Contacts of the helix formed by residues 292 - 313 (chain A) in PDB entry 4X5O
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 ASN 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLY* 3.3 33.6 + - - -
222A ALA* 4.7 7.3 - - - +
223A ILE* 4.0 17.9 - - + +
288A LYS 3.7 8.6 + - - +
289A LEU* 3.1 13.9 + - + +
291A GLN* 1.3 77.7 - - - +
293A LYS* 1.3 63.8 + - - +
294A GLN* 3.3 7.9 + - - +
295A ALA* 2.8 33.2 + - + -
296A LEU* 3.1 26.4 + - - +
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Residues in contact with LYS 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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291A GLN 3.9 3.4 + - - -
292A ASN* 1.3 74.1 - - - +
294A GLN* 1.3 64.2 + - + +
296A LEU* 3.3 11.3 + - - +
297A GLU* 3.3 35.6 + - + +
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Residues in contact with GLN 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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215A ARG* 3.4 41.8 - - + +
218A ASP* 3.5 35.2 + - - +
219A GLY* 4.2 3.9 + - - -
292A ASN* 3.3 10.2 + - - +
293A LYS* 1.3 81.3 - - + +
295A ALA* 1.3 63.7 + - - +
297A GLU* 3.2 18.3 + - - +
298A GLY 3.4 2.4 + - - -
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Residues in contact with ALA 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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215A ARG 4.1 8.2 + - - -
216A ILE* 4.2 12.2 - - + +
219A GLY* 4.5 5.6 - - - -
289A LEU* 3.7 36.8 - - + +
292A ASN* 2.8 28.3 + - + +
294A GLN* 1.3 72.4 - - - +
296A LEU* 1.3 57.3 + - - +
298A GLY* 3.7 0.7 + - - -
299A LEU* 3.1 37.8 + - + +
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Residues in contact with LEU 296 (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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284A LEU* 3.7 28.6 - - + +
289A LEU 3.9 6.7 - - - +
290A SER* 3.3 35.4 - - - +
291A GLN* 4.3 2.5 - - - +
292A ASN 3.1 23.6 + - - +
293A LYS* 3.5 9.6 - - - +
294A GLN 3.1 0.2 - - - -
295A ALA* 1.3 75.8 - - - +
297A GLU* 1.3 61.2 + - + +
299A LEU* 4.0 4.9 - - + +
300A GLY* 3.0 23.2 + - - -
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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
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215A ARG* 3.3 31.9 + - - +
293A LYS* 3.3 27.1 + - + +
294A GLN* 3.2 11.1 + - - +
296A LEU* 1.3 73.9 - - + +
298A GLY* 1.3 56.2 + - - +
300A GLY* 2.9 3.4 + - - -
301A ASP* 2.7 37.1 + - - +
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ASP* 3.7 27.8 - - - +
215A ARG* 3.7 7.2 - - - +
216A ILE* 3.7 13.7 - - - -
294A GLN 3.4 8.0 + - - -
297A GLU* 1.3 79.2 - - - +
299A LEU* 1.3 57.7 + - - +
301A ASP* 3.7 1.8 - - - +
302A LEU* 2.9 34.3 + - - +
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Residues in contact with LEU 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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216A ILE* 3.8 21.9 - - + +
280A VAL* 4.2 19.5 - - + +
283A LEU* 3.8 52.9 - - + +
284A LEU* 3.8 30.6 - - + +
289A LEU* 4.5 13.0 - - + +
295A ALA* 3.1 28.9 + - + +
296A LEU* 4.0 3.6 - - + +
298A GLY* 1.3 73.1 - - - +
300A GLY* 1.3 60.7 + - - +
302A LEU* 3.3 4.0 + - + +
303A LYS* 3.0 30.1 + - - +
320A PHE* 4.6 2.5 - - + -
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Residues in contact with GLY 300 (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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284A LEU* 5.0 4.6 - - - +
296A LEU 3.0 12.5 + - - -
297A GLU* 2.9 6.7 + - - -
299A LEU* 1.3 76.8 - - - +
301A ASP* 1.3 61.3 + - - +
302A LEU 3.2 0.9 + - - -
303A LYS* 3.3 7.6 + - - +
304A LEU* 3.2 22.5 + - - +
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Residues in contact with ASP 301 (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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184A PRO* 4.5 9.4 - - - +
185A MET* 3.5 43.8 - - + +
213A ASP* 4.6 4.9 - - - +
215A ARG* 3.2 32.0 + - - +
297A GLU* 2.7 19.0 + - - +
298A GLY 3.8 4.3 - - - +
300A GLY* 1.3 71.2 - - - +
302A LEU* 1.3 58.0 + - - +
304A LEU* 4.0 4.6 + - - +
305A LEU* 3.2 25.1 + - - +
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Residues in contact with LEU 302 (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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211A VAL* 3.7 18.4 - - + -
212A ASN 5.2 0.2 - - - -
213A ASP* 4.4 10.3 - - + +
216A ILE* 3.6 17.5 - - + -
280A VAL* 4.7 9.2 - - + -
298A GLY 2.9 17.0 + - - +
299A LEU* 3.6 7.2 - - + +
300A GLY 3.1 0.4 - - - -
301A ASP* 1.3 76.7 - - - +
303A LYS* 1.3 60.6 + - - +
304A LEU 3.2 1.1 - - - -
305A LEU* 3.5 27.5 - - + +
306A PHE* 2.9 40.3 + - + -
320A PHE* 3.5 42.0 - - + -
334A VAL* 4.0 12.1 - - + -
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Residues in contact with LYS 303 (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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277A VAL* 4.8 5.9 - - + +
280A VAL* 4.1 19.6 - - + +
281A GLU* 3.2 29.4 + - + +
284A LEU* 4.8 16.8 - - + +
299A LEU 3.0 16.9 + - - +
300A GLY* 3.3 6.9 + - - +
302A LEU* 1.3 76.7 - - - +
304A LEU* 1.3 61.6 + - - +
306A PHE* 3.4 6.3 + - - +
307A GLU* 3.2 22.8 + - - +
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Residues in contact with LEU 304 (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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184A PRO* 4.2 27.6 - - + -
185A MET* 4.2 7.6 - - + -
300A GLY 3.2 12.9 + - - +
301A ASP* 4.1 7.4 - - - +
302A LEU 3.2 0.4 - - - -
303A LYS* 1.3 77.1 - - - +
305A LEU* 1.3 63.9 + - - +
307A GLU* 3.2 30.4 + - - +
308A TYR* 3.2 54.3 + - + +
422B GLU* 6.1 0.2 - - - +
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Residues in contact with LEU 305 (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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185A MET* 4.1 16.4 - - + +
188A ASP 4.0 6.7 - - - +
189A ALA* 3.6 37.7 - - + +
192A LEU* 4.5 9.9 - - + -
211A VAL* 4.8 4.7 - - + -
301A ASP 3.2 18.6 + - - +
302A LEU* 3.5 28.3 - - + +
304A LEU* 1.3 78.2 - - - +
306A PHE* 1.3 61.6 + - + +
308A TYR* 3.5 4.6 + - - +
309A LEU* 3.3 28.7 + - + +
318A ILE* 5.5 1.1 - - + -
334A VAL* 3.7 19.5 - - + -
336A TYR* 3.9 13.7 - - + +
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Residues in contact with PHE 306 (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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211A VAL* 4.9 6.7 - - + -
276A GLY* 3.8 12.3 - - - -
277A VAL* 3.6 42.0 - - + -
280A VAL* 4.1 22.2 - - + -
302A LEU* 2.9 30.3 + - + +
303A LYS 3.6 6.5 - - - +
305A LEU* 1.3 77.2 - - + +
307A GLU* 1.3 63.6 + - - +
309A LEU* 3.2 15.9 + - + +
310A THR* 3.0 17.8 + - - -
315A ASP* 4.1 20.7 - - - +
318A ILE* 4.0 42.8 - - + -
320A PHE* 4.1 17.7 - + + -
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Residues in contact with GLU 307 (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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303A LYS* 3.2 10.9 + - - +
304A LEU* 3.2 27.9 + - - +
306A PHE* 1.3 79.2 - - - +
308A TYR* 1.3 66.5 + - + +
310A THR* 3.5 18.5 + - - -
311A LEU* 3.6 14.2 + - + +
422B GLU* 2.8 32.4 - - - +
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Residues in contact with TYR 308 (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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185A MET* 3.9 34.5 - - + -
186A ILE* 4.2 13.6 - - + +
189A ALA* 3.8 15.3 - - + -
304A LEU* 3.2 48.8 + - + +
305A LEU* 3.8 6.7 - - - +
306A PHE 3.2 0.6 - - - -
307A GLU* 1.3 82.1 - - + +
309A LEU* 1.3 59.4 + - - +
311A LEU* 3.2 15.3 + - + +
312A PHE* 3.1 31.7 + - + -
421B LEU* 3.7 23.5 - - + +
422B GLU* 4.7 15.0 - - - -
425B LEU* 3.7 26.6 - - + +
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Residues in contact with LEU 309 (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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189A ALA* 4.0 13.7 - - + +
192A LEU* 3.6 34.8 - - + -
193A LYS 4.9 0.4 - - - +
305A LEU* 3.3 18.8 + - + +
306A PHE* 3.2 13.5 + - + +
308A TYR* 1.3 74.6 - - - +
310A THR* 1.3 61.3 + - - +
312A PHE* 3.0 11.9 + - + +
313A GLY 2.8 24.4 + - - -
314A ILE* 3.0 30.1 + - + +
315A ASP* 4.0 14.1 - - - +
318A ILE* 3.5 41.5 - - + -
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Residues in contact with THR 310 (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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306A PHE 3.0 15.6 + - - -
307A GLU* 3.6 10.2 + - - -
308A TYR 3.3 0.2 - - - -
309A LEU* 1.3 77.8 - - - +
311A LEU* 1.3 63.4 + - - +
313A GLY* 3.2 13.0 + - - -
315A ASP* 3.6 33.9 + - + +
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Residues in contact with LEU 311 (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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307A GLU* 3.6 18.2 - - + +
308A TYR* 3.2 12.5 + - + +
309A LEU 3.2 0.2 - - - -
310A THR* 1.3 78.9 - - + +
312A PHE* 1.3 62.6 + - - +
313A GLY 3.6 0.2 + - - -
422B GLU* 3.6 52.5 - - + +
425B LEU* 4.2 18.2 - - + -
426B LYS* 3.7 34.9 - - + +
429B SER* 3.6 12.5 + - - -
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Residues in contact with PHE 312 (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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186A ILE* 5.4 2.2 - - + -
189A ALA* 3.4 42.8 - - + -
190A GLU* 3.8 11.0 - - + -
193A LYS* 3.1 44.4 + - + -
308A TYR 3.1 14.2 + - - -
309A LEU* 3.0 17.3 + - + +
311A LEU* 1.3 78.9 - - - +
313A GLY* 1.3 60.0 + - - +
314A ILE* 4.0 11.7 - - + -
425B LEU* 3.6 51.6 - - + -
428B VAL* 5.9 0.7 - - + -
429B SER* 4.0 15.3 + - - -
432B TRP* 4.3 21.5 - + - -
433B ASP* 4.4 3.1 - - - +
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Residues in contact with GLY 313 (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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193A LYS* 5.0 0.3 + - - -
309A LEU 2.8 4.7 + - - -
310A THR* 3.2 12.3 + - - -
311A LEU 3.3 0.6 + - - -
312A PHE* 1.3 79.8 - - - +
314A ILE* 1.3 68.1 + - - +
315A ASP* 3.5 3.8 - - - -
316A ASP* 4.8 5.4 - - - +
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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