Contacts of the helix formed by residues 313 - 329 (chain A) in PDB entry 1EX0
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 GLN 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER 3.0 24.7 + - - +
279A PHE* 3.7 27.6 - - + +
283A TYR* 2.6 33.9 + - - -
289A PRO* 3.5 11.6 - - + +
312A GLY* 1.3 72.6 - - - +
314A CYS* 1.3 69.3 + - - +
315A TRP* 3.2 22.9 - - + -
316A VAL* 3.2 11.0 + - - +
317A PHE* 3.1 26.4 + - - -
559A PHE* 3.8 2.6 - - - -
560A TYR* 3.2 28.4 - - - +
600A GLU* 3.3 10.3 + - - +
601A GLN* 4.1 0.5 - - - +
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Residues in contact with CYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 4.5 3.0 - - - -
313A GLN* 1.3 78.3 - - - +
315A TRP* 1.3 62.7 + - - +
317A PHE* 3.5 3.7 + - - +
318A ALA* 3.0 28.2 + - - +
370A TRP* 3.9 3.4 - - + -
372A TYR* 4.7 0.4 - - - -
373A HIS* 3.3 21.1 - - + +
374A CYS* 3.3 35.0 - - - +
398A THR* 3.4 26.2 + - + +
560A TYR* 3.1 38.6 + - - +
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Residues in contact with TRP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 3.9 25.6 - - + +
223A ARG* 3.2 37.5 - - - +
225A TRP* 4.0 19.0 - + - -
289A PRO* 3.8 28.2 + - + -
290A SER* 3.8 10.8 - - - -
292A TRP 5.4 0.8 + - - -
313A GLN* 3.2 39.5 - - + -
314A CYS* 1.3 81.1 - - - +
316A VAL* 1.3 68.8 + - + +
318A ALA* 3.8 2.6 - - - +
319A GLY* 2.8 28.4 + - - -
334A ILE* 4.8 0.4 - - - +
372A TYR* 3.9 12.6 - - - -
374A CYS* 3.9 26.9 - - - -
560A TYR* 3.8 13.7 - + - -
601A GLN* 3.6 20.9 - - - -
716A HIS* 4.1 1.3 - + - -
718A TYR* 4.6 0.4 + - - -
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TRP* 3.9 13.5 - - + -
275A LEU* 3.9 12.1 - - + -
289A PRO* 3.5 28.0 - - + +
292A TRP* 3.9 11.2 - - + -
298A ILE* 3.8 28.0 - - + -
312A GLY* 4.1 5.6 - - - -
313A GLN 3.2 22.6 + - - +
315A TRP* 1.3 91.9 - - + +
317A PHE* 1.3 65.5 + - - +
319A GLY* 3.8 0.3 - - - -
320A VAL* 3.1 24.8 + - - +
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Residues in contact with PHE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A VAL* 3.6 17.5 - - + +
267A ASN* 3.9 18.6 - - + -
275A LEU* 3.7 37.9 - - + -
277A GLY* 3.8 24.2 - - - -
279A PHE* 5.3 5.2 - + - -
312A GLY* 3.9 18.2 - - - -
313A GLN* 3.1 16.5 + - - -
314A CYS 3.7 3.8 - - - +
316A VAL* 1.3 77.8 - - - +
318A ALA* 1.3 57.2 - - - +
320A VAL* 3.8 2.1 - - - +
321A PHE* 2.9 30.7 + - - +
397A SER* 3.3 20.4 - - - +
398A THR* 3.3 42.4 - - + +
399A PRO* 4.6 1.6 - - + -
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Residues in contact with ALA 318 (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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314A CYS 3.0 18.6 + - - +
315A TRP 4.0 3.4 - - - +
317A PHE* 1.3 72.9 - - - +
319A GLY* 1.3 60.7 + - - +
322A ASN* 2.9 27.4 + - - +
334A ILE* 3.7 23.3 - - + -
374A CYS* 4.3 5.8 - - + -
375A TRP* 4.3 9.6 - - - +
376A ASN* 2.9 33.7 + - - +
397A SER* 4.4 0.6 + - - -
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Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TRP* 3.5 22.2 - - - -
227A TYR* 3.8 2.4 - - - -
295A SER* 3.1 12.5 + - - -
315A TRP 2.8 21.4 + - - -
316A VAL 3.4 0.9 + - - -
317A PHE 3.3 0.2 - - - -
318A ALA* 1.3 72.8 - - - +
320A VAL* 1.3 60.1 + - - +
322A ASN* 3.1 5.4 + - - +
323A THR* 3.0 19.2 + - - -
334A ILE* 3.8 13.0 - - - +
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Residues in contact with VAL 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A TRP* 4.7 1.1 - - + -
266A VAL* 5.0 9.4 - - + -
274A VAL* 4.3 15.0 - - + -
275A LEU* 3.9 11.9 - - + -
295A SER* 3.4 19.5 - - - +
298A ILE* 3.9 30.5 - - + -
299A LEU* 3.8 28.9 - - + +
316A VAL* 3.1 17.3 + - + +
317A PHE 3.8 3.4 - - - +
319A GLY* 1.3 72.3 - - - +
321A PHE* 1.3 67.4 + - - +
323A THR* 3.3 4.3 + - - +
324A PHE* 3.1 21.3 + - + +
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Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A SER* 3.6 13.0 - - - -
262A GLY 3.7 4.3 - - - -
263A SER* 3.3 40.6 - - - -
266A VAL* 4.0 16.5 - - + +
317A PHE 2.9 19.3 + - - +
320A VAL* 1.3 77.1 - - - +
322A ASN* 1.3 59.8 + - - +
324A PHE* 3.4 25.7 + + + -
325A LEU* 3.0 56.0 + - + +
376A ASN* 3.6 27.8 - - + +
395A VAL* 3.5 27.8 - - + -
397A SER* 4.7 4.7 - - - +
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Residues in contact with ASN 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TYR* 3.2 33.5 + - + -
318A ALA 2.9 18.6 + - - +
319A GLY 3.5 4.7 - - - +
321A PHE* 1.3 74.0 - - - +
323A THR* 1.3 59.2 + - - +
325A LEU* 3.4 2.0 + - - +
326A ARG* 3.0 59.5 + - - +
332A ALA* 3.4 11.2 - - - +
333A ARG 3.3 32.4 + - - +
334A ILE* 3.9 8.7 - - + -
376A ASN* 3.5 8.1 + - - +
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Residues in contact with THR 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TYR* 2.7 39.2 + - - +
229A GLN* 4.1 7.8 - - - +
234A ILE* 3.8 18.4 - - + -
295A SER* 2.6 25.6 + - - -
299A LEU* 3.5 24.7 - - + -
319A GLY 3.0 4.1 + - - -
320A VAL 3.4 8.7 - - - -
322A ASN* 1.3 73.3 - - - +
324A PHE* 1.3 66.5 + - - +
326A ARG* 3.3 1.6 + - - +
327A CYS* 2.8 28.1 + - - +
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Residues in contact with PHE 324 (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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238A CYS* 3.6 48.2 - - + -
241A VAL* 4.1 21.5 - - + -
242A MET* 4.0 16.2 - - + -
258A VAL* 3.8 18.4 - - + -
262A GLY* 4.0 21.1 - - - -
299A LEU* 5.1 3.3 - - + +
320A VAL* 3.1 11.3 + - + +
321A PHE* 3.4 30.1 - + + +
323A THR* 1.3 81.1 - - - +
325A LEU* 1.3 69.8 + - + +
327A CYS* 3.6 1.4 - - - +
328A LEU* 3.2 51.5 + - + +
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Residues in contact with LEU 325 (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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259A SER* 3.8 17.0 - - - +
321A PHE* 3.0 55.2 + - + +
322A ASN* 4.0 0.4 - - - +
323A THR 3.4 0.2 - - - -
324A PHE* 1.3 85.3 - - + +
326A ARG* 1.3 62.0 + - - +
328A LEU* 3.2 4.8 + - - +
329A GLY 3.1 5.0 + - - -
330A ILE* 2.8 64.1 + - + +
332A ALA* 3.7 15.9 - - + -
376A ASN* 4.9 4.7 - - + -
377A GLU 4.7 2.2 - - - +
378A ALA* 3.7 22.9 - - + -
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Residues in contact with ARG 326 (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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69A TYR* 4.2 4.3 + - - -
77A ARG* 5.4 0.2 + - - -
203A GLU* 3.2 28.5 + - - -
204A TYR* 3.1 34.9 + - - +
205A VAL* 3.8 13.5 - - - +
207A ASN* 3.0 22.5 + - - +
209A ILE 4.7 1.0 + - - -
227A TYR* 3.2 25.5 + - - -
229A GLN* 3.6 32.2 - - - +
230A PHE* 5.5 0.7 - - - -
322A ASN* 3.0 36.3 + - - +
323A THR 4.2 0.9 - - - +
325A LEU* 1.3 75.8 - - - +
327A CYS* 1.3 61.5 + - - +
329A GLY* 3.0 13.8 + - - +
330A ILE 3.8 4.5 - - - +
332A ALA* 2.6 33.3 + - + -
333A ARG* 4.0 6.3 - - - +
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Residues in contact with CYS 327 (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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69A TYR* 2.7 28.5 + - - -
183A LEU* 3.9 4.9 - - - +
229A GLN* 3.4 35.8 - - + +
234A ILE* 4.0 3.4 - - + -
235A LEU* 3.4 41.6 - - - +
238A CYS* 3.8 15.0 - - - -
323A THR 2.8 18.9 + - - +
324A PHE 3.6 4.3 - - - +
326A ARG* 1.3 77.4 - - - +
328A LEU* 1.3 58.7 + - - +
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Residues in contact with LEU 328 (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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154A VAL* 4.3 10.3 - - + +
183A LEU* 3.4 13.0 - - + +
184A PHE* 3.0 41.2 + - + -
235A LEU* 4.2 10.3 - - + -
238A CYS* 4.0 20.6 - - + -
239A LEU* 4.1 20.9 - - + -
242A MET* 4.0 11.2 - - + -
258A VAL* 3.8 16.2 - - + -
324A PHE* 3.2 55.1 + - + +
325A LEU* 4.0 4.9 - - - +
326A ARG 3.2 0.2 - - - -
327A CYS* 1.3 75.6 - - - +
329A GLY* 1.3 59.0 + - - +
330A ILE* 4.9 1.8 - - + +
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Residues in contact with GLY 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 3.7 21.1 - - - -
184A PHE* 3.4 13.0 - - - +
186A PRO* 3.1 30.7 - - - +
193A VAL* 3.7 1.0 - - - +
205A VAL* 4.4 4.5 - - - -
326A ARG 3.0 15.4 + - - -
327A CYS 3.2 0.6 - - - -
328A LEU* 1.3 78.8 - - - +
330A ILE* 1.3 60.5 + - - +
331A PRO 3.8 0.2 - - - -
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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
------------------------------------------------------------
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