Contacts of the helix formed by residues 273 - 292 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ARG* 4.1 10.3 - - - +
41B VAL 3.5 18.1 + - - +
42B ALA* 4.3 15.2 - - - +
121B GLY* 6.3 4.9 - - - -
122B ASP* 6.4 2.0 - - + -
269B LYS* 3.7 32.5 - - + -
270B ASP* 2.8 41.8 + - - +
272B SER* 1.3 81.0 + - - +
274B VAL* 1.3 66.9 + - - +
275B ASP* 3.1 5.6 - - + +
276B ARG* 3.0 12.7 + - - +
277B SER* 3.1 11.2 + - - -
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA* 4.3 5.4 - - + -
121B GLY 5.4 0.7 - - - +
122B ASP* 4.0 29.6 - - + +
123B GLN 4.9 2.2 - - - +
126B MET* 3.6 21.3 - - + +
272B SER 3.4 4.2 + - - +
273B LYS* 1.3 71.6 - - - +
275B ASP* 1.3 66.4 + - - +
277B SER* 3.5 14.4 - - - +
278B ALA* 2.8 28.1 + - + +
304B TYR* 4.0 30.7 - - + -
341B PRO* 3.9 31.2 - - + -
344B ILE* 5.5 0.4 - - + -
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASP* 5.4 5.1 - - - +
123B GLN 5.0 4.7 - - - +
124B GLY* 5.3 1.6 - - - -
125B LEU 5.2 1.2 - - - +
126B MET* 3.5 23.1 - - - +
264B GLY* 3.8 22.5 + - - +
265B ALA 3.7 7.2 - - - +
266B PHE* 3.4 19.2 - - - -
269B LYS* 2.6 37.9 + - + +
273B LYS* 3.1 4.3 + - + +
274B VAL* 1.3 80.0 - - - +
276B ARG* 1.3 58.1 + - - +
279B ALA* 3.6 8.7 + - - +
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Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 2.8 35.4 + - - -
29B LEU* 3.4 9.7 - - - +
266B PHE* 3.1 35.0 + - + +
269B LYS* 3.0 35.5 + - + +
270B ASP 4.9 5.4 - - - +
271B PRO* 5.3 2.5 - - + -
273B LYS 3.0 6.7 + - - +
274B VAL 3.0 0.2 - - - -
275B ASP* 1.3 78.2 - - + +
277B SER* 1.3 68.0 + - - +
278B ALA 3.3 0.2 - - - -
279B ALA* 3.2 2.9 + - - +
280B TYR* 2.9 62.0 + - + -
355B TYR* 3.4 19.9 - - - -
358B THR* 2.9 28.3 + - - -
363B HIS* 3.7 5.7 - - - -
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO* 3.3 26.7 + - - +
272B SER 5.0 0.5 - - - -
273B LYS 3.1 3.4 + - - -
274B VAL* 3.5 19.8 + - - +
276B ARG* 1.3 79.1 - - - +
278B ALA* 1.3 58.5 + - - +
280B TYR* 3.5 4.9 + - - +
281B ALA 2.9 22.0 + - - -
341B PRO* 4.7 5.3 + - - +
344B ILE* 3.4 30.3 - - - +
345B ILE* 5.2 0.2 - - - -
350B LEU* 4.1 20.6 - - - -
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B MET* 3.6 18.5 - - + +
274B VAL* 2.8 24.8 + - + +
277B SER* 1.3 71.9 + - - +
279B ALA* 1.3 58.4 + - - +
281B ALA* 3.7 2.7 - - - +
282B GLY* 2.8 24.8 + - - -
302B VAL* 4.9 7.8 - - + +
304B TYR* 3.5 37.0 - - + +
339B LEU* 5.8 0.8 - - + +
344B ILE* 4.1 8.3 - - + -
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B MET* 3.9 13.2 - - + +
127B PHE 4.3 18.0 - - - +
254B THR* 6.0 0.2 - - + -
261B HIS* 6.4 0.9 - - + -
266B PHE* 3.5 37.5 - - + -
274B VAL 3.9 2.4 + - - -
275B ASP 3.6 7.4 - - - +
276B ARG 3.2 2.1 + - - +
278B ALA* 1.3 76.3 - - - +
280B TYR* 1.3 61.7 + - - +
282B GLY* 3.2 1.4 + - - -
283B ARG* 3.0 26.9 + - - +
364B PHE* 3.8 7.0 - - + -
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE* 4.2 10.3 - + - -
276B ARG* 2.9 61.4 + - + +
277B SER* 3.7 5.6 - - - +
279B ALA* 1.3 72.1 - - - +
281B ALA* 1.3 66.6 + - - +
283B ARG* 3.2 2.1 + - - +
284B TYR* 3.0 18.5 + - - +
348B LEU* 4.3 7.4 - - + -
350B LEU* 4.6 11.4 - - + -
355B TYR* 3.9 9.2 - + - -
358B THR* 3.6 5.0 + - - -
363B HIS* 2.7 35.1 + - + -
364B PHE* 3.6 27.4 - + - -
373B TRP* 3.4 60.1 - + + +
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B SER 2.9 18.4 + - - +
278B ALA 3.8 4.3 - - - +
280B TYR* 1.3 73.0 - - - +
282B GLY* 1.3 66.2 + - - +
284B TYR* 3.2 8.9 + - - +
285B VAL* 2.8 29.6 + - - +
339B LEU* 4.1 23.1 - - + -
344B ILE* 3.8 21.5 - - + -
347B MET* 4.3 9.0 - - + -
348B LEU* 4.0 5.3 - - - +
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Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PHE 5.0 0.4 - - - -
128B GLY* 3.5 12.1 - - - -
278B ALA 2.8 18.2 + - - -
279B ALA 3.2 2.7 + - - -
280B TYR 3.2 0.2 - - - -
281B ALA* 1.3 77.9 - - - +
283B ARG* 1.3 55.8 + - - +
285B VAL* 3.3 2.6 + - - +
286B ALA* 2.8 31.2 + - - +
300B ILE* 3.4 23.2 - - - +
302B VAL* 5.7 4.0 - - - -
339B LEU* 5.6 0.6 - - - +
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLY* 3.8 2.5 - - - -
129B TYR 2.9 20.2 + - - +
130B ALA* 3.5 7.7 - - - +
136B GLU 2.7 28.7 + - - -
137B LEU 2.8 21.6 + - - -
138B MET* 3.5 22.2 - - - +
255B TYR* 3.5 24.9 - - - +
279B ALA 3.0 12.0 + - - +
280B TYR 3.5 8.1 - - - +
282B GLY* 1.3 76.3 - - - +
284B TYR* 1.3 54.8 + - - +
287B LYS* 2.8 50.8 + - - +
364B PHE* 3.6 27.8 - - + +
365B GLY 4.1 0.2 - - - +
373B TRP* 4.0 8.7 - - + +
374B GLU* 3.0 32.8 + - - +
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Residues in contact with TYR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B TYR 3.0 13.1 + - - +
281B ALA* 3.3 10.1 - - - +
283B ARG* 1.3 75.9 - - - +
285B VAL* 1.3 60.6 - - - +
287B LYS* 3.9 0.8 - - - +
288B ASN* 2.7 43.2 + - - -
337B PHE* 3.7 24.7 - + - -
347B MET* 3.8 42.3 + - + +
348B LEU* 3.8 12.8 - - + -
372B SER 3.9 15.5 - - - -
373B TRP* 3.4 19.0 + - - +
375B ALA 3.2 23.3 - - - -
377B ASP* 2.5 30.0 + - - -
378B LYS* 3.7 17.2 - - + -
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ALA* 2.8 27.5 + - + +
282B GLY 3.6 3.1 - - - +
284B TYR* 1.3 73.3 - - + +
286B ALA* 1.3 59.0 + - - +
288B ASN* 3.1 5.4 + - - +
289B ILE* 2.9 36.6 + - + +
300B ILE* 3.5 31.6 - - + -
333B VAL* 3.6 25.6 - - + -
337B PHE* 3.7 41.3 - - + -
339B LEU* 4.7 8.1 - - + -
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLY 3.9 2.9 - - - +
129B TYR 3.5 33.7 - - - +
130B ALA* 3.4 8.5 - - - +
282B GLY 2.8 20.3 + - - +
283B ARG 3.8 1.1 - - - +
285B VAL* 1.3 72.4 - - - +
287B LYS* 1.3 62.1 + - - +
289B ILE* 3.3 13.6 + - - +
290B VAL* 3.2 21.7 + - - +
298B ALA* 3.6 16.4 - - - +
300B ILE* 4.4 4.7 - - + -
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Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ALA* 3.5 9.6 - - - +
135B PRO 5.5 0.4 - - - -
136B GLU 3.7 12.2 + - - -
137B LEU* 3.7 20.1 - - + +
283B ARG* 2.8 39.6 + - - +
284B TYR* 3.9 4.0 - - - +
286B ALA* 1.3 72.3 - - - +
288B ASN* 1.3 59.0 + - - +
290B VAL 3.3 1.2 + - - -
291B ALA* 2.9 31.1 + - - +
367B GLU* 2.8 27.9 + - - +
373B TRP 4.9 0.2 - - - +
374B GLU* 2.6 67.3 + - - +
375B ALA 5.3 0.2 - - - -
376B ALA* 5.1 11.7 - - + +
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Residues in contact with ASN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B TYR* 2.7 43.7 + - - +
285B VAL 3.5 3.8 - - - +
287B LYS* 1.3 77.0 - - - +
289B ILE* 1.3 59.2 + - - +
291B ALA* 4.5 5.2 - - - +
292B ALA* 2.9 31.4 + - - +
337B PHE* 4.1 5.3 - - + -
375B ALA 3.3 20.4 + - - -
376B ALA* 3.2 10.8 - - - +
378B LYS* 2.8 35.1 + - - -
379B ALA* 3.1 11.1 + - - +
382B LEU* 3.9 17.6 - - + +
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B VAL* 2.9 38.0 + - + +
286B ALA* 3.3 8.5 + - - +
288B ASN* 1.3 78.1 - - - +
290B VAL* 1.3 60.0 + - - +
292B ALA* 3.5 3.6 + - - +
293B GLY 3.5 1.4 + - - -
294B LEU* 3.1 47.3 + - + +
295B ALA* 4.2 9.6 - - + -
298B ALA* 3.9 21.1 - - + -
299B LEU 6.5 0.2 - - - -
300B ILE* 5.7 1.8 - - + -
316B VAL* 4.2 13.2 - - + -
318B THR* 5.0 0.4 - - + -
329B ILE* 3.7 30.7 - - + -
333B VAL* 4.1 6.7 - - + -
382B LEU* 4.4 12.8 - - + -
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ALA* 3.8 25.4 - - + +
131B CYS 4.3 0.9 - - - -
132B ASP* 4.3 10.5 - - + +
137B LEU* 4.0 25.1 - - + -
286B ALA 3.2 13.7 + - - +
287B LYS 3.8 5.6 - - - +
289B ILE* 1.3 74.1 - - - +
291B ALA* 1.3 64.3 + - - +
292B ALA 3.1 1.8 - - - -
293B GLY* 3.1 12.3 + - - -
295B ALA 3.4 23.5 - - - +
296B SER* 3.9 11.9 - - - +
297B ARG* 4.0 12.1 - - - -
298B ALA* 4.0 8.5 - - + +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.8 15.9 - - + +
287B LYS 2.9 17.5 + - - +
288B ASN 4.3 0.4 - - - +
290B VAL* 1.3 78.8 - - - +
292B ALA* 1.3 59.9 + - - +
293B GLY 3.4 0.5 + - - -
376B ALA* 3.9 25.8 - - + -
379B ALA* 3.9 11.4 - - + +
380B LEU* 6.0 0.7 - - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ASN 2.9 21.7 + - - +
289B ILE 3.6 7.4 - - - +
290B VAL 3.1 0.2 - - - -
291B ALA* 1.3 78.1 - - - +
293B GLY* 1.3 57.8 + - - +
294B LEU* 3.4 8.8 - - + +
379B ALA* 3.3 28.0 - - - +
382B LEU* 3.9 15.0 - - + -
383B ALA* 3.4 23.7 - - - +
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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