Contacts of the helix formed by residues 274 - 294 (chain X) in PDB entry 5CQM
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 VAL 274 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200X PHE* 3.6 22.4 - - + +
201X LEU* 3.7 22.7 - - + -
204X VAL* 3.5 38.6 - - + +
205X ASP 3.5 9.6 + - - +
206X TYR 4.5 3.6 - - - +
207X LEU* 4.5 12.3 - - + -
272X GLY 3.8 0.2 + - - -
273X SER* 1.3 74.0 - - - +
275X GLN* 1.3 63.7 + - - +
277X VAL* 3.3 0.9 + - - +
278X GLN* 2.9 51.9 + - + +
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Residues in contact with GLN 275 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201X LEU* 4.4 13.5 - - + +
273X SER* 3.2 7.8 + - - +
274X VAL* 1.3 79.7 - - - +
276X GLU* 1.3 60.4 + - - +
278X GLN* 3.4 6.2 + - - +
279X ARG* 3.0 73.3 + - + +
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Residues in contact with GLU 276 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227X PRO* 3.1 38.4 - - + +
228X LEU* 4.3 20.9 - - + +
273X SER* 3.1 16.6 + - - +
275X GLN* 1.3 79.4 + - + +
277X VAL* 1.3 58.9 + - - +
279X ARG* 2.8 40.0 + - - +
280X LEU* 3.0 27.9 + - - +
309X TYR* 4.6 8.7 + - - -
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Residues in contact with VAL 277 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207X LEU* 3.8 30.3 - - + +
209X CYS* 3.9 18.8 - - - -
228X LEU* 5.3 2.0 - - + -
270X PHE* 4.4 6.3 - - + -
271X GLY* 3.5 13.7 - - - +
272X GLY* 3.4 27.8 - - - +
273X SER 2.9 20.3 + - - +
274X VAL 3.9 2.9 - - - +
276X GLU* 1.3 76.2 - - - +
278X GLN* 1.3 59.1 + - + +
280X LEU* 3.2 6.1 + - - +
281X THR* 2.9 39.7 + - + +
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Residues in contact with GLN 278 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198X ARG 4.5 11.5 + - - +
200X PHE* 3.9 20.6 - - + +
201X LEU* 4.0 21.3 - - - +
207X LEU* 5.1 6.7 - - + -
274X VAL* 2.9 42.6 + - + +
275X GLN* 3.9 5.3 - - - +
277X VAL* 1.3 78.3 - - + +
279X ARG* 1.3 56.0 + - - +
281X THR* 3.2 7.7 + - - +
282X ARG* 2.9 55.3 + - - +
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Residues in contact with ARG 279 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275X GLN* 3.0 54.7 + - + +
276X GLU* 2.8 43.9 + - - +
277X VAL 3.3 0.2 - - - -
278X GLN* 1.3 75.2 - - - +
280X LEU* 1.3 63.7 + - - +
282X ARG* 3.7 22.3 - - - +
283X ALA* 3.0 25.1 + - - +
309X TYR* 3.7 15.5 + - - +
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Residues in contact with LEU 280 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228X LEU* 4.0 20.9 - - + -
229X PHE 5.9 0.2 - - - +
270X PHE* 4.1 24.0 - - + -
276X GLU 3.0 14.7 + - - +
277X VAL* 3.6 8.7 - - - +
279X ARG* 1.3 77.9 - - - +
281X THR* 1.3 76.0 + - + +
283X ALA* 3.2 3.1 + - - +
284X CYS* 3.0 35.4 + - + +
306X LEU* 3.7 28.0 - - + -
309X TYR* 3.6 38.3 + - + -
310X LEU* 4.3 4.3 - - + -
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Residues in contact with THR 281 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209X CYS* 5.9 0.9 - - - -
270X PHE* 4.6 10.3 - - + -
277X VAL* 2.9 27.0 + - + +
278X GLN* 3.2 14.2 + - - +
280X LEU* 1.3 88.7 - - + +
282X ARG* 1.3 59.9 + - - +
284X CYS* 3.9 4.6 - - - +
285X HIS* 2.9 31.6 + - - +
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Residues in contact with ARG 282 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278X GLN* 2.9 42.3 + - - +
279X ARG* 3.7 33.8 - - - +
281X THR* 1.3 78.4 + - - +
283X ALA* 1.3 63.5 + - - +
285X HIS* 3.3 5.5 + - - +
286X GLN* 3.0 49.7 + - + +
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Residues in contact with ALA 283 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279X ARG 3.0 18.7 + - - +
280X LEU 3.7 1.1 - - - +
282X ARG* 1.3 75.9 - - - +
284X CYS* 1.3 62.8 + - - +
286X GLN* 3.4 9.7 + - - +
287X ALA* 3.0 24.9 + - - +
309X TYR* 3.6 29.2 - - + -
313X HIS* 5.7 0.4 - - + -
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Residues in contact with CYS 284 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280X LEU* 3.0 34.2 + - + +
281X THR* 3.9 6.7 - - - +
283X ALA* 1.3 75.7 - - - +
285X HIS* 1.3 57.8 + - - +
287X ALA* 3.3 4.0 + - - +
288X MET* 2.9 42.2 + - - +
302X ASP 5.4 0.7 - - - -
305X HIS* 3.8 41.9 + - + -
306X LEU* 3.9 5.6 - - - -
309X TYR* 4.5 8.1 - - - -
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Residues in contact with HIS 285 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281X THR 2.9 18.5 + - - +
282X ARG* 3.7 6.5 - - - +
284X CYS* 1.3 77.8 - - - +
286X GLN* 1.3 63.7 + - + +
288X MET* 3.4 15.1 + - + +
289X MET* 3.0 63.2 + - + +
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Residues in contact with GLN 286 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253X GLN* 5.4 0.4 - - - -
282X ARG* 3.0 40.3 + - + +
283X ALA* 3.9 7.4 - - - +
285X HIS* 1.3 79.7 - - + +
287X ALA* 1.3 57.2 + - - +
289X MET* 3.2 14.5 + - - +
290X VAL* 3.0 34.1 + - + +
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Residues in contact with ALA 287 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253X GLN* 3.8 32.7 - - + +
283X ALA 3.0 17.4 + - - +
284X CYS* 3.7 3.4 - - - +
286X GLN* 1.3 76.3 - - - +
288X MET* 1.3 57.9 + - - +
290X VAL* 3.3 3.1 + - - +
291X ASP* 2.9 32.1 + - - +
305X HIS* 3.7 21.8 - - + +
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Residues in contact with MET 288 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284X CYS* 2.9 32.2 + - - +
285X HIS* 3.6 15.3 - - + +
287X ALA* 1.3 74.5 - - - +
289X MET* 1.3 59.2 + - - +
291X ASP* 3.3 4.4 + - - +
292X GLN* 3.0 44.5 + - - +
301X HIS* 5.5 9.4 - - + +
302X ASP* 5.7 5.8 - - - +
305X HIS* 3.5 35.0 - - + +
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Residues in contact with MET 289 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285X HIS* 3.0 59.1 + - + +
286X GLN* 3.2 15.7 + - - +
288X MET* 1.3 75.4 - - + +
290X VAL* 1.3 59.2 + - + +
292X GLN* 3.2 16.6 + - - +
293X ALA* 2.9 29.0 + - - +
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Residues in contact with VAL 290 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253X GLN* 3.7 30.5 - - + +
286X GLN* 3.0 16.3 + - + +
287X ALA 3.6 7.4 - - - +
288X MET 3.3 0.2 - - - -
289X MET* 1.3 74.4 - - + +
291X ASP* 1.3 65.1 + - - +
293X ALA* 3.3 8.4 + - + +
294X ASN* 3.0 37.8 + - - +
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Residues in contact with ASP 291 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251X GLN 4.2 1.0 - - - +
252X SER* 2.6 31.2 + - - -
253X GLN* 2.8 29.4 + - - +
287X ALA 2.9 18.1 + - - +
288X MET* 3.3 7.6 + - - +
290X VAL* 1.3 76.1 - - - +
292X GLN* 1.3 61.8 + - - +
294X ASN* 3.0 9.2 + - - +
295X GLY 3.0 0.2 + - - -
296X ILE* 2.9 51.1 + - + +
297X GLU* 5.1 6.0 - - - -
305X HIS* 3.5 16.8 + - + +
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Residues in contact with GLN 292 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288X MET* 3.0 29.6 + - - +
289X MET* 3.2 19.1 + - - +
291X ASP* 1.3 75.9 - - - +
293X ALA* 1.3 61.9 + - - +
295X GLY* 3.0 14.4 + - - -
296X ILE 3.9 5.8 - - - +
297X GLU* 3.9 22.5 + - - +
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Residues in contact with ALA 293 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289X MET 2.9 12.9 + - - +
290X VAL* 3.5 11.7 - - + +
292X GLN* 1.3 78.4 - - - +
294X ASN* 1.3 66.9 + - - +
295X GLY 3.3 1.1 + - - -
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Residues in contact with ASN 294 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251X GLN 4.7 7.1 - - - +
290X VAL* 3.0 31.9 + - - +
291X ASP* 3.0 4.1 + - - +
293X ALA* 1.3 83.9 + - - +
295X GLY* 1.3 59.7 + - - +
296X ILE* 3.4 22.3 + - + +
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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