Contacts of the helix formed by residues 272 - 285 (chain P) in PDB entry 3L73
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 GLU 272 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89P SER* 5.4 1.6 + - - -
132P TYR* 3.4 32.4 + - + -
251P LEU* 3.8 22.3 - - - +
252P GLY* 4.6 2.9 - - - -
253P ASP* 4.4 11.4 + - - +
270P LYS* 5.5 0.2 - - - +
271P PRO* 1.3 78.4 - - - +
273P TRP* 1.3 73.5 + - - +
274P TYR* 3.7 31.7 + - + +
275P PHE* 2.9 12.8 + - - -
276P LEU 3.4 4.2 + - - -
3001P JZZ 2.8 35.5 + - + +
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Residues in contact with TRP 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P SER* 2.7 39.5 + - - -
92P PHE* 4.1 1.3 - - + -
93P ILE* 3.5 46.4 - - + -
96P PHE* 3.6 26.9 - + - -
251P LEU* 3.9 36.2 + - + +
270P LYS* 5.5 1.6 - - - +
271P PRO 3.7 1.2 + - - -
272P GLU* 1.3 74.1 + - - +
274P TYR* 1.3 80.3 + + - +
275P PHE 2.7 13.3 + - - -
276P LEU* 2.8 38.2 + - + +
277P PHE* 4.4 1.2 + - - -
337P THR* 4.6 8.8 - - + +
3007P PEE 4.6 15.4 - - + +
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Residues in contact with TYR 274 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P ALA* 4.3 5.4 - - + +
89P SER* 3.9 19.3 - - - -
92P PHE* 3.7 53.3 - + + -
96P PHE* 3.9 9.2 - - + -
125P MET* 5.5 0.3 - - - +
128P ALA* 4.1 3.6 - - + +
132P TYR* 5.5 0.2 - - - -
272P GLU* 3.7 24.2 + - + +
273P TRP* 1.3 105.9 - + + +
275P PHE* 1.3 95.6 + + - +
277P PHE* 3.8 18.6 - - - -
501P HEM 4.0 17.3 - - - +
3001P JZZ 3.6 30.9 - - - -
3007P PEE 6.1 0.7 - - - -
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Residues in contact with PHE 275 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P PHE* 4.0 13.0 - + - -
125P MET* 3.8 36.1 - - + -
129P PHE* 4.3 9.2 - + + -
271P PRO* 3.7 17.9 - - + -
272P GLU 2.9 3.2 + - - +
273P TRP 2.7 1.6 + - - -
274P TYR* 1.3 108.5 - + - +
276P LEU* 1.3 66.9 + - - +
277P PHE* 3.3 4.5 - - - -
278P ALA* 2.9 16.9 + - - +
279P TYR* 2.9 11.4 + - - +
3001P JZZ 3.4 91.4 - + + +
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Residues in contact with LEU 276 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270P LYS* 4.6 7.6 - - + +
271P PRO* 3.6 31.4 - - + +
272P GLU 3.4 2.0 + - - +
273P TRP* 2.8 35.9 + - + +
275P PHE* 1.3 75.6 - - - +
277P PHE* 1.3 56.6 + - - +
279P TYR* 2.7 24.1 + - - +
280P ALA* 2.9 12.1 + - - +
336P LEU 4.4 0.2 - - - -
337P THR* 3.4 34.8 - - + +
340P GLY* 3.6 27.9 - - - +
341P SER* 3.8 16.8 - - - +
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Residues in contact with PHE 277 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96P PHE* 4.6 7.4 - + - -
125P MET* 5.1 7.6 - - + -
273P TRP 4.4 0.8 + - - -
274P TYR 3.8 23.1 - - - -
275P PHE* 4.4 0.7 - - - -
276P LEU* 1.3 78.6 - - - +
278P ALA* 1.3 84.9 + - + +
280P ALA* 3.3 4.5 - - - +
281P ILE* 3.2 33.3 + - + +
298P SER* 4.4 17.3 - - - -
299P VAL* 4.4 13.7 - - + -
333P LEU* 4.4 15.7 - - + +
336P LEU* 3.9 21.7 - - + +
337P THR* 3.8 20.8 + - - +
359P TYR* 5.6 2.2 - + - -
3007P PEE 3.8 49.4 - - + -
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Residues in contact with ALA 278 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P MET* 5.3 1.3 - - + -
275P PHE 2.9 9.0 + - - +
277P PHE* 1.3 102.5 - - + +
279P TYR* 1.3 60.9 + - - +
280P ALA 3.1 0.4 - - - -
281P ILE* 3.5 5.0 + - - +
282P LEU* 3.0 26.9 + - - +
295P LEU* 3.6 30.1 - - + +
298P SER* 4.7 1.6 - - - +
299P VAL* 5.5 0.7 - - + -
3001P JZZ 4.1 17.5 - - + -
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Residues in contact with TYR 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146P VAL* 4.6 13.2 - - + +
147P ILE* 4.8 0.2 - - + -
269P ILE* 3.2 34.1 + - - +
270P LYS* 4.1 2.0 - - + -
271P PRO* 3.2 30.1 - - + -
275P PHE 2.9 10.0 + - - +
276P LEU* 2.7 9.7 + - - +
278P ALA* 1.3 77.8 - - - +
280P ALA* 1.3 62.1 + - - +
282P LEU* 3.2 39.6 - - + +
283P ARG* 3.2 52.1 + - - +
295P LEU* 6.2 0.2 - - - -
340P GLY* 3.8 13.7 - - - -
3001P JZZ 3.9 26.4 - + + +
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Residues in contact with ALA 280 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276P LEU 2.9 6.8 + - - +
277P PHE 3.3 8.5 - - - +
279P TYR* 1.3 74.1 - - - +
281P ILE* 1.3 66.9 + - - +
282P LEU 3.1 0.5 + - - -
283P ARG* 3.2 8.0 + - - +
284P SER* 3.0 21.8 + - - -
336P LEU* 3.2 39.7 - - + +
339P ILE* 4.2 13.1 - - + +
340P GLY* 3.7 13.4 - - - +
352P GLY* 5.9 1.5 - - - -
356P SER* 4.6 1.3 - - - -
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Residues in contact with ILE 281 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277P PHE* 3.2 20.3 + - + +
278P ALA* 3.9 7.9 - - - +
279P TYR 3.4 0.2 - - - -
280P ALA* 1.3 79.6 - - - +
282P LEU* 1.3 62.0 + - - +
284P SER* 2.6 21.9 + - - +
285P ILE 4.0 0.7 + - - -
294P ALA* 3.6 39.4 - - + +
295P LEU* 4.2 1.1 - - - +
298P SER* 3.6 23.8 - - - -
336P LEU* 3.9 23.6 - - + -
356P SER* 3.5 22.7 - - - +
359P TYR* 4.3 18.2 - - + -
360P PHE* 4.4 9.9 - - + -
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Residues in contact with LEU 282 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146P VAL* 5.8 1.1 - - + -
147P ILE* 4.7 6.5 - - + -
150P LEU* 3.9 36.6 - - + -
278P ALA 3.0 13.7 + - - +
279P TYR* 3.2 37.5 - - + +
280P ALA 3.0 0.2 - - - -
281P ILE* 1.3 80.4 - - - +
283P ARG* 1.3 67.6 + - + +
284P SER 3.3 0.3 + - - -
285P ILE 3.5 4.9 + - - +
288P LYS 5.4 0.4 - - - +
291P GLY* 3.1 54.9 - - - +
292P VAL* 3.9 3.8 - - + +
295P LEU* 4.1 16.8 - - + -
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Residues in contact with ARG 283 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269P ILE 4.7 2.0 + - - -
270P LYS* 6.0 0.4 - - - +
279P TYR* 3.2 57.5 + - + +
280P ALA* 4.1 4.8 - - - +
282P LEU* 1.3 77.5 - - + +
284P SER* 1.3 65.6 + - - +
285P ILE 3.0 11.0 + - - -
286P PRO* 3.9 6.1 - - - +
339P ILE* 4.2 3.2 + - - +
340P GLY* 3.4 23.6 + - - -
342P GLN 3.1 25.7 + - - -
343P PRO* 4.8 1.6 - - - +
344P VAL* 3.5 38.3 - - + +
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Residues in contact with SER 284 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280P ALA 3.0 9.9 + - - -
281P ILE* 2.6 21.6 + - - +
283P ARG* 1.3 76.9 - - - +
285P ILE* 1.3 71.5 + - - +
286P PRO* 3.2 10.7 - - - +
294P ALA* 5.0 0.2 - - - +
349P ILE 5.9 0.2 - - - -
352P GLY* 4.3 3.8 - - - -
353P GLN* 3.4 35.9 + - - +
356P SER* 3.2 34.2 + - - -
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Residues in contact with ILE 285 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282P LEU 3.5 5.6 + - - +
283P ARG* 3.1 3.3 - - - +
284P SER* 1.3 92.3 + - - +
286P PRO* 1.3 74.0 - - + +
287P ASN* 3.0 13.0 + - + +
290P GLY* 3.9 11.7 - - - +
291P GLY* 3.7 26.3 + - - +
294P ALA* 3.9 23.1 - - + -
356P SER* 6.2 0.4 - - - -
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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