Contacts of the helix formed by residues 272 - 285 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C SER* 5.4 1.4 + - - -
132C TYR* 3.2 33.4 + - + -
251C LEU* 3.6 22.9 - - - +
252C GLY* 4.6 3.0 - - - -
253C ASP* 4.4 12.0 + - - +
270C LYS* 5.6 0.4 - - - +
271C PRO* 1.3 76.6 - - - +
273C TRP* 1.3 73.3 + - + +
274C TYR* 3.8 38.1 + - + +
275C PHE 2.9 13.7 + - - -
276C LEU 3.4 3.8 + - - -
2001C JZZ 2.9 27.0 + - - +
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Residues in contact with TRP 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C SER* 2.9 40.0 + - - -
92C PHE* 4.1 2.2 - - + -
93C ILE* 3.5 44.9 - - + -
96C PHE* 3.6 28.3 - + - -
251C LEU* 4.1 36.7 + - + +
270C LYS* 5.5 1.6 - - - +
271C PRO 3.8 1.2 + - - -
272C GLU* 1.3 72.7 + - + +
274C TYR* 1.3 79.3 + + - +
275C PHE 2.8 12.5 + - - -
276C LEU* 2.8 38.8 + - + +
277C PHE* 4.4 1.4 + - - -
337C THR* 4.5 9.7 - - + +
2007C PEE 4.4 16.5 - - + +
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Residues in contact with TYR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ALA* 4.2 4.9 - - + +
89C SER* 3.9 19.1 - - - -
92C PHE* 3.6 50.6 - + + -
96C PHE* 3.9 10.7 - - + -
125C MET* 5.6 0.3 - - - +
128C ALA* 3.9 3.7 - - + +
132C TYR* 5.4 0.2 - - - -
272C GLU* 2.9 26.8 + - + +
273C TRP* 1.3 111.6 - + + +
275C PHE* 1.3 96.2 + + - +
277C PHE* 3.8 18.0 - - - -
501C HEM 3.9 19.1 - - - +
2001C JZZ 3.7 22.6 - - - -
2007C PEE 6.1 0.9 - - - -
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Residues in contact with PHE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 4.0 13.2 - + - -
125C MET* 3.8 36.3 - - + -
128C ALA* 4.7 0.9 - - + -
129C PHE* 4.3 7.2 - + + -
271C PRO* 3.7 17.7 - - + -
272C GLU 2.9 6.1 + - - +
273C TRP 2.8 1.8 + - - -
274C TYR* 1.3 105.1 - + - +
276C LEU* 1.3 69.5 + - - +
277C PHE* 3.4 5.2 - + - -
278C ALA* 3.0 16.2 + - - +
279C TYR* 3.0 10.6 + - - +
2001C JZZ 3.6 90.5 - + + +
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Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LYS* 4.6 7.9 - - + +
271C PRO* 3.5 33.6 - - + +
272C GLU 3.4 1.6 + - - +
273C TRP* 2.8 35.4 + - + +
275C PHE* 1.3 75.6 - - - +
277C PHE* 1.3 55.6 + - - +
279C TYR* 2.7 26.2 + - - +
280C ALA* 2.9 11.1 + - - +
336C LEU 4.4 0.2 - - - -
337C THR* 3.4 33.7 - - + +
340C GLY* 3.6 27.6 - - - +
341C SER* 3.9 16.2 - - - +
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Residues in contact with PHE 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PHE* 4.7 6.1 - + - -
125C MET* 5.1 7.4 - - + -
273C TRP 4.4 0.6 + - - -
274C TYR 3.8 23.8 - - - -
275C PHE* 4.4 1.1 - - - -
276C LEU* 1.3 77.8 - - - +
278C ALA* 1.3 85.2 + - + +
280C ALA* 3.3 4.0 + - - +
281C ILE* 3.2 32.7 + - + +
298C SER* 4.5 16.4 - - - -
299C VAL* 4.4 14.4 - - + -
333C LEU* 4.4 17.3 - - + +
336C LEU* 3.9 25.2 - - + +
337C THR* 3.8 18.6 + - - +
359C TYR* 5.5 2.5 - + - -
2007C PEE 3.8 48.2 - - + -
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C MET* 5.4 1.8 - - + -
275C PHE 3.0 10.0 + - - +
277C PHE* 1.3 101.7 - - + +
279C TYR* 1.3 62.2 + - - +
280C ALA 3.1 1.8 - - - -
281C ILE* 3.3 6.0 + - - +
282C LEU* 2.9 28.1 + - - +
295C LEU* 3.5 30.7 - - + +
298C SER* 4.7 2.0 - - - +
299C VAL* 5.5 0.7 - - + -
2001C JZZ 4.3 15.5 - - + -
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Residues in contact with TYR 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C VAL* 4.6 13.3 - - + +
269C ILE* 3.0 34.9 + - - +
270C LYS* 4.3 2.0 - - + -
271C PRO* 3.4 26.5 - - + -
275C PHE 3.0 10.7 + - - +
276C LEU* 2.7 13.3 + - - +
278C ALA* 1.3 73.1 - - - +
280C ALA* 1.3 62.7 + - - +
282C LEU* 3.3 26.4 - - + +
283C ARG* 3.2 66.6 + - - +
295C LEU* 6.3 0.4 - - - -
340C GLY 3.8 13.0 - - - +
2001C JZZ 3.7 28.0 - + + +
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU 2.9 4.8 + - - +
277C PHE 3.3 8.1 - - - +
278C ALA 3.1 0.2 - - - -
279C TYR* 1.3 75.0 - - - +
281C ILE* 1.3 66.8 + - - +
282C LEU 3.1 0.3 + - - -
283C ARG* 3.1 9.0 + - - +
284C SER* 3.0 19.9 + - - -
336C LEU* 3.3 41.1 - - + +
339C ILE* 4.1 13.1 - - + +
340C GLY* 3.7 14.5 - - - +
352C GLY* 5.9 1.9 - - - -
356C SER* 4.6 1.6 - - - -
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Residues in contact with ILE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C PHE* 3.2 19.8 + - + +
278C ALA* 3.3 7.4 + - - +
280C ALA* 1.3 78.9 - - - +
282C LEU* 1.3 63.2 + - - +
284C SER* 2.4 23.1 + - - +
285C ILE 3.9 0.5 + - - -
294C ALA* 3.6 39.7 - - + +
295C LEU* 4.2 1.6 - - - +
298C SER* 3.6 24.2 - - - -
336C LEU* 3.9 23.8 - - + -
356C SER* 3.4 23.8 - - - +
359C TYR* 4.1 18.6 - - + -
360C PHE* 4.4 9.0 - - + -
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Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C VAL* 5.8 1.3 - - + -
147C ILE* 4.7 6.5 - - + -
150C LEU* 3.8 35.9 - - + -
278C ALA 2.9 13.8 + - - +
279C TYR* 3.3 35.4 - - + +
280C ALA 3.0 0.2 - - - -
281C ILE* 1.3 79.8 - - - +
283C ARG* 1.3 65.8 + - + +
284C SER 3.3 0.3 + - - -
285C ILE 3.6 5.9 + - - +
288C LYS 5.4 1.1 - - - +
291C GLY* 3.4 52.1 - - - +
292C VAL* 3.9 5.6 - - + +
295C LEU* 4.2 15.5 - - + +
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Residues in contact with ARG 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C ILE 5.0 1.8 + - - -
279C TYR* 3.3 57.3 + - + +
280C ALA* 3.1 7.4 + - - +
282C LEU* 1.3 77.5 - - + +
284C SER* 1.3 63.6 + - - +
285C ILE 3.2 6.5 + - - -
286C PRO* 4.3 5.2 - - - +
339C ILE* 3.7 11.7 + - - +
340C GLY* 3.7 15.8 + - - -
342C GLN 2.6 29.3 + - - -
343C PRO* 4.3 3.6 + - - +
344C VAL* 3.3 43.5 - - + +
349C ILE* 6.0 1.9 - - - +
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Residues in contact with SER 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ALA 3.0 8.8 + - - -
281C ILE* 2.4 25.4 + - - +
283C ARG* 1.3 80.6 - - - +
285C ILE* 1.3 72.8 + - - +
286C PRO* 3.2 11.3 - - - +
294C ALA* 4.9 0.2 - - - +
352C GLY* 4.4 3.4 - - - -
353C GLN* 3.4 35.2 + - - +
356C SER* 3.3 32.6 + - - -
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Residues in contact with ILE 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C LEU 3.6 5.1 + - - +
283C ARG* 3.2 2.9 - - - -
284C SER* 1.3 94.0 + - - +
286C PRO* 1.3 73.5 - - + +
287C ASN* 3.0 12.7 + - + +
290C GLY* 3.8 11.0 - - - +
291C GLY* 3.7 26.2 + - - +
294C ALA* 3.8 23.1 - - + -
353C GLN* 6.3 0.2 - - + -
356C SER* 6.3 0.9 - - - -
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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