Contacts of the helix formed by residues 279 - 299 (chain A) in PDB entry 3CQ6
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 GLY 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ALA 3.2 9.8 + - - -
276A ASP 3.1 13.6 + - - -
278A LEU* 1.3 77.3 - - - +
280A THR* 1.3 59.5 + - - +
281A VAL 3.3 0.7 + - - -
282A GLU* 3.5 30.5 + - - +
283A LYS* 4.2 8.9 + - - +
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Residues in contact with THR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 2.9 22.8 + - - +
39A TYR* 3.7 41.0 - - + -
229A ALA 4.3 2.3 + - - -
231A ASP* 6.0 0.9 - - - -
276A ASP 4.2 3.1 + - - +
277A THR* 2.9 24.5 + - + +
278A LEU 4.5 0.3 - - - -
279A GLY* 1.3 75.5 - - - +
281A VAL* 1.3 66.4 + - - +
283A LYS* 3.2 22.7 + - - +
284A LEU* 3.1 24.8 + - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 5.7 0.2 - - - +
202A GLU* 3.6 24.5 - - + +
203A PHE* 3.9 23.1 - - + -
229A ALA* 3.9 28.9 - - + -
278A LEU* 3.4 26.2 - - + +
279A GLY 3.2 0.2 - - - -
280A THR* 1.3 81.4 + - - +
282A GLU* 1.3 60.4 + - + +
284A LEU* 3.1 2.6 + - - +
285A SER* 2.8 46.6 + - - +
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU 5.6 0.7 - - - +
279A GLY* 3.5 20.2 + - - +
280A THR 3.3 0.6 - - - -
281A VAL* 1.3 80.2 - - + +
283A LYS* 1.3 63.4 + - + +
285A SER* 3.4 5.2 + - - -
286A VAL* 3.3 27.1 + - - +
319E HIS* 3.6 41.5 + - + +
323E GLN* 4.8 0.4 - - - +
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 3.4 43.1 - - + +
279A GLY 4.6 11.2 - - - +
280A THR* 3.2 20.8 + - - +
282A GLU* 1.3 80.9 - - + +
284A LEU* 1.3 58.2 + - - +
286A VAL* 3.4 6.4 + - - +
287A GLU* 3.0 33.9 + - + +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 4.0 19.3 - - - +
38A PRO* 3.7 32.1 - - + -
39A TYR* 3.9 11.9 - - + +
203A PHE* 3.8 30.1 - - + -
280A THR 3.1 21.6 + - - +
281A VAL 3.7 3.6 - - - +
283A LYS* 1.3 75.7 - - - +
285A SER* 1.3 61.0 + - - +
287A GLU* 3.4 3.8 + - + -
288A ARG* 3.0 28.1 + - - +
307A SER 5.3 0.3 - - - +
308A ASN* 4.8 9.3 - - + +
345A ILE* 3.6 16.5 - - + +
346A GLY 3.6 24.2 - - - +
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE* 4.0 15.0 + - - -
281A VAL* 2.8 31.2 + - - +
282A GLU* 4.0 4.5 - - - -
283A LYS 3.3 0.2 - - - -
284A LEU* 1.3 76.9 - - - +
286A VAL* 1.3 60.5 + - - +
288A ARG* 3.6 18.1 + - - +
289A VAL* 3.3 26.7 + - - +
307A SER 5.4 2.1 - - - -
323E GLN* 3.6 30.7 + - - +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU 3.3 18.1 + - - +
283A LYS* 3.9 4.5 - - - +
284A LEU 3.3 0.2 - - - -
285A SER* 1.3 74.4 - - - +
287A GLU* 1.3 63.2 + - + +
289A VAL* 3.3 7.6 + - - +
290A ARG* 3.0 26.0 + - - +
24E PRO* 5.2 7.0 - - + -
26E LEU* 4.3 24.3 - - + +
319E HIS* 5.4 2.7 - - + +
322E TRP* 3.7 36.3 - - + -
323E GLN* 3.8 5.6 - - - +
326E LEU* 4.7 1.1 - - + -
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 6.0 0.7 - - - +
283A LYS* 3.0 22.6 + - + +
284A LEU* 3.7 1.1 - - - +
286A VAL* 1.3 77.3 - - - +
288A ARG* 1.3 55.1 + - - +
290A ARG* 2.8 43.4 + - - +
291A VAL* 2.8 37.9 + - - +
345A ILE* 3.6 13.5 - - + -
346A GLY 4.5 3.4 - - - +
348A PRO* 3.7 25.8 - - + +
351A ASN* 2.7 35.6 + - - +
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PHE 4.2 4.4 + - - -
284A LEU 3.0 17.9 + - - +
285A SER* 3.6 19.2 + - - +
286A VAL 3.3 0.2 - - - -
287A GLU* 1.3 77.2 - - - +
289A VAL* 1.3 76.3 + - - +
291A VAL* 3.8 0.9 - - - +
292A ALA* 2.9 35.6 + - - +
305A SER* 3.2 35.7 + - - +
306A GLU* 3.5 20.7 + - - -
307A SER 2.9 25.8 + - - +
309A PHE 4.2 1.6 - - - +
310A VAL* 3.7 19.3 - - + +
345A ILE* 3.8 19.7 - - + +
323E GLN* 4.0 6.1 - - - +
327E ASP* 3.0 34.2 + - - +
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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
----------------------------------------------------------
285A SER 3.3 16.2 - - - +
286A VAL 3.3 7.1 + - - +
287A GLU 3.2 0.2 - - - -
288A ARG* 1.3 94.0 - - - +
290A ARG* 1.3 65.9 + - - +
292A ALA* 4.0 3.5 - - - +
293A ALA* 2.9 26.9 + - - +
26E LEU* 4.0 7.4 - - + -
28E VAL* 3.6 27.6 - - + -
323E GLN* 4.0 2.0 - - - +
326E LEU* 3.8 42.8 - - + +
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A VAL 3.0 13.9 + - - +
287A GLU* 2.8 46.4 + - - +
289A VAL* 1.3 77.1 - - - +
291A VAL* 1.3 63.6 + - - +
293A ALA* 3.2 4.8 + - - +
294A ARG* 3.0 25.0 + - + +
348A PRO* 3.6 12.3 + - - +
351A ASN* 3.7 8.8 - - - +
352A ASP* 2.8 29.1 + - - -
355A LEU* 3.6 18.8 - - + +
26E LEU* 4.0 25.7 - - + +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 2.8 24.3 + - - +
288A ARG 3.9 2.7 - - - +
290A ARG* 1.3 73.4 - - - +
292A ALA* 1.3 64.1 + - - +
294A ARG* 3.2 3.3 + - - +
295A LEU* 3.0 28.4 + - + +
310A VAL* 4.8 2.7 - - + -
343A THR* 4.6 3.6 - - + -
345A ILE* 3.9 19.1 - - + -
351A ASN* 3.7 37.2 - - + +
354A PHE* 3.7 32.3 - - + -
355A LEU* 4.0 17.6 - - + +
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Residues in contact with ALA 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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288A ARG* 2.9 25.5 + - - +
289A VAL* 4.0 4.0 - - - +
291A VAL* 1.3 74.0 - - - +
293A ALA* 1.3 62.1 + - - +
295A LEU* 3.4 4.7 + - - +
296A GLU* 3.2 29.3 + - - +
302A VAL* 3.9 23.5 - - + +
304A PRO* 6.4 1.1 - - + -
305A SER* 6.2 2.7 - - - +
310A VAL* 4.1 15.3 - - + -
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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
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289A VAL 2.9 20.5 + - - +
290A ARG* 3.6 5.8 - - - +
292A ALA* 1.3 76.3 - - - +
294A ARG* 1.3 56.0 + - - +
296A GLU* 3.3 12.4 + - - +
297A GLU* 2.9 27.6 + - - +
26E LEU* 6.0 0.2 - - + -
27E ASN* 3.6 29.3 - - + +
28E VAL* 4.3 14.6 - - + -
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Residues in contact with ARG 294 (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 ARG* 3.0 19.0 + - + +
291A VAL 3.7 3.6 - - - +
293A ALA* 1.3 73.4 - - - +
295A LEU* 1.3 61.3 + - - +
297A GLU* 3.3 37.2 + - - +
298A LEU* 2.9 60.2 + - + +
355A LEU* 3.5 33.9 + - + +
359A ALA* 4.7 10.1 - - - +
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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
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291A VAL* 3.0 20.8 + - + +
292A ALA 3.7 1.1 - - - +
294A ARG* 1.3 75.7 - - - +
296A GLU* 1.3 59.9 + - - +
298A LEU* 3.2 12.7 + - + +
299A GLY 3.2 0.5 + - - -
300A TYR* 3.0 50.5 + - + +
302A VAL* 3.7 12.3 - - + -
310A VAL* 4.2 16.8 - - + -
312A PHE* 3.9 31.6 - - + -
343A THR* 4.8 0.4 - - + -
354A PHE* 3.9 25.6 - - + -
355A LEU* 4.4 5.2 - - + -
358A ALA* 3.7 24.5 - - + -
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Residues in contact with GLU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA* 3.2 15.0 + - - +
293A ALA* 3.7 12.5 - - - +
295A LEU* 1.3 73.8 - - - +
297A GLU* 1.3 66.7 + - - +
299A GLY* 3.0 14.0 + - - -
300A TYR 3.9 12.9 - - - +
302A VAL* 3.6 36.6 + - + +
304A PRO* 6.2 0.3 - - - +
29E ASP* 4.8 9.5 - - - +
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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 ALA 2.9 13.9 + - - +
294A ARG* 3.3 44.5 + - - +
296A GLU* 1.3 75.1 - - - +
298A LEU* 1.3 62.2 + - - +
299A GLY* 3.2 1.7 + - - -
27E ASN* 3.6 29.3 + - - +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 2.9 70.6 + - + +
295A LEU* 3.3 14.6 - - + +
296A GLU 3.2 0.4 - - - -
297A GLU* 1.3 75.8 - - - +
299A GLY* 1.3 58.3 + - - +
300A TYR* 4.0 11.2 - - + -
355A LEU* 4.2 7.2 - - + +
358A ALA* 4.3 10.1 - - + -
359A ALA* 4.1 35.9 - - + +
362A ILE* 3.6 20.4 - - + +
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Residues in contact with GLY 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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296A GLU 3.0 12.9 + - - -
297A GLU 3.2 1.5 - - - -
298A LEU* 1.3 80.0 - - - +
300A TYR* 1.3 65.8 + - - +
301A ALA 4.0 0.2 + - - -
362A ILE* 3.6 10.9 - - - +
405A PO4 4.3 8.7 + - - -
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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