Contacts of the helix formed by residues 288 - 306 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A LEU 4.9 2.0 - - - -
248A PRO* 4.1 22.7 - - - -
287A ASP* 1.3 88.6 - - - +
289A VAL* 1.3 66.4 + - - +
290A GLN* 3.8 12.1 - - - -
291A ALA* 3.2 37.4 + - + +
292A ARG* 3.4 13.9 + - - +
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Residues in contact with VAL 289 (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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288A CYS* 1.3 70.3 - - - +
290A GLN* 1.3 73.3 + - + +
292A ARG* 3.0 32.4 + - - +
293A ALA* 2.8 28.3 + - - +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 3.5 23.4 - - + +
248A PRO* 2.7 39.7 + - + +
251A ALA* 2.9 30.7 - - - +
255A PRO 5.5 0.8 + - - -
258A PRO* 3.8 12.5 - - + +
288A CYS* 3.3 8.2 - - - -
289A VAL* 1.3 91.7 - - + +
291A ALA* 1.3 61.6 + - - +
293A ALA* 3.2 18.0 + - - +
294A ALA 3.2 10.0 + - - -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 4.1 30.4 - - + +
247A LEU* 4.3 3.8 - - - +
282A TYR* 5.3 9.9 - - + -
287A ASP 4.6 2.5 - - - +
288A CYS* 3.2 28.1 - - + +
290A GLN* 1.3 78.3 - - - +
292A ARG* 1.3 62.9 + - - +
294A ALA* 3.3 6.2 + - - +
295A LEU* 3.2 27.3 + - + +
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP* 4.5 16.2 - - - +
288A CYS 3.4 13.3 + - - +
289A VAL* 3.0 37.2 + - - +
291A ALA* 1.3 76.0 - - - +
293A ALA* 1.3 60.0 + - - +
295A LEU* 3.3 11.3 + - + +
296A ASP* 2.9 53.9 + - - +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO* 3.9 16.3 - - + -
259A GLN* 4.7 9.7 - - - +
289A VAL 2.8 12.1 + - - +
290A GLN* 3.3 13.0 - - - +
292A ARG* 1.3 78.2 - - - +
294A ALA* 1.3 61.1 + - - +
296A ASP* 3.3 7.6 + - - +
297A LYS* 3.0 24.6 + - - +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 3.9 19.5 - - + -
247A LEU* 5.0 1.8 - - + -
258A PRO* 3.3 29.8 + - + +
261A VAL* 4.2 6.3 - - + -
262A GLY* 3.2 18.9 - - - +
265A ILE* 4.8 2.2 - - + -
290A GLN 3.2 9.1 + - - +
291A ALA* 3.5 9.4 - - - +
292A ARG 3.3 0.2 - - - -
293A ALA* 1.3 80.2 - - - +
295A LEU* 1.3 60.9 + - - +
297A LYS* 3.3 1.7 + - - -
298A ALA* 3.1 19.1 + - - +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 4.2 20.9 - - + -
265A ILE* 4.4 9.4 - - + -
278A TYR* 4.8 3.8 - - + -
279A ILE* 4.0 40.4 - - + +
282A TYR* 3.8 38.6 - - + +
291A ALA* 3.2 17.3 + - + +
292A ARG* 3.8 11.4 - - + +
294A ALA* 1.3 80.4 - - - +
296A ASP* 1.3 60.7 + - - +
298A ALA* 3.3 5.7 + - - +
299A THR* 2.9 33.9 + - - -
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 2.9 39.2 + - - +
293A ALA* 3.7 7.4 + - - +
295A LEU* 1.3 75.3 - - - +
297A LYS* 1.3 64.6 + - - +
299A THR* 3.5 7.4 + - - -
300A VAL* 3.1 33.6 + - + +
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Residues in contact with LYS 297 (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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259A GLN* 3.7 34.8 - - + +
262A GLY* 4.1 4.7 - - - -
263A GLN* 4.0 19.3 - - - +
293A ALA 3.0 16.5 + - - +
294A ALA 3.6 5.4 - - - +
296A ASP* 1.3 74.1 - - - +
298A ALA* 1.3 66.4 + - - +
300A VAL* 3.5 5.3 + - - +
301A LEU* 3.0 52.5 + - + +
337A GLU* 3.0 40.1 + - - +
346A GLU* 3.5 22.7 - - + -
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLY* 3.7 21.7 - - - +
265A ILE* 3.8 25.8 - - + -
266A ALA* 4.1 7.9 - - + +
279A ILE* 4.3 8.7 - - + -
294A ALA 3.1 12.3 + - - +
295A LEU* 3.5 10.1 - - - +
297A LYS* 1.3 77.8 - - - +
299A THR* 1.3 57.7 + - - +
301A LEU* 3.3 2.6 + - - +
302A LEU* 2.9 35.9 + - - +
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ILE* 3.4 21.6 - - + +
280A ASP* 5.7 3.6 - - - +
295A LEU 2.9 18.7 + - - -
296A ASP* 3.8 8.1 + - - -
298A ALA* 1.3 75.7 - - - +
300A VAL* 1.3 57.1 + - + +
302A LEU* 3.1 7.6 + - - +
303A SER* 2.8 44.1 + - - -
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Residues in contact with VAL 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASP* 3.1 20.6 + - + +
297A LYS* 3.9 5.8 - - - +
299A THR* 1.3 77.2 - - + +
301A LEU* 1.3 63.3 + - - +
303A SER* 3.6 6.5 + - - -
304A MET* 3.1 30.2 + - + +
337A GLU* 3.8 34.1 - - + +
340A LEU* 4.1 27.1 - - + -
341A SER* 6.2 4.0 - - - -
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Residues in contact with LEU 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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263A GLN* 3.7 36.1 - - + +
266A ALA* 3.9 14.6 - - + -
297A LYS* 3.0 53.1 + - + +
298A ALA 3.7 3.6 - - - +
300A VAL* 1.3 75.6 - - - +
302A LEU* 1.3 58.2 + - - +
304A MET* 3.7 25.7 - - + +
305A SER* 3.2 26.3 + - - -
333A MET* 5.5 6.2 - - + +
337A GLU* 4.0 7.6 - - - +
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Residues in contact with LEU 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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266A ALA* 3.4 32.8 - - + +
269A VAL* 3.8 32.3 - - + -
270A GLY* 4.5 5.4 - - - +
276A ASN* 4.0 9.4 - - - +
279A ILE* 3.9 24.9 - - + -
298A ALA 2.9 20.8 + - - +
299A THR* 3.7 4.7 - - - +
301A LEU* 1.3 76.1 - - - +
303A SER* 1.3 65.1 + - - +
305A SER* 3.0 19.1 + - - +
306A LYS* 3.1 11.3 + - - -
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Residues in contact with SER 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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299A THR* 2.8 29.3 + - - +
300A VAL* 3.6 8.0 + - - -
302A LEU* 1.3 72.2 - - - +
304A MET* 1.3 59.9 + - - +
306A LYS* 3.0 28.8 + - - +
340A LEU* 5.0 6.4 - - - +
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Residues in contact with MET 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 VAL 3.1 15.6 + - - +
301A LEU* 3.7 40.8 - - + +
303A SER* 1.3 80.4 + - - +
305A SER* 1.3 60.3 + - - +
306A LYS* 3.0 14.4 + - - +
333A MET* 3.3 60.8 - - + +
336A LYS* 3.8 35.3 + - + +
337A GLU* 4.0 11.4 - - + +
340A LEU* 4.7 12.8 - - + -
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU 3.2 20.7 + - - -
302A LEU* 3.0 13.9 + - - +
304A MET* 1.3 78.0 - - - +
306A LYS* 1.3 67.4 + - - +
333A MET* 5.7 7.9 - - - -
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Residues in contact with LYS 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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302A LEU 3.1 7.1 + - - -
303A SER* 3.0 23.0 + - - +
304A MET* 3.9 9.6 - - - +
305A SER* 1.3 84.7 - - - +
336A LYS* 6.1 2.1 - - - +
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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