Contacts of the helix formed by residues 273 - 292 (chain C) in PDB entry 3IML
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 273 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ARG* 3.9 11.3 - - - +
41C VAL 3.3 26.5 + - - +
42C ALA* 4.5 10.5 - - - +
121C GLY* 6.4 0.4 - - - -
122C ASP* 6.4 2.0 - - + -
269C LYS* 4.1 26.7 - - + -
270C ASP* 2.4 45.4 + - - +
271C PRO 3.7 1.6 - - - +
272C SER* 1.3 83.3 + - - +
274C VAL* 1.3 60.0 + - - +
275C ASP* 3.2 5.4 - - + +
276C ARG* 3.1 18.8 + - - +
277C SER* 3.2 11.9 + - - -
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ALA* 4.6 6.5 - - + -
121C GLY 5.3 1.3 - - - +
122C ASP* 4.1 24.7 - - + +
123C GLN 5.0 3.6 - - - +
126C MET* 3.3 19.5 - - + +
272C SER 3.5 3.8 + - - +
273C LYS* 1.3 69.4 - - - +
275C ASP* 1.3 65.1 + - - +
276C ARG 3.2 0.2 - - - -
277C SER* 3.6 11.7 - - - +
278C ALA* 2.9 33.6 + - + +
304C TYR* 4.1 30.3 - - + -
341C PRO* 3.8 35.9 - - + -
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Residues in contact with ASP 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ASP* 5.1 6.1 - - - +
123C GLN 5.0 3.1 - - - +
124C GLY* 4.9 5.4 - - - -
125C LEU 4.8 2.9 - - - +
126C MET* 3.1 27.5 - - - +
264C GLY* 3.8 24.2 + - - +
265C ALA 4.0 5.4 - - - +
266C PHE* 3.2 22.2 - - - -
269C LYS* 3.2 32.7 + - + +
273C LYS* 4.5 2.9 - - + +
274C VAL* 1.3 78.9 - - - +
276C ARG* 1.3 56.5 + - - +
279C ALA* 3.3 10.7 - - - +
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Residues in contact with ARG 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ASP* 2.8 43.4 + - - -
29C LEU* 3.3 9.1 - - - +
265C ALA 4.9 0.4 + - - -
266C PHE* 3.1 35.2 + - + +
269C LYS* 3.0 34.7 + - + +
270C ASP 4.7 6.7 - - - +
271C PRO* 5.2 2.9 - - + -
273C LYS* 3.1 9.7 + - - +
275C ASP* 1.3 79.0 - - - +
277C SER* 1.3 60.9 + - - +
278C ALA 3.4 0.2 - - - -
279C ALA* 3.2 4.3 + - - +
280C TYR* 2.9 64.8 + - + -
350C LEU* 6.5 0.2 - - + -
355C TYR* 3.5 22.1 - - - -
358C THR* 3.1 20.0 + - - -
363C HIS* 3.7 6.1 - - - -
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Residues in contact with SER 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C PRO* 3.2 26.9 + - - -
273C LYS 3.2 6.7 + - - -
274C VAL* 3.6 11.6 - - - +
276C ARG* 1.3 81.0 - - - +
278C ALA* 1.3 59.6 + - - +
280C TYR* 3.7 3.8 - - - +
281C ALA 2.8 23.0 + - - -
341C PRO* 4.7 4.2 + - - +
344C ILE* 3.2 29.5 - - - +
345C ILE* 5.2 1.3 - - - -
350C LEU* 3.8 24.9 - - - -
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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
----------------------------------------------------------
126C MET* 3.4 19.6 - - + +
274C VAL* 2.9 24.8 + - + +
277C SER* 1.3 73.5 + - - +
279C ALA* 1.3 58.9 + - - +
281C ALA* 3.6 7.9 - - - +
282C GLY* 2.8 24.8 + - - -
302C VAL* 4.2 10.9 - - + +
304C TYR* 3.6 31.6 - - + +
344C ILE* 4.8 2.7 - - + -
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Residues in contact with ALA 279 (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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126C MET* 4.1 12.4 - - + +
127C PHE 4.4 15.7 - - - +
254C THR* 5.8 0.2 - - + -
261C HIS* 6.4 0.2 - - + -
266C PHE* 3.3 27.8 - - + -
274C VAL 3.8 2.6 + - - -
275C ASP 3.3 20.8 + - - +
276C ARG 3.2 2.1 + - - +
278C ALA* 1.3 75.5 - - - +
280C TYR* 1.3 61.3 + - - +
282C GLY* 3.3 1.6 + - - -
283C ARG* 3.0 22.9 + - - +
364C PHE* 3.7 11.1 - - + -
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Residues in contact with TYR 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C PHE* 4.0 14.1 - + - -
276C ARG* 2.9 53.9 + - + +
277C SER* 3.7 5.4 - - - +
279C ALA* 1.3 74.0 - - + +
281C ALA* 1.3 65.0 + - - +
283C ARG* 3.3 1.7 + - - +
284C TYR* 3.1 22.2 + - - +
348C LEU* 4.1 13.9 - - + -
350C LEU* 4.3 11.2 - - + -
355C TYR* 3.9 16.8 - + - -
358C THR* 3.7 4.5 + - - +
363C HIS* 2.7 37.7 + - + -
364C PHE* 3.8 17.3 - + - -
373C TRP* 3.6 52.3 - + + +
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Residues in contact with ALA 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C SER 2.8 22.1 + - - +
278C ALA* 3.6 7.9 - - - +
279C ALA 3.3 0.2 - - - -
280C TYR* 1.3 72.4 - - - +
282C GLY* 1.3 55.6 + - - +
284C TYR* 3.0 21.1 + - - +
285C VAL* 3.0 20.3 + - - +
339C LEU* 4.9 8.5 - - + -
344C ILE* 3.4 33.2 - - + -
347C MET* 4.8 7.0 - - + -
348C LEU* 4.1 9.7 - - - +
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Residues in contact with GLY 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C MET 6.1 0.4 - - - -
127C PHE 5.0 0.2 - - - -
128C GLY* 3.4 22.8 - - - -
278C ALA 2.8 18.0 + - - -
279C ALA 3.6 2.2 - - - -
280C TYR 3.3 0.4 - - - -
281C ALA* 1.3 75.4 - - - +
283C ARG* 1.3 58.3 + - - +
285C VAL* 3.1 24.3 - - - +
286C ALA* 3.2 14.2 + - - +
300C ILE* 5.1 5.4 - - - -
302C VAL* 6.1 3.6 - - - -
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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
----------------------------------------------------------
128C GLY* 4.0 1.2 - - - -
129C TYR 3.0 18.1 + - - -
130C ALA* 3.5 8.3 - - - +
136C GLU 3.0 27.7 + - - -
137C LEU 3.0 19.0 + - - -
138C MET* 3.5 26.5 - - - +
255C TYR* 3.4 24.5 - - - +
279C ALA 3.0 6.2 + - - +
280C TYR 3.7 4.9 - - - +
281C ALA 3.3 0.4 - - - -
282C GLY* 1.3 74.7 - - - +
284C TYR* 1.3 59.3 + - - +
286C ALA* 4.5 1.8 - - - -
287C LYS* 2.8 39.1 + - - +
364C PHE* 3.5 29.4 - - + +
373C TRP* 4.1 9.2 - - + +
374C GLU* 2.8 39.0 + - - +
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Residues in contact with TYR 284 (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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280C TYR 3.1 12.2 + - - +
281C ALA* 3.0 12.0 + - - +
283C ARG* 1.3 77.2 - - - +
285C VAL* 1.3 60.7 + - - +
287C LYS* 4.0 1.3 - - - +
288C ASN* 3.0 37.7 + - - -
337C PHE* 3.6 33.9 - + - -
347C MET* 4.1 24.6 + - + +
348C LEU* 3.8 20.4 - - + -
372C SER 3.5 17.3 - - - -
373C TRP* 3.4 25.8 - - + +
375C ALA 3.2 26.0 - - - -
377C ASP* 2.5 28.1 + - - -
378C LYS* 3.9 11.4 - - + +
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ALA* 3.0 14.5 + - + +
282C GLY* 3.1 17.0 - - - +
284C TYR* 1.3 76.1 - - + +
286C ALA* 1.3 69.2 + - - +
288C ASN* 3.3 2.4 + - - +
289C ILE* 2.9 38.1 + - + +
300C ILE* 3.0 31.9 - - + -
333C VAL* 4.5 8.1 - - + -
337C PHE* 3.2 53.8 - - + -
339C LEU* 4.7 7.2 - - + -
347C MET* 5.6 0.4 - - + -
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLY 4.0 2.5 - - - +
129C TYR 3.5 34.3 - - - +
130C ALA* 3.4 10.0 - - - +
282C GLY 3.2 15.2 + - - +
283C ARG 3.9 0.9 - - - +
285C VAL* 1.3 81.6 - - - +
287C LYS* 1.3 63.0 + - - +
289C ILE* 3.4 3.8 + - - +
290C VAL* 3.2 20.4 + - - +
298C ALA* 3.7 19.2 - - + +
300C ILE* 4.6 6.1 - - + -
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Residues in contact with LYS 287 (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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130C ALA* 3.6 9.8 - - - +
135C PRO 5.6 0.2 - - - -
136C GLU 3.6 17.7 + - - -
137C LEU* 3.8 21.6 - - + +
283C ARG* 2.8 35.8 + - - +
284C TYR* 4.0 4.9 - - + +
286C ALA* 1.3 71.4 - - - +
288C ASN* 1.3 58.6 + - - +
290C VAL* 3.7 0.5 - - - +
291C ALA* 2.8 33.0 + - + +
367C GLU* 2.9 30.0 + - - +
373C TRP 4.6 0.7 - - - +
374C GLU* 2.7 63.7 + - - +
375C ALA 5.2 2.9 - - - +
376C ALA* 5.3 7.4 - - + +
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Residues in contact with ASN 288 (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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284C TYR* 3.0 44.0 + - - +
285C VAL 3.3 3.6 + - - +
287C LYS* 1.3 74.3 - - - +
289C ILE* 1.3 57.3 + - - +
291C ALA* 2.9 5.0 + - - +
292C ALA* 2.6 40.7 + - + +
337C PHE* 4.4 11.6 - - + -
375C ALA 3.5 19.0 + - - -
376C ALA* 3.6 14.7 - - - +
378C LYS* 3.0 42.9 + - - +
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Residues in contact with ILE 289 (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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285C VAL* 2.9 29.7 + - + +
286C ALA* 3.7 6.7 - - - +
288C ASN* 1.3 71.1 - - + +
290C VAL* 1.3 58.8 + - - +
293C GLY 3.6 0.2 + - - -
294C LEU* 2.9 64.3 + - + +
295C ALA* 3.8 11.8 + - + +
298C ALA* 3.8 19.7 - - + -
300C ILE* 5.3 6.3 - - + -
316C VAL* 6.1 3.8 - - + -
329C ILE* 5.1 19.5 - - + +
332C LEU* 6.2 3.8 - - + -
333C VAL* 5.8 7.6 - - + -
337C PHE* 5.9 5.8 - - + -
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Residues in contact with VAL 290 (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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130C ALA* 4.0 14.6 - - + +
131C CYS 4.4 13.7 - - - +
132C ASP* 4.6 5.4 - - + +
137C LEU* 4.4 18.4 - - + -
286C ALA 3.2 9.4 + - - +
287C LYS 3.9 2.5 - - - +
288C ASN 3.1 0.4 - - - -
289C ILE* 1.3 72.3 - - - +
291C ALA* 1.3 66.1 + - - +
292C ALA 3.1 1.8 - - - -
293C GLY* 3.1 14.4 + - - -
295C ALA 3.5 22.5 - - - +
296C SER* 4.0 12.3 - - - +
298C ALA* 3.7 34.5 - - + +
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 3.8 18.6 - - + -
287C LYS* 2.8 23.7 + - + +
288C ASN* 2.9 8.7 + - - +
290C VAL* 1.3 74.3 - - - +
292C ALA* 1.3 57.0 + - - +
293C GLY 3.4 1.6 + - - -
376C ALA* 4.2 21.8 - - + -
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Residues in contact with ALA 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ASN 2.6 19.9 + - - +
290C VAL 3.1 0.2 - - - -
291C ALA* 1.3 73.6 - - - +
293C GLY* 1.3 58.8 + - - +
294C LEU* 3.3 24.5 + - + +
378C LYS 5.1 13.9 - - - +
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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