Contacts of the helix formed by residues 291 - 307 (chain A) in PDB entry 2CW9
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 PHE 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A GLY 3.1 1.2 - - - -
290A LEU* 1.3 103.8 - - + +
292A SER* 1.3 58.5 + - - +
293A LYS 3.3 3.1 - - - -
294A THR* 3.1 14.1 + - - +
295A GLU* 2.9 50.8 + - + +
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Residues in contact with SER 292 (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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287A LEU 4.8 2.7 - - - -
288A GLY* 3.7 14.9 - - - -
289A GLY* 2.7 33.7 + - - -
290A LEU 3.5 0.6 - - - -
291A PHE* 1.3 78.5 - - - +
293A LYS* 1.3 76.4 + - - +
295A GLU* 4.1 7.3 - - - +
296A MSE 3.1 26.2 + - - +
379A MSE 5.4 9.2 - - - +
380A GLY 5.6 1.2 + - - +
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Residues in contact with LYS 293 (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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290A LEU 5.1 2.1 + - - +
291A PHE 3.3 1.0 - - - -
292A SER* 1.3 90.0 - - - +
294A THR* 1.3 65.3 + - + +
296A MSE 4.0 3.6 - - - +
297A SER* 3.3 22.5 + - - -
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PHE* 3.1 24.5 + - - +
293A LYS* 1.3 77.2 - - + +
295A GLU* 1.3 61.3 + - - +
297A SER* 3.4 6.3 + - - -
298A GLU* 2.8 43.6 + - - +
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Residues in contact with GLU 295 (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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291A PHE* 2.9 45.5 + - + +
292A SER* 4.1 6.8 - - - +
294A THR* 1.3 80.0 - - - +
296A MSE 1.3 62.0 + - - +
298A GLU* 3.4 15.8 + - - +
299A VAL* 3.1 30.2 + - + +
379A MSE 5.0 7.8 - - - +
380A GLY 3.9 16.6 - - - +
381A LYS* 5.4 4.9 - - - +
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Residues in contact with MSE 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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292A SER 3.1 19.3 + - - +
293A LYS* 4.0 4.5 - - - +
295A GLU* 1.3 74.2 - - - +
297A SER* 1.3 67.3 + - - +
299A VAL* 3.2 5.6 + - - +
300A LEU* 3.0 33.4 + - + +
312A LYS* 4.1 19.1 - - - +
377A LEU* 3.7 33.4 - - + -
378A ALA 4.6 1.8 - - - +
379A MSE 3.4 35.9 - - - +
380A GLY* 4.3 9.1 + - - +
389A LEU* 4.1 20.9 - - - -
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Residues in contact with SER 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LYS 3.3 15.6 + - - -
294A THR* 3.7 7.6 - - - -
296A MSE 1.3 80.7 - - - +
298A GLU* 1.3 58.8 + - - +
300A LEU* 3.4 12.5 + - - +
301A THR* 3.0 28.5 + - - -
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Residues in contact with GLU 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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294A THR* 2.8 36.4 + - - +
295A GLU* 3.6 19.3 - - - +
296A MSE 3.2 0.2 - - - -
297A SER* 1.3 76.1 - - - +
299A VAL* 1.3 64.1 + - + +
301A THR* 3.4 16.2 + - - -
302A GLU* 3.4 13.9 + - - +
382A MSE 4.7 7.7 - - + +
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Residues in contact with VAL 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 GLU 3.1 18.4 + - - +
296A MSE 3.2 5.8 + - - +
298A GLU* 1.3 73.9 - - + +
300A LEU* 1.3 66.9 + - - +
302A GLU* 3.2 5.0 + - - +
303A ILE* 3.1 30.9 + - + +
380A GLY* 3.8 2.5 - - - -
381A LYS* 3.4 36.6 - - - +
382A MSE 4.0 15.5 - - + +
387A PRO* 3.7 22.7 - - + -
388A VAL 3.8 16.4 - - - +
389A LEU* 4.1 8.1 - - + -
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Residues in contact with LEU 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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296A MSE 3.0 31.5 + - + +
297A SER* 3.7 9.0 - - - +
298A GLU 3.3 0.2 - - - -
299A VAL* 1.3 76.2 - - + +
301A THR* 1.3 58.8 + - - +
303A ILE* 3.7 8.7 - - + +
304A LEU* 2.8 48.9 + - + +
310A PHE* 3.9 31.2 - - + -
312A LYS* 3.2 42.8 - - + +
389A LEU* 5.4 2.2 - - + -
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Residues in contact with THR 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 SER* 3.0 18.1 + - - -
298A GLU* 3.5 13.1 - - - -
299A VAL 3.2 0.2 - - - -
300A LEU* 1.3 77.3 - - - +
302A GLU* 1.3 63.1 + - + +
304A LEU* 3.6 9.3 + - - +
305A ARG* 3.2 45.5 + - - +
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Residues in contact with GLU 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 GLU 3.4 5.9 + - - +
299A VAL 3.2 9.3 + - - +
301A THR* 1.3 79.3 - - + +
303A ILE* 1.3 64.6 + - - +
305A ARG* 3.4 37.8 + - - +
306A VAL 3.9 0.2 + - - -
382A MSE 3.9 34.8 - - + +
387A PRO* 4.5 4.3 - - + +
429A GLN* 2.9 41.6 + - - +
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Residues in contact with ILE 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 VAL* 3.1 31.4 + - + +
300A LEU* 3.3 10.3 + - + +
302A GLU* 1.3 75.2 - - - +
304A LEU* 1.3 60.1 + - + +
306A VAL* 3.1 6.2 + - - +
307A ASP* 2.8 25.8 + - + +
310A PHE* 3.7 39.9 - - + -
387A PRO* 3.8 18.4 - - + -
389A LEU* 4.1 15.0 - - + -
427A ARG* 4.2 16.9 + - - +
429A GLN* 4.3 6.9 - - - +
438A TRP* 3.8 24.2 - - + -
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Residues in contact with LEU 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 LEU* 2.8 39.0 + - + +
301A THR* 3.9 9.0 - - - +
303A ILE* 1.3 75.4 - - + +
305A ARG* 1.3 65.1 + - - +
306A VAL 3.2 0.2 - - - -
307A ASP 3.6 10.5 - - - +
308A PRO* 3.2 48.0 - - + +
310A PHE* 4.1 21.5 - - + +
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Residues in contact with ARG 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 THR* 3.2 36.9 + - - +
302A GLU* 3.5 30.9 + - - +
303A ILE 3.1 1.0 - - - -
304A LEU* 1.3 77.4 - - - +
306A VAL* 1.3 64.7 + - + +
308A PRO* 4.7 4.9 - - - +
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Residues in contact with VAL 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 GLU 4.5 0.4 - - - +
303A ILE 3.1 6.0 + - - +
305A ARG* 1.3 85.3 - - + +
307A ASP* 1.3 55.7 - - - +
308A PRO* 3.4 9.0 - - - +
427A ARG* 3.7 23.8 - - - +
429A GLN* 3.8 50.3 - - + +
431A GLU 4.8 7.6 - - - +
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Residues in contact with ASP 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 ILE* 2.8 11.2 + - + +
304A LEU* 3.6 9.2 - - - -
306A VAL* 1.3 78.4 - - - +
308A PRO* 1.3 57.6 - - - +
309A ALA* 3.5 15.4 + - - +
310A PHE* 3.0 52.2 + - + +
427A ARG* 3.8 21.3 + - - +
434A PRO* 3.9 24.2 - - + +
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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