Contacts of the helix formed by residues 285 - 308 (chain A) in PDB entry 3L0I
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 PRO 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ASN* 6.1 0.2 - - - +
284A LEU* 1.3 100.3 - - + +
286A GLU* 1.3 60.8 + - - +
287A GLU* 3.3 5.2 - - + +
288A GLN* 2.9 34.5 + - + +
289A ILE* 3.0 10.4 + - - +
335A LEU* 5.8 0.7 - - + -
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 2.9 53.7 + - - +
282A ASN* 5.9 0.8 + - - -
284A LEU 3.4 4.3 + - - -
285A PRO* 1.3 70.1 - - - +
287A GLU* 1.3 58.4 + - - +
289A ILE* 3.1 7.4 + - - +
290A ALA* 2.8 38.3 + - + +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PRO* 3.3 5.3 - - + +
286A GLU* 1.3 78.3 - - - +
288A GLN* 1.3 59.2 + - - +
290A ALA* 4.3 4.2 - - - +
291A ARG* 3.0 54.4 + - - +
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Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 4.3 5.2 - - + -
285A PRO* 2.9 28.3 + - + +
287A GLU* 1.3 78.3 - - - +
289A ILE* 1.3 62.9 + - - +
291A ARG* 2.9 48.2 + - - +
292A ILE* 3.4 22.8 + - - +
331A LYS* 4.7 7.1 + - - +
332A ILE* 5.5 1.2 - - - +
335A LEU* 3.4 55.1 + - + +
338A GLN* 5.0 5.2 + - - +
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Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ILE* 3.9 25.0 - - + +
278A LEU* 3.7 43.1 - - + +
279A ARG* 3.8 31.4 - - + +
282A ASN* 5.8 0.2 - - - -
284A LEU* 3.4 38.1 - - + +
285A PRO 3.0 14.0 + - - +
286A GLU* 3.7 10.5 - - - +
288A GLN* 1.3 73.8 - - - +
290A ALA* 1.3 66.1 + - - +
292A ILE* 2.9 22.3 + - + +
293A GLU* 3.0 9.9 + - - +
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 3.6 14.6 - - - +
286A GLU* 2.8 33.2 + - + +
287A GLU* 4.3 4.9 - - - +
289A ILE* 1.3 73.5 - - - +
291A ARG* 1.3 52.5 + - - +
293A GLU* 3.2 3.0 + - - +
294A SER* 2.8 36.3 + - - -
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 3.0 52.7 + - - +
288A GLN* 2.9 36.3 - - - +
289A ILE 3.1 0.4 - - - -
290A ALA* 1.3 79.6 - - - +
292A ILE* 1.3 61.0 + - - +
294A SER* 4.1 5.4 - - - +
295A VAL* 3.2 26.9 + - - +
328A GLU* 3.6 51.6 + - + +
331A LYS* 3.6 31.8 - - - +
332A ILE* 3.9 15.9 - - + -
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 4.2 21.9 - - + +
251A MSE 4.9 5.4 - - + -
252A LEU* 4.5 13.5 - - + -
255A LEU* 4.1 20.9 - - + -
275A ILE* 4.4 15.3 - - + -
278A LEU* 5.7 2.9 - - + -
284A LEU* 4.8 4.3 - - + -
288A GLN 3.4 16.8 + - - +
289A ILE* 2.9 11.1 + - + +
291A ARG* 1.3 75.7 - - - +
293A GLU* 1.3 58.7 + - - +
295A VAL* 4.3 0.5 - - - +
296A TYR* 3.1 28.0 + - + +
332A ILE* 4.2 31.2 - - + -
335A LEU* 3.9 23.6 - - + -
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ILE* 3.5 26.9 - - + +
279A ARG* 2.7 43.1 + - - -
289A ILE 3.0 11.0 + - - +
290A ALA* 3.2 10.1 + - - +
292A ILE* 1.3 76.5 - - - +
294A SER* 1.3 64.7 + - - +
296A TYR* 4.0 1.7 - - - +
297A ASN* 3.1 29.1 + - + +
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Residues in contact with SER 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ALA 2.8 19.5 + - - -
291A ARG* 4.1 5.6 - - - -
293A GLU* 1.3 73.3 - - - +
295A VAL* 1.3 59.5 + - - +
297A ASN* 4.0 4.9 - - - +
298A GLN* 2.9 39.8 + - - +
328A GLU* 6.2 1.3 - - - -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 3.9 24.0 - - + -
248A ILE* 4.7 6.5 - - + -
291A ARG 3.2 18.5 + - - +
292A ILE 4.3 1.1 - - - +
294A SER* 1.3 77.9 - - - +
296A TYR* 1.3 58.8 + - - +
297A ASN 3.2 1.6 - - - -
298A GLN* 3.2 11.8 + - - +
299A ALA* 2.9 28.8 + - - +
325A MSE 4.4 10.0 - - + +
328A GLU* 3.7 34.5 - - + -
329A VAL* 3.9 15.7 - - + -
332A ILE* 4.2 15.5 - - + -
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Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A MSE 4.7 20.0 - - + +
248A ILE* 3.7 30.4 - - + +
249A ASP* 3.4 28.1 + - - -
252A LEU* 4.9 3.4 - - + -
271A ALA* 3.9 30.0 - - + +
272A PRO* 5.5 4.0 - - + -
275A ILE* 5.4 7.4 - - + -
292A ILE* 3.1 20.4 + - + +
293A GLU* 4.1 4.0 - - - +
295A VAL* 1.3 76.6 - - - +
297A ASN* 1.3 59.8 + - - +
299A ALA* 3.7 5.8 - - - +
300A MSE 3.1 60.3 + - + +
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU* 3.1 20.9 + - + +
294A SER* 4.0 6.6 + - - +
296A TYR* 1.3 79.7 - - + +
298A GLN* 1.3 62.7 + - - +
300A MSE 3.3 15.4 - - - +
301A SER* 3.0 36.9 + - - -
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Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A SER* 2.9 30.2 + - - +
295A VAL* 3.2 13.7 + - - +
297A ASN* 1.3 78.9 - - + +
299A ALA* 1.3 61.5 + - - +
301A SER* 3.4 7.7 + - - -
302A LYS* 3.0 28.9 + - - +
324A ALA* 5.7 6.9 - - - +
325A MSE 3.7 38.4 - - + +
328A GLU* 6.1 0.2 - - - +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL* 4.0 13.6 - - + +
244A ILE* 4.0 20.0 - - + -
245A MSE 3.7 26.5 - - + -
295A VAL 2.9 17.7 + - - +
296A TYR* 3.7 7.9 - - - +
298A GLN* 1.3 73.6 - - - +
300A MSE 1.3 59.1 + - - +
302A LYS* 3.1 2.3 + - - +
303A ARG* 2.9 31.4 + - - +
325A MSE 4.1 5.5 - - - -
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Residues in contact with MSE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A MSE 4.6 10.6 - - - -
272A PRO* 6.1 4.5 - - + -
296A TYR* 3.1 49.7 + - + +
297A ASN* 3.3 20.2 - - - +
299A ALA* 1.3 75.9 - - - +
301A SER* 1.3 62.0 + - - +
303A ARG* 3.6 3.0 + - - +
304A PHE* 3.3 22.3 + - - +
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ASN* 3.0 23.3 + - - -
298A GLN* 3.6 11.7 - - - -
299A ALA 3.3 0.2 - - - -
300A MSE 1.3 77.4 - - - +
302A LYS* 1.3 57.4 + - - +
304A PHE* 3.6 6.2 + - - +
305A GLU* 3.0 34.3 + - - +
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Residues in contact with LYS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL* 4.3 10.1 - - + -
298A GLN 3.0 17.3 + - - +
299A ALA* 3.1 4.9 + - - +
301A SER* 1.3 75.1 - - - +
303A ARG* 1.3 66.1 + - - +
305A GLU* 3.2 28.6 + - - +
306A LEU* 2.9 45.9 + - + +
317A MSE 3.8 39.7 - - + -
318A PRO* 6.2 0.4 - - - -
321A ASP* 4.0 23.0 + - - +
325A MSE 4.9 13.5 - - + -
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Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL* 4.5 7.9 - - + +
241A LYS* 4.6 14.1 - - - +
245A MSE 4.1 35.8 - - - +
299A ALA 2.9 16.2 + - - +
300A MSE 4.0 4.3 - - - +
302A LYS* 1.3 75.3 - - - +
304A PHE* 1.3 57.8 + - - +
306A LEU* 3.8 4.8 - - - -
307A HIS* 2.9 73.9 + - + +
314A HIS 5.0 0.9 - - - -
315A ASP* 3.6 27.4 + - - +
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A MSE 3.3 15.1 + - - +
301A SER* 3.7 6.5 - - - +
303A ARG* 1.3 79.5 - - - +
305A GLU* 1.3 67.7 + - + +
307A HIS* 3.4 6.5 + - + +
308A ALA* 3.2 33.8 + - + +
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A SER* 3.0 23.3 + - - +
302A LYS* 3.2 35.7 + - + +
304A PHE* 1.3 82.0 - - + +
306A LEU* 1.3 60.5 + - + +
308A ALA* 3.7 4.9 + - - +
309A GLU* 3.0 35.0 - - - +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL* 3.6 31.0 - - + -
302A LYS* 2.9 32.4 + - + +
303A ARG* 3.9 2.0 - - - +
305A GLU* 1.3 76.2 - - + +
307A HIS* 1.3 60.4 + - - +
308A ALA 3.0 5.9 + - - -
309A GLU* 3.4 20.1 + - + +
310A HIS* 3.9 16.1 - - - +
313A GLU 4.3 3.8 - - - +
314A HIS* 3.2 32.1 - - - +
316A GLU 3.9 19.5 - - - +
317A MSE 3.7 22.7 - - + -
318A PRO* 5.1 4.7 - - + -
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Residues in contact with HIS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ARG* 2.9 65.5 + - + +
304A PHE* 3.4 7.2 + - + +
306A LEU* 1.3 76.2 - - - +
308A ALA* 1.3 56.8 + - - +
309A GLU 3.4 4.2 + - - +
314A HIS* 3.3 37.1 + - + +
315A ASP* 3.5 22.1 + - - -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 3.2 27.6 + - + +
305A GLU* 3.9 8.3 - - - +
306A LEU 3.0 1.4 - - - -
307A HIS* 1.3 78.1 - - - +
309A GLU* 1.3 68.4 + - - +
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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