Contacts of the helix formed by residues 288 - 306 (chain B) in PDB entry 3EIJ
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 CYS 288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B LEU 4.8 2.2 - - - -
248B PRO* 4.6 22.2 - - - -
287B ASP* 1.3 94.0 + - - +
289B VAL* 1.3 65.8 + - - +
290B GLN* 3.9 10.3 - - - -
291B ALA* 3.1 41.2 - - + +
292B ARG* 3.4 18.6 + - - +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B CYS* 1.3 70.7 - - - +
290B GLN* 1.3 78.5 + - + +
292B ARG* 3.3 28.0 + - - +
293B ALA* 3.1 22.7 + - - +
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 3.6 22.7 - - + +
248B PRO* 2.7 42.1 + - + +
251B ALA* 3.4 24.1 - - - +
255B PRO 5.6 1.0 + - - -
258B PRO* 3.8 11.3 - - + +
288B CYS* 3.2 7.7 - - - -
289B VAL* 1.3 85.7 - - + +
291B ALA* 1.3 65.0 + - - +
293B ALA* 3.3 9.5 + - - +
294B ALA* 3.3 16.5 + - - +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 4.0 30.7 - - + +
247B LEU* 4.3 5.1 - - - +
282B TYR* 5.1 9.9 - - + -
287B ASP 4.7 2.0 - - - +
288B CYS* 3.1 33.0 - - + +
290B GLN* 1.3 75.0 - - - +
292B ARG* 1.3 62.0 + - - +
294B ALA* 3.3 6.4 + - - +
295B LEU* 3.2 26.7 + - + +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASP* 4.3 22.4 + - - +
288B CYS 3.4 11.4 + - - +
289B VAL* 3.3 31.0 + - - +
290B GLN 3.2 0.4 - - - -
291B ALA* 1.3 76.9 - - - +
293B ALA* 1.3 55.7 + - - +
295B LEU* 3.0 14.2 + - + +
296B ASP* 2.7 53.5 + - - +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PRO* 4.3 6.7 - - + -
259B GLN* 4.2 18.3 - - - +
289B VAL 3.1 13.4 + - - +
290B GLN* 3.4 11.9 - - - +
292B ARG* 1.3 76.5 - - - +
294B ALA* 1.3 57.4 + - - +
296B ASP* 3.2 9.1 + - - +
297B LYS* 2.9 30.9 + - - +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 4.0 17.9 - - + -
247B LEU* 4.9 2.0 - - + -
258B PRO* 3.2 33.5 - - + +
261B VAL* 4.4 4.9 - - + -
262B GLY* 3.2 19.0 - - - +
265B ILE* 5.0 2.0 - - + -
290B GLN 3.3 7.3 + - - +
291B ALA* 3.4 10.1 - - - +
292B ARG 3.2 0.4 - - - -
293B ALA* 1.3 77.9 - - - +
295B LEU* 1.3 59.3 + - - +
297B LYS* 3.4 1.5 + - - -
298B ALA* 3.0 23.4 + - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 4.2 13.2 - - + -
265B ILE* 4.1 20.2 - - + -
278B TYR* 4.9 3.1 - - + -
279B ILE* 3.7 38.9 - - + +
282B TYR* 3.8 39.3 - - + +
291B ALA* 3.2 17.2 + - + +
292B ARG* 3.0 13.9 + - + +
294B ALA* 1.3 76.6 - - - +
296B ASP* 1.3 55.3 - - - +
298B ALA* 3.4 5.4 + - - +
299B THR* 2.6 37.3 + - - -
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ARG* 2.7 40.8 + - - +
293B ALA* 3.6 7.9 + - - +
295B LEU* 1.3 72.5 - - - +
297B LYS* 1.3 59.9 + - - +
299B THR* 3.2 9.3 + - - -
300B VAL* 2.9 38.9 + - + +
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Residues in contact with LYS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLN* 3.6 37.2 - - + +
262B GLY* 4.1 4.0 - - - -
263B GLN* 3.9 19.1 - - - +
293B ALA 2.9 13.6 + - - +
294B ALA 3.5 9.0 - - - +
296B ASP* 1.3 76.1 - - - +
298B ALA* 1.3 62.9 + - - +
300B VAL* 3.3 5.7 + - + +
301B LEU* 3.0 53.7 + - + +
337B GLU* 3.1 35.5 + - - +
346B GLU* 3.1 30.1 - - + +
350B CYS* 4.7 4.0 - - - -
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLY* 3.8 19.4 - - - +
265B ILE* 4.0 24.5 - - + -
266B ALA* 4.1 8.1 - - - +
279B ILE* 4.1 10.3 - - + -
294B ALA 3.0 14.7 + - - +
295B LEU* 3.6 10.5 - - - +
297B LYS* 1.3 75.7 - - - +
299B THR* 1.3 64.0 + - - +
301B LEU* 3.4 1.4 + - - +
302B LEU* 3.1 31.2 + - - +
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 3.4 19.4 - - + +
280B ASP* 5.0 5.5 + - - +
295B LEU 2.6 23.8 + - - -
296B ASP* 3.2 11.3 + - - -
298B ALA* 1.3 76.1 - - - +
300B VAL* 1.3 60.3 + - + +
302B LEU* 3.2 7.0 + - - +
303B SER* 2.9 33.0 + - - -
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ASP* 2.9 26.2 + - + +
297B LYS* 3.9 5.2 - - + +
299B THR* 1.3 78.8 - - + +
301B LEU* 1.3 62.0 + - - +
303B SER* 3.2 6.4 + - - +
304B MET* 3.1 24.3 + - - +
337B GLU* 3.7 41.5 - - + +
340B LEU* 4.2 17.3 - - + -
341B SER* 4.5 15.3 - - - -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLY 4.2 0.2 - - - +
263B GLN* 3.8 36.3 - - + +
266B ALA* 3.8 21.3 - - + -
297B LYS* 3.0 40.1 + - + +
298B ALA 3.8 0.2 - - - +
300B VAL* 1.3 77.3 - - - +
302B LEU* 1.3 58.5 + - - +
304B MET* 3.7 19.7 - - + +
305B SER* 3.1 27.2 + - - -
337B GLU* 3.4 24.5 - - - +
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA* 3.8 29.2 - - + +
269B VAL* 3.9 24.2 - - + -
270B GLY* 4.7 4.9 - - - +
276B ASN* 3.8 24.0 - - - +
279B ILE* 4.0 23.6 - - + -
298B ALA 3.1 21.6 + - - +
299B THR* 3.8 4.3 - - - +
301B LEU* 1.3 77.2 - - - +
303B SER* 1.3 63.3 + - - +
305B SER* 3.4 9.1 + - - -
306B LYS* 3.3 18.2 + - - -
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Residues in contact with SER 303 (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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299B THR* 2.9 18.5 + - - -
300B VAL* 3.2 13.3 + - - +
302B LEU* 1.3 72.8 - - - +
304B MET* 1.3 69.1 + - - +
306B LYS* 3.3 22.5 + - - +
340B LEU* 3.7 14.3 - - - +
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Residues in contact with MET 304 (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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300B VAL 3.1 15.4 + - - +
301B LEU* 3.7 22.2 - - + +
303B SER* 1.3 82.9 + - - +
305B SER* 1.3 82.7 + - - +
306B LYS* 3.3 14.0 + - - +
333B MET* 3.3 58.6 - - + +
336B LYS* 3.7 29.3 - - + +
337B GLU* 4.2 11.0 - - - +
340B LEU* 3.7 17.9 - - + -
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU 3.1 20.4 + - - -
302B LEU* 3.6 14.4 - - - -
303B SER 3.2 0.4 - - - -
304B MET* 1.3 88.2 - - - +
306B LYS* 1.3 72.7 + - - +
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Residues in contact with LYS 306 (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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302B LEU 3.3 7.4 + - - -
303B SER* 3.3 17.1 + - - +
304B MET* 3.2 16.3 - - - +
305B SER* 1.3 90.9 + - - +
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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