - +
277A ASN* 1.3 68.3 + - - +
278A PHE 3.1 0.2 + - - -
279A PHE* 3.4 7.3 + - - +
280A LYS* 3.2 26.0 + - - +
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Residues in contact with ASN 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 ILE* 3.1 15.2 + - - +
274A PHE 3.2 2.9 + - - +
275A ARG 3.1 0.2 - - - -
276A LYS* 1.3 81.8 - - - +
278A PHE* 1.3 65.8 + - - +
280A LYS* 4.4 1.9 - - - +
281A ASP* 3.3 25.6 + - - +
368A PRO 3.3 14.2 + - - +
369A LYS* 3.0 23.7 - - - +
370A MET 2.5 29.6 - - - +
371A GLY 3.2 15.4 - - - +
372A MET* 3.3 12.8 - - - +
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Residues in contact with PHE 278 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A VAL* 4.5 14.1 - - + -
260A PHE* 3.3 56.5 - + + -
274A PHE* 3.1 15.5 + - + +
275A ARG* 2.7 15.0 + - - +
277A ASN* 1.3 75.8 - - - +
279A PHE* 1.3 83.7 + - - +
281A ASP* 2.9 9.9 + - - +
282A TRP* 2.9 65.1 + + + +
297A LEU* 3.6 18.6 - - + -
302A PHE* 4.1 5.4 - + - -
360A LEU* 4.3 17.0 - - + -
371A GLY 3.2 10.9 + - - +
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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 ARG 3.0 8.4 + - - +
276A LYS* 3.6 11.9 - - - +
278A PHE* 1.3 87.5 - - + +
280A LYS* 1.3 63.1 + - - +
282A TRP* 3.0 24.0 + + - +
283A ARG* 3.0 53.2 + - - +
294A ILE* 3.8 10.1 - - + -
295A THR 3.7 4.9 - - - -
296A ASN* 3.6 15.5 - - - -
297A LEU* 3.4 59.2 - - + -
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Residues in contact with LYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A LYS 3.2 12.8 + - - +
277A ASN* 4.4 2.7 - - - +
278A PHE 3.0 1.2 + - - -
279A PHE* 1.3 79.5 - - - +
281A ASP* 1.3 73.6 + - - +
283A ARG* 3.2 26.6 - - + +
284A LYS* 3.0 39.7 + - - +
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Residues in contact with ASP 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 ASN* 3.3 20.1 + - - +
278A PHE* 2.9 6.6 + - - +
280A LYS* 1.3 85.9 + - - +
282A TRP* 1.3 63.1 + - - +
284A LYS* 3.2 13.7 + - - +
285A GLU* 2.7 30.1 - - - +
360A LEU* 6.1 0.2 - - + -
371A GLY 5.2 0.2 - - - +
372A MET* 3.3 24.1 - - - +
373A LEU* 2.8 43.5 + - + +
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Residues in contact with TRP 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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240A PHE* 4.6 12.3 - + - -
249A LEU* 4.5 10.1 - - + -
253A ALA* 3.1 25.0 + - - +
256A VAL* 3.1 26.9 - - + +
257A ALA* 3.2 28.1 - - + +
278A PHE* 2.9 39.5 + + + +
279A PHE* 3.0 20.4 - + - +
281A ASP* 1.3 74.1 - - - +
283A ARG* 1.3 59.8 + - - +
285A GLU* 2.5 37.3 + - - +
286A MET* 3.7 22.8 - - + +
294A ILE* 4.9 12.6 - - + -
297A LEU* 4.8 4.5 - - + -
300A CYS* 4.5 12.3 - - - -
302A PHE* 3.3 28.9 - + - -
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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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279A PHE* 3.1 65.5 - - - +
280A LYS* 3.2 18.0 - - + +
282A TRP* 1.3 78.2 - - - +
284A LYS* 1.3 67.2 + - + +
285A GLU 2.9 0.5 + - - -
286A MET* 2.9 35.4 + - - +
291A LYS* 3.4 29.6 + - + +
294A ILE 3.9 14.3 + - - -
295A THR* 4.1 13.9 + - - +
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Residues in contact with LYS 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 LYS* 3.0 46.5 - - - +
281A ASP* 3.2 9.6 + - - +
282A TRP 3.1 0.2 + - - -
283A ARG* 1.3 79.6 - - + +
285A GLU* 1.3 76.3 + - - +
286A MET 3.1 8.7 + - - +
291A LYS* 5.1 4.1 + - - +
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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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252A LYS* 3.5 12.9 - - + +
253A ALA* 3.0 23.3 + - - -
256A VAL* 3.6 22.7 - - + -
281A ASP* 2.7 27.7 - - - +
282A TRP* 2.5 20.8 + - + +
284A LYS* 1.3 87.6 - - - +
286A MET* 1.3 58.9 + - - +
373A LEU* 3.7 31.5 - - + +
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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