Contacts of the helix formed by residues 273 - 292 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 4.5 14.7 - - - +
41D VAL 3.4 15.1 - - - +
42D ALA* 4.0 16.9 - - + +
57D GLU* 5.7 2.4 + - - +
269D LYS* 3.8 27.6 - - + -
270D ASP* 3.0 43.1 + - - +
271D PRO 3.7 1.4 - - - +
272D SER* 1.3 77.0 - - - +
274D VAL* 1.3 65.1 + - - +
275D ASP* 3.3 3.1 - - + +
276D ARG* 3.0 14.9 + - - +
277D SER* 3.3 10.2 + - - -
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Residues in contact with VAL 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D GLN 5.9 0.9 - - - +
124D GLY* 5.2 3.4 - - - +
126D MET* 3.3 16.6 - - + +
272D SER 3.4 6.9 + - - +
273D LYS* 1.3 66.0 - - - +
275D ASP* 1.3 67.6 + - - +
276D ARG 3.0 3.5 + - - -
277D SER* 3.5 11.2 - - - +
278D ALA* 3.0 24.9 + - + +
304D TYR* 3.2 59.0 - - + +
341D PRO* 4.9 12.1 - - + +
344D ILE* 6.4 0.2 - - + -
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Residues in contact with ASP 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D GLN 5.0 3.1 - - - +
124D GLY* 4.7 6.8 - - - -
125D LEU 4.6 0.9 - - - +
126D MET* 2.9 28.5 - - - +
264D GLY* 3.4 28.2 + - - +
265D ALA 4.1 2.9 - - - +
266D PHE* 3.3 21.1 - - - -
269D LYS* 3.2 33.7 + - + +
273D LYS* 3.3 2.2 + - + +
274D VAL* 1.3 78.5 - - - +
276D ARG* 1.3 56.6 + - - +
279D ALA* 3.6 8.5 - - - +
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Residues in contact with ARG 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASP* 2.9 42.6 + - - -
29D LEU* 3.5 6.1 - - - +
266D PHE* 3.1 38.8 + - + +
269D LYS* 3.1 31.6 + - + +
270D ASP 4.8 5.4 - - - +
271D PRO* 5.3 2.9 - - + -
273D LYS* 3.0 9.3 + - - +
274D VAL 3.0 0.6 - - - -
275D ASP* 1.3 78.4 - - - +
277D SER* 1.3 67.0 + - - +
278D ALA 3.3 1.6 - - - -
279D ALA* 3.3 2.4 + - - +
280D TYR* 3.0 60.3 + - + -
350D LEU* 6.4 0.2 - - + -
355D TYR* 3.5 20.8 - - - -
358D THR* 3.0 21.6 + - - -
363D HIS* 3.6 7.3 - - - -
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Residues in contact with SER 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D PRO* 3.1 26.2 + - - +
272D SER 4.8 0.3 - - - -
273D LYS 3.3 7.8 + - - -
274D VAL* 3.5 13.2 - - - +
276D ARG* 1.3 80.1 - - - +
278D ALA* 1.3 59.2 + - - +
280D TYR* 3.4 4.6 + - - +
281D ALA 3.0 21.7 + - - -
341D PRO 4.8 5.5 + - - -
344D ILE* 3.4 22.6 - - - +
345D ILE* 4.9 3.6 - - - -
350D LEU* 3.9 24.9 - - - -
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Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D MET* 3.5 22.6 - - + +
127D PHE 5.3 0.9 - - - +
274D VAL* 3.0 19.9 + - + +
277D SER* 1.3 76.5 + - - +
279D ALA* 1.3 59.7 + - - +
281D ALA* 3.3 2.9 + - - +
282D GLY* 2.9 24.6 + - - -
302D VAL* 5.6 3.9 - - + +
304D TYR* 3.7 28.9 - - + +
344D ILE* 4.0 11.0 - - + -
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Residues in contact with ALA 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D MET* 4.3 11.0 - - + +
127D PHE 4.3 17.3 - - - +
254D THR* 5.7 0.4 - - + -
255D TYR* 4.8 0.2 + - - -
266D PHE* 3.5 37.9 - - + -
274D VAL 4.1 2.0 + - - -
275D ASP 3.6 7.6 + - - +
276D ARG 3.3 2.9 + - - +
278D ALA* 1.3 74.1 - - - +
280D TYR* 1.3 66.0 + - - +
282D GLY* 3.4 1.9 + - - -
283D ARG* 3.1 21.3 + - - +
364D PHE* 3.8 9.0 - - + -
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Residues in contact with TYR 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D PHE* 4.4 8.1 - + - -
276D ARG* 3.0 53.6 + - + -
277D SER* 3.6 9.4 - - - +
279D ALA* 1.3 77.2 - - + +
281D ALA* 1.3 63.1 + - - +
283D ARG* 3.1 5.2 + - - +
284D TYR* 2.9 18.7 + - - +
348D LEU* 4.1 13.2 - - + -
350D LEU* 4.1 12.1 - - + -
355D TYR* 3.8 13.9 - + - -
358D THR* 3.7 6.4 + - - +
363D HIS* 3.0 36.3 + - + -
364D PHE* 3.9 16.6 - + - -
373D TRP* 3.2 56.4 - + + +
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Residues in contact with ALA 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D SER 3.0 14.5 + - - +
278D ALA 3.4 9.0 - - - +
279D ALA 3.2 0.2 - - - -
280D TYR* 1.3 75.6 - - - +
282D GLY* 1.3 57.7 + - - +
284D TYR* 3.1 6.7 + - - +
285D VAL* 2.9 35.2 + - + +
339D LEU* 5.5 6.1 - - + -
344D ILE* 3.6 31.9 - - + -
347D MET* 4.8 7.6 - - + -
348D LEU* 4.1 9.6 - - - +
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Residues in contact with GLY 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D PHE 4.8 1.1 - - - -
128D GLY* 3.6 21.0 - - - -
278D ALA 2.9 14.7 + - - -
279D ALA 3.4 3.6 + - - -
280D TYR 3.3 0.2 - - - -
281D ALA* 1.3 74.7 - - - +
283D ARG* 1.3 56.5 + - - +
285D VAL 3.7 0.2 + - - -
286D ALA* 3.1 30.1 + - - +
300D ILE* 3.8 21.8 - - - +
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Residues in contact with ARG 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLY* 4.2 0.6 - - - -
129D TYR 3.3 7.7 + - - -
130D ALA* 3.3 21.4 - - - +
136D GLU 2.9 27.7 + - - -
137D LEU 3.0 19.2 + - - -
138D MET* 3.5 22.3 - - - +
255D TYR* 3.7 23.8 - - - +
279D ALA 3.1 5.4 + - - +
280D TYR 3.1 9.7 + - - +
282D GLY* 1.3 74.8 - - - +
284D TYR* 1.3 60.2 + - - +
286D ALA* 3.2 1.7 + - - -
287D LYS* 2.8 43.4 + - - +
364D PHE* 3.5 29.5 - - + +
373D TRP* 4.1 9.0 - - + +
374D GLU* 2.9 37.8 + - - +
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Residues in contact with TYR 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D TYR 2.9 11.0 + - - +
281D ALA* 3.3 9.6 - - - +
283D ARG* 1.3 76.7 - - - +
285D VAL* 1.3 64.2 + - + +
287D LYS* 4.0 1.0 - - - -
288D ASN* 3.1 43.4 + - - +
337D PHE* 3.5 31.4 - + - -
347D MET* 3.8 29.5 + - + +
348D LEU* 3.7 17.3 - - + -
372D SER 3.6 22.7 - - - -
373D TRP* 3.4 19.5 + - + +
375D ALA 3.4 20.9 - - - -
377D ASP* 3.2 22.2 + - + +
378D LYS* 3.2 22.1 - - - -
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Residues in contact with VAL 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ALA* 2.9 23.4 + - + +
284D TYR* 1.3 71.8 - - + +
286D ALA* 1.3 65.3 + - - +
288D ASN* 3.2 2.6 + - - +
289D ILE* 3.0 41.1 + - + +
300D ILE* 3.5 31.0 - - + -
337D PHE* 3.9 41.3 - - + -
339D LEU* 4.4 20.0 - - + -
347D MET* 6.0 1.3 - - + -
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Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D GLY 4.3 1.6 - - - -
129D TYR 3.6 32.8 - - - +
130D ALA* 3.6 5.8 - - + +
282D GLY 3.1 16.9 + - - +
283D ARG 3.8 2.0 - - - +
285D VAL* 1.3 81.6 - - - +
287D LYS* 1.3 62.8 + - - +
289D ILE* 3.3 11.4 + - - +
290D VAL* 3.2 25.1 + - - +
298D ALA* 3.8 11.2 - - - +
300D ILE* 4.7 5.6 - - + +
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Residues in contact with LYS 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ALA* 3.6 9.3 - - - +
135D PRO 5.4 0.4 - - - -
136D GLU 3.8 11.5 + - - -
137D LEU* 3.4 24.6 - - + +
283D ARG* 2.8 35.5 + - - +
284D TYR 4.2 2.7 - - - +
286D ALA* 1.3 73.7 - - - +
288D ASN* 1.3 59.7 + - - +
290D VAL 4.8 0.2 - - - +
291D ALA* 3.1 26.4 + - + +
367D GLU* 3.1 33.1 + - - +
373D TRP 4.7 1.3 - - - +
374D GLU* 2.6 62.8 + - - +
375D ALA 5.2 1.3 - - - +
376D ALA* 5.0 9.6 - - - +
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Residues in contact with ASN 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D TYR* 3.1 39.4 + - - +
285D VAL 3.2 0.2 + - - -
287D LYS* 1.3 76.9 - - - +
289D ILE* 1.3 69.1 + - - +
291D ALA* 3.9 3.8 - - - +
292D ALA* 3.2 23.4 + - - +
294D LEU* 4.7 0.3 - - - +
337D PHE* 3.7 18.2 - - + -
375D ALA 2.7 26.0 + - - -
376D ALA* 3.4 4.0 - - - +
377D ASP 3.0 6.2 + - - +
378D LYS* 2.7 46.0 + - + +
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Residues in contact with ILE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D VAL* 3.0 37.6 + - + +
286D ALA* 3.4 10.8 - - - +
288D ASN* 1.3 78.4 - - - +
290D VAL* 1.3 66.0 + - - +
292D ALA 3.2 6.8 + - - -
294D LEU* 3.3 54.0 + - + +
295D ALA* 4.3 7.2 - - + +
298D ALA* 4.2 22.0 - - + -
300D ILE* 4.5 13.2 - - + -
337D PHE* 5.4 4.2 - - + -
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Residues in contact with VAL 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ALA* 3.9 25.6 - - + +
131D CYS 4.2 5.6 - - - -
132D ASP* 4.3 5.4 - - - +
137D LEU* 3.9 26.1 - - + +
286D ALA 3.2 16.2 + - - +
287D LYS 4.2 2.9 - - - +
289D ILE* 1.3 80.7 - - + +
291D ALA* 1.3 61.8 + - - +
293D GLY* 3.2 14.0 + - - -
295D ALA 3.5 23.9 - - - +
296D SER* 3.8 13.2 - - - +
297D ARG* 4.2 2.7 - - - -
298D ALA* 4.0 18.4 - - + +
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Residues in contact with ALA 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 3.8 15.0 - - + +
287D LYS 3.1 21.1 + - - +
288D ASN* 3.9 5.6 - - - +
289D ILE 3.2 0.2 - - - -
290D VAL* 1.3 77.9 - - - +
292D ALA* 1.3 57.8 + - - +
293D GLY 3.2 2.8 + - - -
376D ALA* 3.9 26.2 - - + -
378D LYS 5.9 1.3 - - - +
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Residues in contact with ALA 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D ASN 3.2 17.6 + - - +
289D ILE 3.2 0.4 + - - -
291D ALA* 1.3 75.5 - - - +
293D GLY* 1.3 60.7 + - - +
294D LEU* 3.3 21.9 + - + +
378D LYS 4.6 13.5 - - - +
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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
------------------------------------------------------------
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