Contacts of the helix formed by residues 301 - 313 (chain X) in PDB entry 5CQL
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 HIS 301 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288X MET* 4.4 4.3 - - + -
297X GLU 5.8 7.9 - - - -
299X VAL 3.5 5.3 + - - +
300X TRP* 1.3 74.0 - - - +
302X ASP* 1.3 67.5 + - + +
304X SER* 3.0 22.6 + - - -
305X HIS* 3.1 19.3 - - - -
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Residues in contact with ASP 302 (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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267X GLY* 4.7 12.6 - - - +
284X CYS* 5.4 0.7 - - - -
288X MET* 3.9 17.8 - - + +
300X TRP 3.0 2.0 + - - -
301X HIS* 1.3 80.3 - - + +
303X ALA* 1.3 57.0 + - - +
305X HIS* 3.4 2.4 + - - +
306X LEU* 2.9 30.1 + - - +
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Residues in contact with ALA 303 (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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264X TYR* 4.0 19.5 - - + +
265X TYR 4.8 0.9 - - - +
266X MET* 5.5 0.9 - - - -
267X GLY* 3.9 30.8 - - - +
300X TRP* 3.1 16.2 + - + +
302X ASP* 1.3 78.4 - - - +
304X SER* 1.3 62.0 + - - +
306X LEU* 3.8 1.7 - - - +
307X ASN* 2.8 34.9 + - - +
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Residues in contact with SER 304 (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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245X THR 5.3 1.6 - - - -
246X TYR* 4.8 3.1 - - - +
247X GLU* 3.9 35.2 + - - +
254X ALA* 3.8 11.4 - - - +
256X ILE* 5.1 0.9 - - - +
264X TYR* 5.6 1.3 - - - -
299X VAL* 4.6 4.4 + - - -
300X TRP* 3.9 19.0 + - - +
301X HIS* 3.0 19.7 + - - -
303X ALA* 1.3 78.7 - - - +
305X HIS* 1.3 63.7 + - - +
307X ASN* 3.3 6.1 + - - +
308X LYS* 3.1 26.9 + - - +
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Residues in contact with HIS 305 (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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253X GLN 5.0 0.2 - - - -
254X ALA* 3.7 20.3 - - + +
284X CYS* 3.9 21.3 - - + -
287X ALA* 3.8 20.3 - - + +
288X MET* 3.6 48.1 - - + +
291X ASP* 3.7 24.8 + - - +
301X HIS* 3.1 25.2 + - - -
302X ASP 3.4 6.1 + - - +
304X SER* 1.3 82.6 + - - +
306X LEU* 1.3 65.6 + - - +
308X LYS* 3.3 4.6 + - - +
309X TYR* 3.0 23.0 + - - +
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Residues in contact with LEU 306 (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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230X GLY* 5.9 0.4 - - - -
265X TYR* 4.5 6.3 - - + +
266X MET 3.2 27.8 - - - +
267X GLY* 3.8 10.5 - - - +
270X PHE* 4.1 27.4 - - + -
280X LEU* 3.7 35.9 - - + -
284X CYS* 4.1 7.9 - - - -
302X ASP 2.9 18.9 + - - +
303X ALA* 3.8 4.0 - - - +
305X HIS* 1.3 76.4 - - - +
307X ASN* 1.3 59.1 + - - +
309X TYR* 3.2 3.1 + - + +
310X LEU* 2.9 49.3 + - + +
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Residues in contact with ASN 307 (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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246X TYR* 3.5 35.5 - - + -
256X ILE* 4.0 4.3 - - + +
263X PHE 3.5 1.0 - - - +
264X TYR* 3.6 13.4 - - - -
265X TYR* 2.9 61.9 + - - +
303X ALA* 2.8 29.4 + - - +
304X SER* 3.7 5.2 - - - +
306X LEU* 1.3 80.5 - - - +
308X LYS* 1.3 56.3 + - - +
310X LEU* 3.5 1.0 + - - +
311X LEU* 3.0 28.9 + - - +
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Residues in contact with LYS 308 (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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253X GLN 2.8 33.1 + - - +
254X ALA* 3.9 14.4 - - - +
255X TYR* 2.8 32.1 + - - +
256X ILE* 3.9 13.8 - - + +
304X SER 3.1 14.2 + - - +
305X HIS* 3.7 7.6 - - - +
306X LEU 3.3 0.2 - - - -
307X ASN* 1.3 73.7 - - - +
309X TYR* 1.3 65.0 + - - +
311X LEU* 3.3 4.2 + - + +
312X ARG* 3.1 64.6 + - + +
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Residues in contact with TYR 309 (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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228X LEU* 4.0 11.2 - - + -
276X GLU* 4.6 7.4 + - - -
279X ARG* 3.8 23.5 - - - +
280X LEU* 3.7 42.3 + - + -
283X ALA* 3.6 32.5 - - + -
284X CYS* 4.6 7.2 - - - -
305X HIS 3.0 13.5 + - - +
306X LEU* 3.5 10.5 - - - +
308X LYS* 1.3 74.7 - - - +
310X LEU* 1.3 58.7 + - + +
312X ARG* 3.1 3.8 + - - -
313X HIS* 2.7 88.4 + + + +
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Residues in contact with LEU 310 (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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228X LEU* 3.8 38.1 - - + -
229X PHE 4.9 2.5 - - - +
230X GLY* 4.1 16.2 - - - +
262X ASP* 4.8 0.9 - - - +
265X TYR* 3.6 50.8 + - + -
270X PHE* 5.5 0.2 - - + -
280X LEU* 4.5 2.9 - - + -
306X LEU* 2.9 37.9 + - + +
307X ASN 4.2 0.4 - - - +
309X TYR* 1.3 82.4 - - + +
311X LEU* 1.3 65.2 + - - +
313X HIS 3.3 14.6 - - - +
314X LYS* 3.6 13.0 - - - +
315X PRO* 3.6 14.5 - - + +
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Residues in contact with LEU 311 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246X TYR* 5.4 1.1 - - - +
256X ILE* 3.7 39.5 - - + -
260X GLU* 3.7 19.7 - - + +
261X GLY* 3.8 28.5 - - - +
262X ASP* 3.9 9.9 - - - +
265X TYR* 5.0 1.9 - - - -
307X ASN 3.0 17.9 + - - +
308X LYS* 3.5 6.5 - - + +
309X TYR 3.2 0.2 - - - -
310X LEU* 1.3 77.0 - - - +
312X ARG* 1.3 75.6 + - - +
314X LYS* 2.8 41.2 + - - +
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Residues in contact with ARG 312 (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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255X TYR 5.1 2.8 + - - -
257X PRO* 5.3 3.0 - - - +
260X GLU* 3.1 30.1 + - - -
308X LYS* 3.1 49.4 + - + +
309X TYR* 3.8 4.0 - - - +
311X LEU* 1.3 90.9 - - - +
313X HIS* 1.3 74.7 + - + +
314X LYS* 3.9 3.0 + - - +
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Residues in contact with HIS 313 (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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228X LEU* 3.8 12.3 - - + +
283X ALA* 5.8 0.2 - - + -
309X TYR* 2.7 71.1 + + + +
310X LEU* 3.3 16.4 - - - +
312X ARG* 1.3 87.2 - - + +
314X LYS* 1.3 67.3 + - - +
315X PRO* 3.4 1.7 - - - +
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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
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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