Contacts of the helix formed by residues 267 - 280 (chain X) in PDB entry 2EXC
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 ASP 267 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227X ARG* 6.0 4.3 - - - +
265X GLY 4.5 1.1 - - - -
266X ARG* 1.3 102.5 + - - +
268X TYR* 1.3 63.6 + - - +
269X ILE* 3.1 26.4 - - - +
270X ASP* 3.0 18.0 + - - +
271X GLN* 2.8 31.1 + - - +
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Residues in contact with TYR 268 (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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227X ARG* 3.5 39.2 + - + +
230X ARG* 2.5 37.2 + - - -
234X VAL* 4.3 10.3 - - - +
235X ILE* 3.7 57.8 - - + +
267X ASP* 1.3 74.4 - - - +
269X ILE* 1.3 60.6 + - + +
271X GLN* 4.1 9.0 - - - -
272X TRP* 3.2 25.1 + - - +
297X TYR* 6.0 0.2 - - - -
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Residues in contact with ILE 269 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266X ARG* 6.2 1.6 - - - +
267X ASP* 3.1 18.8 + - - +
268X TYR* 1.3 76.8 - - + +
270X ASP* 1.3 67.5 + - + +
272X TRP* 3.3 4.2 + - - +
273X ASN* 3.2 28.9 + - - +
297X TYR* 3.4 39.7 + - + +
301X ARG* 4.0 13.2 - - - +
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Residues in contact with ASP 270 (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 PRO 4.0 0.9 - - - +
265X GLY* 3.5 2.4 - - - -
266X ARG* 3.0 49.7 + - + +
267X ASP* 3.0 20.7 + - - +
269X ILE* 1.3 79.2 - - + +
271X GLN* 1.3 63.8 + - - +
273X ASN* 3.2 18.2 + - - +
274X LYS* 3.1 48.7 + - - +
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Residues in contact with GLN 271 (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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227X ARG* 2.6 34.2 + - + +
228X TYR* 3.2 30.1 + - + +
230X ARG 4.5 2.0 + - - -
235X ILE* 3.8 28.5 - - + +
247X TRP* 5.6 0.2 - - - +
263X PHE* 3.5 30.7 + - - +
265X GLY* 4.0 15.8 - - - +
267X ASP 2.8 15.3 + - - +
268X TYR* 4.0 9.3 - - - +
270X ASP* 1.3 77.4 - - - +
272X TRP* 1.3 62.7 + - - +
274X LYS* 3.0 16.5 + - - +
275X VAL* 3.0 19.8 + - - +
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Residues in contact with TRP 272 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232X PRO* 4.2 18.4 - - + -
235X ILE* 4.5 16.4 - - + +
236X LEU* 3.9 32.8 - - + -
268X TYR 3.2 17.2 + - - +
269X ILE 3.3 3.6 + - - +
271X GLN* 1.3 78.0 - - - +
273X ASN* 1.3 64.1 + - - +
275X VAL* 3.0 32.6 + - + +
276X ILE* 3.2 43.5 + - + +
282X PRO* 4.1 12.3 - - + -
286X PHE* 4.3 1.6 - + - -
297X TYR* 4.2 21.3 - + + +
298X VAL* 4.0 34.0 + - + +
301X ARG* 4.3 19.3 - - + +
342X ILE* 4.1 20.0 - - + -
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Residues in contact with ASN 273 (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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269X ILE* 3.2 18.6 + - - +
270X ASP* 3.2 20.6 + - - +
272X TRP* 1.3 77.9 - - - +
274X LYS* 1.3 57.5 + - + +
276X ILE* 3.6 11.0 - - - +
277X GLU* 2.8 42.7 + - - +
297X TYR* 4.5 0.5 + - - -
301X ARG* 3.0 38.1 + - - +
302X PRO* 5.9 0.7 - - - +
304X TYR* 5.1 1.3 - - - -
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Residues in contact with LYS 274 (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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262X LEU 5.2 0.2 - - - +
263X PHE* 4.1 14.8 - - + -
264X PRO* 2.9 44.6 + - + +
270X ASP* 3.1 35.9 + - - +
271X GLN* 3.0 11.0 + - - +
273X ASN* 1.3 78.9 - - + +
275X VAL* 1.3 63.6 + - - +
277X GLU* 3.7 20.1 + - - +
278X GLN* 3.0 35.7 + - - +
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Residues in contact with VAL 275 (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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232X PRO* 5.2 1.3 - - + -
235X ILE* 4.6 14.4 - - + -
247X TRP* 3.8 39.0 - - + -
263X PHE* 3.9 21.3 - - + -
271X GLN* 3.0 20.2 + - - +
272X TRP* 3.0 24.9 + - + +
274X LYS* 1.3 80.0 - - - +
276X ILE* 1.3 57.1 + - - +
278X GLN* 3.2 3.6 + - - +
279X LEU* 3.0 29.4 + - + +
342X ILE* 3.8 22.9 - - + -
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Residues in contact with ILE 276 (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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272X TRP* 3.3 54.5 - - + +
273X ASN* 3.6 14.1 - - - +
275X VAL* 1.3 74.0 - - - +
277X GLU* 1.3 59.9 + - - +
278X GLN 2.9 7.3 + - - -
280X GLY* 2.9 50.3 + - - +
281X THR* 4.3 6.3 - - + +
282X PRO* 3.9 9.6 - - + -
301X ARG* 4.5 16.4 - - + -
302X PRO* 3.8 23.6 - - + +
304X TYR* 3.3 21.8 - - + +
342X ILE* 4.4 3.1 - - + -
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Residues in contact with GLU 277 (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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273X ASN* 2.8 33.0 + - - +
274X LYS* 3.7 24.2 - - - +
276X ILE* 1.3 74.2 - - - +
278X GLN* 1.3 65.3 + - + +
304X TYR* 3.8 43.6 + - + +
306X GLY* 5.1 3.5 - - - -
307X LEU* 5.1 6.2 - - - +
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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
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258X ARG* 3.5 30.4 + - - +
262X LEU 3.8 10.1 + - - -
263X PHE* 3.8 21.5 - - + -
274X LYS* 3.0 26.3 + - - +
275X VAL 3.2 6.0 + - - +
276X ILE 2.9 4.0 - - - -
277X GLU* 1.3 89.5 + - + +
279X LEU* 1.3 63.5 + - + +
280X GLY 3.4 0.7 - - - -
306X GLY* 3.4 1.4 - - - -
307X LEU* 2.9 45.3 + - + +
312X LEU* 3.7 18.5 - - + +
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Residues in contact with LEU 279 (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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247X TRP* 3.4 31.6 - - + -
263X PHE* 4.7 9.0 - - + -
275X VAL* 3.0 17.3 + - + +
278X GLN* 1.3 78.7 - - + +
280X GLY* 1.3 60.9 + - - +
281X THR 5.1 0.5 - - - +
305X ALA 4.0 8.1 - - - +
306X GLY* 4.4 0.6 - - - -
307X LEU 4.9 3.0 - - - +
309X PHE* 4.2 11.2 - - + -
312X LEU* 3.7 28.3 - - + -
340X LEU* 3.3 36.3 - - + +
342X ILE* 4.1 19.0 - - + +
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Residues in contact with GLY 280 (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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276X ILE* 2.9 25.6 + - - -
278X GLN 3.4 2.0 + - - -
279X LEU* 1.3 82.1 - - - +
281X THR* 1.3 68.2 + - - -
282X PRO* 3.4 2.9 - - - +
304X TYR 3.1 13.2 - - - -
305X ALA 3.7 12.6 - - - -
306X GLY 3.9 0.2 - - - -
342X ILE* 3.6 14.9 - - - +
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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