Contacts of the helix formed by residues 289 - 305 (chain A) in PDB entry 1CEC
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 LEU 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ALA 3.3 3.1 + - - -
288A ASP* 1.3 72.3 - - - +
290A GLU* 1.3 64.4 + - - +
292A ARG* 3.2 14.4 + - + +
293A ILE* 2.9 49.6 + - + +
330A VAL* 4.3 26.7 - - + +
331A SER* 4.5 13.2 - - - +
334A LEU* 5.2 2.2 - - + -
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Residues in contact with GLU 290 (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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225A TYR 5.0 0.2 - - - -
288A ASP* 3.2 9.6 + - - +
289A LEU* 1.3 78.9 - - - +
291A SER* 1.3 62.8 + - - +
293A ILE* 3.8 6.6 - - - +
294A LYS* 3.1 27.9 + - + +
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Residues in contact with SER 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PHE* 3.7 17.4 - - - -
224A LYS* 3.5 5.0 - - - +
225A TYR* 3.0 42.0 + - - -
287A ALA* 5.5 0.2 - - - -
288A ASP* 2.7 34.0 + - - -
290A GLU* 1.3 73.2 - - - +
292A ARG* 1.3 66.1 + - - +
294A LYS* 3.2 1.6 + - - +
295A TRP* 2.9 27.2 + - - +
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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
----------------------------------------------------------
205A PHE* 4.3 0.8 - - - -
283A VAL* 2.8 48.4 + - + +
284A ILE 3.6 12.0 + - - -
285A ALA* 3.9 21.1 + - - +
287A ALA* 4.6 4.7 - - + +
288A ASP 2.9 16.0 + - - +
289A LEU* 3.2 15.7 + - + +
291A SER* 1.3 79.0 - - - +
293A ILE* 1.3 62.5 + - + +
295A TRP* 3.7 1.2 + - - +
296A HIS* 2.7 38.0 + - + -
313A TRP 4.9 1.0 + - - -
320A PHE* 2.9 30.9 + - - +
321A GLU 2.9 20.8 + - - -
322A ILE* 3.8 13.2 - - - +
330A VAL* 4.4 13.7 - - - +
334A LEU* 4.1 19.4 - - + +
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Residues in contact with ILE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 2.9 41.2 + - + +
290A GLU* 3.8 6.7 - - - +
292A ARG* 1.3 76.0 - - - +
294A LYS* 1.3 59.2 + - - +
296A HIS* 3.2 5.4 + - - +
297A GLU* 2.9 31.6 + - - +
331A SER* 3.7 23.3 - - - +
333A GLU* 4.6 13.9 - - + +
334A LEU* 4.3 18.6 - - + +
337A ILE* 3.9 22.9 - - + +
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Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TYR* 4.0 16.6 - - + +
226A PRO* 4.3 17.3 - - + -
290A GLU* 3.1 19.6 + - + +
291A SER 3.7 3.1 - - - +
293A ILE* 1.3 77.2 - - + +
295A TRP* 1.3 64.5 + - - +
297A GLU* 2.9 43.1 + - - +
298A ASP* 3.0 59.3 + - - +
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Residues in contact with TRP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 3.8 25.8 - + - -
201A ASN 2.8 29.3 + - - -
202A PRO* 3.7 5.6 - - + +
205A PHE* 3.6 30.7 - + + -
206A THR* 3.8 12.2 - - + +
225A TYR* 3.6 28.8 - + + -
258A LEU* 3.7 11.2 - - + +
281A PHE* 4.0 19.1 - + + -
282A GLY* 3.7 34.5 - - - -
283A VAL* 3.4 17.5 - - + -
291A SER 2.9 16.5 + - - +
292A ARG 4.0 0.2 - - - +
294A LYS* 1.3 76.3 - - - +
296A HIS* 1.3 66.4 + + - +
298A ASP* 3.7 1.6 - - - +
299A TYR* 2.9 44.9 + + + +
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Residues in contact with HIS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 4.3 3.8 - + - -
282A GLY* 3.7 17.0 - - - -
283A VAL* 3.6 29.6 - - + +
292A ARG* 2.7 37.2 + - + -
293A ILE 3.2 8.3 + - - +
295A TRP* 1.3 93.9 - + - +
297A GLU* 1.3 54.5 + - - +
299A TYR* 3.9 0.8 - - - +
300A ILE* 2.8 39.2 + - - +
312A VAL* 3.7 14.6 - - + +
313A TRP 5.0 0.2 + - - -
322A ILE* 4.6 2.4 - - + +
334A LEU* 3.6 25.0 - - + +
337A ILE* 4.2 4.5 - - + -
338A LEU* 3.7 26.7 - - + -
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ILE* 2.9 21.6 + - - +
294A LYS* 2.9 38.1 + - - +
296A HIS* 1.3 76.7 - - - +
298A ASP* 1.3 61.7 + - - +
300A ILE* 4.0 1.6 - - - +
301A SER* 3.0 25.0 + - - -
337A ILE* 3.9 31.4 - - + +
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Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TYR* 2.6 37.7 + - - +
226A PRO* 5.0 2.1 - - - +
255A LYS* 4.0 26.5 + - + +
258A LEU* 4.0 7.6 - - + -
294A LYS* 3.0 42.1 + - - +
295A TRP 3.7 3.6 - - - +
297A GLU* 1.3 76.6 - - - +
299A TYR* 1.3 61.2 + - - +
301A SER* 2.6 22.5 + - - -
302A LEU* 3.2 14.9 + - - +
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Residues in contact with TYR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 3.4 12.1 - - - -
199A PHE* 3.1 54.4 - + - +
258A LEU* 4.1 9.2 - - + +
262A LEU* 3.9 10.7 - - + +
278A CYS* 3.4 10.9 - - - -
281A PHE* 3.6 44.2 - + + -
295A TRP* 2.9 34.0 + + + +
296A HIS 3.9 2.5 - - - +
298A ASP* 1.3 75.1 - - - +
300A ILE* 1.3 63.9 + - - +
302A LEU* 3.0 16.8 + - + +
303A LEU* 3.0 51.0 + - + +
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Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 3.9 28.5 - - + -
296A HIS 2.8 23.7 + - - +
297A GLU 4.1 2.9 - - - +
299A TYR* 1.3 72.3 - - - +
301A SER* 1.3 57.8 + - - +
303A LEU* 3.2 9.7 + - + +
304A GLU* 2.8 50.9 + - + +
337A ILE* 3.9 30.7 - - + +
338A LEU* 4.2 18.2 - - + +
340A ARG* 3.9 26.5 - - + +
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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
----------------------------------------------------------
255A LYS* 3.1 26.8 + - - -
297A GLU* 3.0 14.4 + - - -
298A ASP* 2.6 26.2 + - - -
300A ILE* 1.3 76.2 - - - +
302A LEU* 1.3 56.8 + - - +
304A GLU* 3.8 11.5 - - - +
305A GLU* 2.9 30.7 + - - +
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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
----------------------------------------------------------
255A LYS* 4.2 14.1 - - + +
258A LEU* 3.7 20.0 - - + -
259A ARG* 3.6 66.9 - - + +
262A LEU* 3.9 16.8 - - + -
298A ASP 3.4 12.8 - - - +
299A TYR* 3.0 13.3 + - + +
301A SER* 1.3 79.9 + - - +
303A LEU* 1.3 65.4 + - - +
305A GLU* 3.2 4.1 + - - +
306A TYR* 3.0 44.5 + - + -
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 4.6 1.3 - - + -
262A LEU* 4.5 6.5 - - + -
278A CYS* 4.4 9.6 - - + -
281A PHE* 4.2 17.5 - - + -
299A TYR* 3.0 58.2 + - + +
300A ILE* 3.2 12.5 + - + +
302A LEU* 1.3 75.7 - - - +
304A GLU* 1.3 57.8 + - - +
306A TYR 3.4 0.3 + - - -
307A ASP 2.9 9.5 + - - -
308A ILE* 2.8 67.0 + - + +
309A GLY 4.9 1.8 - - - +
340A ARG* 3.6 20.4 - - - +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ILE* 2.8 34.1 + - - +
301A SER* 3.8 10.2 - - - +
303A LEU* 1.3 76.8 - - - +
305A GLU* 1.3 62.2 + - - +
307A ASP* 3.1 14.4 + - - +
340A ARG* 3.4 49.7 - - - +
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LYS* 5.3 4.2 + - - -
259A ARG* 2.9 31.6 + - - -
301A SER 2.9 19.2 + - - +
302A LEU* 3.2 9.8 + - - +
304A GLU* 1.3 78.1 - - - +
306A TYR* 1.3 86.7 + - + +
307A ASP* 3.3 1.1 + - - +
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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
------------------------------------------------------------
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