Contacts of the helix formed by residues 272 - 288 (chain I) in PDB entry 5IIO
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 ASP 272 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I TYR* 2.9 30.0 + - + +
268I SER* 4.9 0.4 - - - -
270I GLN* 3.4 5.3 + - + +
271I GLY* 1.3 71.6 - - - +
273I LYS* 1.3 62.6 + - - +
274I TRP* 4.0 3.1 + - - +
275I ARG* 2.5 58.1 + - - +
276I ALA* 3.0 24.4 + - - +
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Residues in contact with LYS 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268I SER* 5.7 1.6 - - - +
271I GLY 2.8 14.2 + - - +
272I ASP* 1.3 72.3 + - - +
274I TRP* 1.3 107.6 + - + +
276I ALA* 3.4 5.5 + - - +
277I LEU* 3.0 25.5 + - - +
5J 8OG 6.1 0.6 + - - -
4K T 6.2 3.8 - - - -
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Residues in contact with TRP 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I ASP* 3.4 3.2 + - - +
273I LYS* 1.3 118.3 - - + +
275I ARG* 1.3 65.4 + - - +
277I LEU* 3.3 18.1 + - + +
278I GLY 3.0 18.4 + - - -
4J C 3.3 60.6 - + + +
5J 8OG 5.0 5.6 - - - -
1L G 3.2 36.4 + - + -
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Residues in contact with ARG 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I TYR* 3.6 37.0 - - + -
272I ASP* 2.5 65.3 + - - +
274I TRP* 1.3 77.0 - - - +
276I ALA* 1.3 63.5 + - - +
278I GLY* 3.2 3.5 + - - -
279I TYR* 3.1 29.9 + - + -
1L G 3.3 65.1 + - - +
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Residues in contact with ALA 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264I ALA* 3.6 27.2 - - + +
267I TYR* 4.1 4.6 - - + +
268I SER* 3.8 20.9 - - - +
272I ASP 3.0 17.7 + - - +
273I LYS* 3.7 4.7 - - - +
275I ARG* 1.3 78.0 - - - +
277I LEU* 1.3 62.3 + - - +
279I TYR* 3.3 7.4 + - - +
280I ALA* 2.9 23.4 + - - +
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Residues in contact with LEU 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273I LYS 3.0 14.5 + - - +
274I TRP* 3.4 27.8 - - + +
275I ARG 3.3 0.2 - - - -
276I ALA* 1.3 75.8 - - - +
278I GLY* 1.3 57.6 + - - +
280I ALA* 3.1 9.3 + - + +
281I LYS* 2.9 39.3 + - + +
511I HIS* 5.9 0.2 - - + -
514I ARG* 3.4 47.3 - - - +
4J C 3.5 38.4 - - + +
1L G 4.3 1.3 - - - +
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Residues in contact with GLY 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I TRP 3.0 10.9 + - - -
275I ARG 3.2 2.7 + - - -
277I LEU* 1.3 76.6 - - - +
279I TYR* 1.3 60.4 + - - +
281I LYS* 3.6 6.5 + - - +
282I ALA* 3.1 22.2 + - - +
304I GLY 4.6 2.8 - - - +
309I MET* 4.1 3.0 - - - +
1L G 3.2 38.5 - - - +
2L C 4.8 5.3 - - - +
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Residues in contact with TYR 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I LEU* 4.0 27.1 - - + -
263I LEU* 3.7 24.4 - - + +
264I ALA* 3.6 21.5 - - + -
267I TYR* 3.5 25.5 - + - -
275I ARG* 3.1 26.5 + - + -
276I ALA* 3.3 4.0 + - - +
278I GLY* 1.3 72.4 - - - +
280I ALA* 1.3 61.0 + - - +
282I ALA* 3.1 2.4 + - - +
283I ILE* 2.8 37.2 + - + +
309I MET* 3.9 27.8 - - + -
312I LYS* 3.1 16.1 - - + -
1L G 2.5 50.0 + - - -
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Residues in contact with ALA 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264I ALA* 4.7 3.1 - - + +
276I ALA 2.9 13.6 + - - +
277I LEU* 3.3 15.5 - - + +
279I TYR* 1.3 76.0 - - - +
281I LYS* 1.3 57.8 + - - +
283I ILE* 3.3 11.5 + - - +
284I ASN* 3.0 35.1 + - - +
511I HIS* 4.1 24.0 - - + +
514I ARG* 5.1 0.2 - - - +
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Residues in contact with LYS 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I LEU* 2.9 35.4 + - + +
278I GLY* 4.0 5.1 - - - +
280I ALA* 1.3 74.2 - - - +
282I ALA* 1.3 59.9 + - - +
284I ASN* 3.6 8.1 + - - +
285I ALA* 3.1 27.0 + - - +
304I GLY* 4.6 20.4 - - - -
514I ARG* 4.0 24.9 - - - +
4J C 5.8 0.7 - - - +
1L G 5.3 7.4 + - - +
2L C 5.0 10.3 + - - -
3L C 5.2 9.3 + - - -
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Residues in contact with ALA 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I LEU* 5.2 2.0 - - + -
278I GLY 3.1 13.6 + - - +
279I TYR 3.1 8.4 + - - +
281I LYS* 1.3 74.9 - - - +
283I ILE* 1.3 59.4 + - + +
285I ALA* 3.1 7.6 + - - +
286I LEU* 2.9 34.7 + - + +
304I GLY 3.6 22.8 + - - +
305I ILE* 4.3 4.3 - - + +
309I MET* 3.7 31.2 - - + -
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Residues in contact with ILE 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257I THR* 4.0 15.5 - - + +
260I LEU* 3.8 24.2 - - + -
261I GLU* 3.6 45.5 - - + +
264I ALA* 4.0 9.4 - - + -
279I TYR* 2.8 29.6 + - + +
280I ALA* 3.6 7.9 - - - +
282I ALA* 1.3 72.9 - - - +
284I ASN* 1.3 60.4 + - - +
286I LEU* 3.1 6.7 + - - +
287I LYS* 2.9 54.9 + - - +
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Residues in contact with ASN 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280I ALA 3.0 21.7 + - - +
281I LYS* 3.9 8.0 - - - +
283I ILE* 1.3 78.8 - - - +
285I ALA* 1.3 63.5 + - - +
287I LYS* 3.2 11.5 + - - +
288I SER* 3.1 24.1 + - - -
511I HIS* 3.6 29.9 + - - +
514I ARG* 5.0 1.0 - - - +
575I TRP* 3.5 62.3 + - + +
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Residues in contact with ALA 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I LYS 3.1 16.0 + - - +
282I ALA* 3.4 11.2 - - - +
284I ASN* 1.3 76.8 - - - +
286I LEU* 1.3 61.7 + - - +
288I SER* 3.6 8.8 + - - -
289I PHE* 3.4 20.8 + - - +
302I ILE* 3.9 17.6 - - + +
303I PRO 3.5 24.7 - - - +
305I ILE* 4.5 3.4 - - + -
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Residues in contact with LEU 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251I ASN* 3.8 3.0 - - - +
253I ASN* 3.2 30.3 + - + +
256I ILE* 3.6 32.5 - - + -
257I THR* 3.6 13.9 - - + -
260I LEU* 3.7 19.5 - - + -
282I ALA* 2.9 15.9 + - + +
283I ILE 3.1 8.7 + - - +
285I ALA* 1.3 78.5 - - - +
287I LYS* 1.3 60.8 + - - +
289I PHE* 3.4 8.6 + - + +
293I VAL* 3.8 28.9 - - + -
302I ILE* 4.3 2.7 - - + -
305I ILE* 3.7 22.2 - - + -
313I ILE* 3.9 13.9 - - + -
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Residues in contact with LYS 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250I THR 3.8 7.6 - - - +
251I ASN* 3.5 48.1 - - + +
254I LEU* 6.1 0.9 - - - -
257I THR* 4.1 10.8 - - + -
261I GLU* 3.0 27.8 + - - -
283I ILE* 2.9 30.9 + - + +
284I ASN* 3.2 11.6 + - - +
286I LEU* 1.3 78.1 - - - +
288I SER* 1.3 56.4 + - - +
289I PHE 3.2 4.1 + - - +
575I TRP* 3.7 34.0 - - + -
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Residues in contact with SER 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284I ASN 3.1 12.9 + - - -
285I ALA* 3.7 8.5 + - - -
286I LEU 3.3 0.4 - - - -
287I LYS* 1.3 75.8 - - - +
289I PHE* 1.3 61.8 + - - +
290I HIS 3.8 1.4 + - - -
575I TRP* 3.7 24.8 + - - -
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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