Contacts of the helix formed by residues 295 - 311 (chain A) in PDB entry 2ILU
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A VAL 3.9 1.2 + - - -
294A GLN* 1.3 68.9 - - - +
296A GLY* 1.3 56.1 + - - +
297A ILE 2.8 13.0 + - - -
298A TYR* 2.9 21.5 + - + +
299A ASP* 4.1 11.4 - - - +
393A ALA* 4.0 24.9 + - + +
394A PHE* 3.4 14.0 + - - +
395A ASP* 3.1 38.6 + - - +
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Residues in contact with GLY 296 (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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262A ASP* 3.0 22.9 + - - +
294A GLN* 3.1 2.8 + - - +
295A LYS* 1.3 76.9 - - - +
297A ILE* 1.3 57.0 + - - +
299A ASP* 5.5 1.6 - - - +
300A GLN* 4.9 7.1 - - - +
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Residues in contact with ILE 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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260A VAL* 4.2 9.2 - - + +
261A MET 3.8 10.5 - - - +
262A ASP* 2.6 49.4 + - + +
264A ALA 3.8 15.9 - - - +
266A LEU* 4.1 26.9 - - + -
293A VAL* 3.5 20.0 - - + -
294A GLN 3.0 2.0 + - - +
295A LYS 2.8 0.6 + - - -
296A GLY* 1.3 74.2 - - - +
298A TYR* 1.3 70.2 + - - +
299A ASP* 3.2 3.3 + - - -
300A GLN* 3.3 18.4 + - + +
301A PHE* 2.9 22.1 + - + +
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Residues in contact with TYR 298 (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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293A VAL* 3.6 24.7 - - + -
294A GLN 2.9 10.6 + - - +
295A LYS* 2.9 18.5 + - + +
297A ILE* 1.3 76.3 - - - +
299A ASP* 1.3 76.1 + - - +
301A PHE* 3.7 0.5 - - - +
302A VAL* 2.9 45.5 + - + +
350A ARG* 5.3 3.0 + - - -
371A LEU* 3.7 31.4 - - + +
372A ASP* 3.9 8.5 + - - -
391A VAL* 3.5 30.2 + - + -
393A ALA* 4.0 29.8 - - + -
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Residues in contact with ASP 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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295A LYS 4.1 10.1 - - - +
296A GLY 5.5 1.6 - - - +
297A ILE 3.2 1.0 + - - -
298A TYR* 1.3 88.4 - - - +
300A GLN* 1.3 67.5 + - + +
302A VAL* 3.5 3.1 + - - +
303A ASN* 2.8 30.8 + - - +
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 3.4 28.0 - - + +
296A GLY 4.9 6.3 - - - +
297A ILE* 3.3 17.0 + - + +
299A ASP* 1.3 77.6 - - + +
301A PHE* 1.3 65.1 + - - +
303A ASN* 3.1 20.4 + - - +
304A ARG* 3.2 19.0 + - + +
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Residues in contact with PHE 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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260A VAL* 3.9 22.4 - - + -
266A LEU* 3.6 19.6 - - + +
269A ALA* 4.1 2.5 - - + -
270A VAL* 3.8 30.3 - - + -
273A ILE* 3.5 29.6 - - + -
291A VAL* 3.8 8.1 - - + -
293A VAL* 3.5 37.0 - - + -
297A ILE* 2.9 20.1 + - + +
298A TYR 3.7 2.7 - - - +
300A GLN* 1.3 76.0 - - - +
302A VAL* 1.3 69.8 - - + +
304A ARG* 3.6 1.6 + - - +
305A LEU* 3.0 54.3 + - + +
391A VAL* 5.0 2.2 - - + -
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Residues in contact with VAL 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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298A TYR* 2.9 53.9 + - + +
299A ASP* 3.9 4.5 - - - +
301A PHE* 1.3 82.0 - - + +
303A ASN* 1.3 55.7 + - - +
305A LEU* 3.4 6.4 + - + +
306A GLY* 2.7 32.6 + - - -
352A ALA* 5.6 0.2 - - + -
369A LEU* 4.5 8.9 - - + +
371A LEU* 3.4 37.7 - - + -
391A VAL* 4.7 3.4 - - + -
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Residues in contact with ASN 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 ASP* 2.8 27.0 + - - +
300A GLN* 3.1 8.5 + - - +
302A VAL* 1.3 76.3 - - - +
304A ARG* 1.3 63.1 + - + +
306A GLY* 3.1 1.6 + - - -
307A GLU* 2.8 44.3 + - - +
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Residues in contact with ARG 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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266A LEU* 3.5 29.5 - - + +
267A GLU* 3.0 45.8 + - - +
270A VAL* 3.8 23.9 - - + +
300A GLN* 3.2 16.1 + - + +
303A ASN* 1.3 77.1 - - + +
305A LEU* 1.3 52.4 - - - +
307A GLU* 3.2 10.7 + - - +
308A ALA* 2.8 35.2 + - - +
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Residues in contact with LEU 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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270A VAL* 3.7 15.4 - - + +
273A ILE* 4.5 11.9 - - + -
274A VAL* 3.7 26.2 - - + -
291A VAL* 5.3 0.7 - - + -
301A PHE* 3.0 51.6 + - + +
302A VAL* 3.5 5.6 - - + +
304A ARG* 1.3 74.6 - - - +
306A GLY* 1.3 65.6 + - - +
308A ALA* 3.2 2.6 + - - +
309A MET* 2.9 48.5 + - + +
369A LEU* 4.3 11.4 - - + -
389A LEU* 4.3 16.8 - - + -
391A VAL* 4.4 7.4 - - + -
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Residues in contact with GLY 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 VAL 2.7 20.9 + - - -
303A ASN* 3.6 1.8 - - - -
305A LEU* 1.3 73.0 - - - +
307A GLU* 1.3 62.1 + - - +
309A MET* 3.3 20.5 + - - +
310A GLN* 3.4 20.9 + - - +
353A PHE* 5.0 5.9 - - - -
369A LEU* 4.1 8.7 - - - -
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Residues in contact with GLU 307 (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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303A ASN* 2.8 29.5 + - - +
304A ARG* 3.5 8.3 - - - +
306A GLY* 1.3 76.8 - - - +
308A ALA* 1.3 63.1 + - - +
310A GLN* 3.2 29.9 + - - +
311A ALA* 3.8 5.7 + - - +
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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
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270A VAL* 4.1 8.5 - - + -
274A VAL* 3.7 29.3 - - + +
304A ARG 2.8 20.4 + - - +
305A LEU 3.6 4.5 - - - +
307A GLU* 1.3 74.5 - - - +
309A MET* 1.3 61.0 + - - +
310A GLN 3.5 0.2 + - - -
311A ALA* 3.6 14.8 + - - +
312A VAL* 3.8 11.0 - - - +
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Residues in contact with MET 309 (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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274A VAL* 4.9 7.9 - - + -
305A LEU* 2.9 46.2 + - + +
306A GLY* 3.7 5.6 - - - +
307A GLU 3.2 0.4 - - - -
308A ALA* 1.3 75.4 - - - +
310A GLN* 1.3 65.4 + - - +
311A ALA 3.3 0.2 - - - -
312A VAL* 3.2 26.9 + - + +
353A PHE* 3.6 22.2 - - + -
367A PRO* 4.1 12.8 - - + +
368A THR 4.5 10.8 - - - +
369A LEU* 3.2 52.7 - - + -
389A LEU* 4.7 15.5 - - + -
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Residues in contact with GLN 310 (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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306A GLY 3.4 14.5 + - - +
307A GLU* 3.2 21.2 + - - +
309A MET* 1.3 79.2 - - - +
311A ALA* 1.3 62.7 + - - +
312A VAL 3.1 7.1 + - - +
313A GLN* 5.0 4.5 - - - +
353A PHE* 3.5 37.0 - - + -
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Residues in contact with ALA 311 (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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307A GLU 3.8 5.3 + - - +
308A ALA* 3.6 11.7 + - - +
309A MET 3.3 0.6 - - - -
310A GLN* 1.3 78.3 - - - +
312A VAL* 1.3 56.7 + - - +
313A GLN* 3.0 20.8 + - - +
324A ALA* 5.4 0.5 - - - +
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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
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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