Contacts of the helix formed by residues 295 - 314 (chain A) in PDB entry 4XK8
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 TRP 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ARG* 3.2 55.4 - - + +
285A GLY 3.1 29.5 + - - -
286A GLY 4.1 4.2 + - - -
287A LEU 3.7 9.8 + - - -
288A ASP* 3.1 34.5 - - + -
289A PRO* 3.5 35.0 - - + -
290A LEU* 5.5 2.5 - - + -
294A LEU* 1.3 70.4 - - - +
296A LEU* 1.3 61.9 + - - +
297A THR* 3.7 13.7 - - + +
298A ASP* 3.0 26.3 + - - +
299A ILE* 3.0 27.4 + - - +
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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
----------------------------------------------------------
155A ALA* 4.2 15.7 - - + +
222A GLN* 4.9 6.9 - - - +
226A SER* 4.4 13.0 - - - +
227A LEU* 3.6 19.0 - - + +
230A ASN* 3.7 44.0 - - + +
234A ASN* 5.1 8.7 - - - +
288A ASP* 5.4 5.6 - - - +
291A THR* 5.6 7.6 - - + -
294A LEU 4.2 9.6 - - - +
295A TRP* 1.3 73.6 - - - +
297A THR* 1.3 57.6 + - - +
299A ILE* 3.3 15.9 + - + +
300A ALA* 2.9 28.8 + - - +
381A PRO 6.1 0.4 - - - +
383A PRO* 5.6 11.0 - - + -
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Residues in contact with THR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.7 17.5 - - + -
259A TYR* 4.6 7.6 - - + +
279A ASP 4.2 7.2 - - - +
280A PHE* 3.3 37.8 - - - +
282A THR* 2.6 32.7 + - + +
284A ARG* 4.0 10.1 + - - +
295A TRP* 3.7 11.5 - - + +
296A LEU* 1.3 74.8 - - - +
298A ASP* 1.3 59.4 + - - +
300A ALA* 3.4 1.0 + - - +
301A HIS* 3.0 29.8 + - - +
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Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A THR* 2.6 44.4 + - - -
283A PHE* 4.2 2.2 - - - -
284A ARG* 3.1 8.4 + - - -
285A GLY* 2.8 30.8 + - - -
286A GLY 5.4 0.2 - - - +
294A LEU* 5.8 2.0 - - + -
295A TRP* 3.0 27.7 + - + +
297A THR* 1.3 80.5 + - - +
299A ILE* 1.3 59.4 + - + +
301A HIS* 3.5 1.7 + - - +
302A HIS* 2.9 28.5 + - - +
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Residues in contact with ILE 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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222A GLN* 3.3 26.7 - - - +
294A LEU* 4.1 28.5 - - + +
295A TRP 3.0 15.3 + - - +
296A LEU* 3.6 17.0 - - + +
297A THR 3.2 0.4 - - - -
298A ASP* 1.3 76.0 - - + +
300A ALA* 1.3 58.9 + - - +
302A HIS* 3.2 8.3 + - + +
303A HIS* 2.9 50.9 + - + -
381A PRO* 3.5 29.2 - - + +
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Residues in contact with ALA 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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219A ALA* 4.1 8.3 - - + +
222A GLN* 3.3 26.2 + - + +
223A VAL* 4.9 6.3 - - + +
227A LEU* 4.4 15.5 - - + -
281A LEU* 4.3 13.5 - - + -
296A LEU 2.9 17.0 + - - +
297A THR 3.4 4.0 + - - +
299A ILE* 1.3 72.7 - - - +
301A HIS* 1.3 66.3 + - - +
303A HIS* 3.2 3.3 + - - +
304A LEU* 2.9 23.4 + - - +
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Residues in contact with HIS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 3.9 39.4 - - + +
282A THR 3.0 26.7 + - - +
283A PHE* 4.4 17.8 - + + -
297A THR 3.0 18.3 + - - +
298A ASP 3.7 2.5 - - - +
300A ALA* 1.3 75.4 - - - +
302A HIS* 1.3 63.8 + - - +
304A LEU* 3.2 8.9 + - + +
305A ALA* 2.9 31.2 + - + +
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Residues in contact with HIS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ASP 2.9 18.9 + - - +
299A ILE* 3.2 10.3 - - + +
300A ALA 3.2 0.2 - - - -
301A HIS* 1.3 78.4 - - - +
303A HIS* 1.3 80.1 + + - +
305A ALA* 3.4 4.6 + - - +
306A ILE* 2.9 59.7 + - + +
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Residues in contact with HIS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A SER* 3.5 35.4 + - - +
218A TRP* 3.6 28.7 - + - -
219A ALA* 3.9 7.6 - - + -
222A GLN* 2.9 18.1 + - - +
299A ILE* 2.9 37.5 + - + +
300A ALA 3.8 3.6 - - - +
302A HIS* 1.3 88.6 + + - +
304A LEU* 1.3 61.1 + - - +
306A ILE* 4.2 4.5 - - + -
307A ALA* 2.9 29.3 + - - +
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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
----------------------------------------------------------
216A LEU* 4.1 22.4 - - + -
219A ALA* 4.0 11.6 - - + +
269A PHE* 6.0 9.0 - - + -
281A LEU* 3.8 33.2 - - + -
300A ALA 2.9 13.0 + - - +
301A HIS* 3.5 13.7 - - + +
303A HIS* 1.3 74.4 - - - +
305A ALA* 1.3 65.3 + - - +
307A ALA* 3.1 5.8 + - - +
308A ILE* 3.0 38.0 + - + +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A HIS* 2.9 25.0 + - + +
302A HIS* 3.8 4.9 - - - +
304A LEU* 1.3 76.8 - - - +
306A ILE* 1.3 64.1 + - + +
308A ILE* 3.1 11.5 + - - +
309A LEU* 2.9 22.8 + - - +
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Residues in contact with ILE 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 LEU* 5.4 0.7 - - + +
215A SER* 3.6 16.8 - - - +
302A HIS* 2.9 48.8 + - + +
303A HIS* 3.8 7.0 - - + +
305A ALA* 1.3 75.5 - - + +
307A ALA* 1.3 64.7 + - - +
309A LEU* 3.2 19.1 + - + +
310A PHE* 2.9 49.7 + - + -
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Residues in contact with ALA 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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212A GLY* 3.5 17.0 - - - +
215A SER* 3.3 15.2 + - - +
216A LEU* 3.6 28.7 - - + +
303A HIS 2.9 19.4 + - - +
304A LEU 3.3 6.3 - - - +
306A ILE* 1.3 77.0 - - - +
308A ILE* 1.3 62.1 + - - +
310A PHE* 3.5 1.0 + - - +
311A LEU* 2.9 32.3 + - + +
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Residues in contact with ILE 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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216A LEU* 5.3 3.6 - - + -
269A PHE* 6.5 1.3 - - + -
304A LEU* 3.0 33.1 + - + +
305A ALA* 3.1 8.7 + - - +
307A ALA* 1.3 76.0 - - + +
309A LEU* 1.3 63.2 + - - +
311A LEU* 3.2 13.4 + - + +
312A ILE* 3.0 42.7 + - + +
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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
----------------------------------------------------------
305A ALA 2.9 11.7 + - - +
306A ILE* 3.5 24.2 - - + +
308A ILE* 1.3 76.6 - - - +
310A PHE* 1.3 67.4 + - + +
312A ILE* 3.2 21.6 - - + +
313A ALA* 2.9 32.0 + - + +
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Residues in contact with PHE 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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207A LEU* 3.2 46.5 - - + +
208A ALA* 3.7 0.2 - - - -
211A LEU* 3.5 38.8 - - + -
212A GLY* 3.7 12.3 - - - -
306A ILE* 2.9 53.1 + - + +
309A LEU* 1.3 82.5 - - + +
311A LEU* 1.3 60.1 + - - +
313A ALA* 3.2 6.8 + - + +
314A GLY 2.9 24.1 + - - -
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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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208A ALA* 3.5 31.3 - - + +
212A GLY* 4.3 5.6 - - - +
213A LEU* 4.0 17.0 - - + -
216A LEU* 4.3 23.8 - - + -
307A ALA* 2.9 30.0 + - + +
308A ILE* 3.2 14.3 + - + +
310A PHE* 1.3 79.9 - - - +
312A ILE* 1.3 62.5 + - + +
314A GLY* 3.5 3.8 + - - -
315A HIS* 2.9 31.3 + - + -
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Residues in contact with ILE 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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308A ILE* 3.0 26.7 + - + +
309A LEU* 3.2 26.2 - - + +
311A LEU* 1.3 75.1 - - + +
313A ALA* 1.3 69.5 + - - +
315A HIS* 3.3 21.5 + - - +
316A MET* 4.5 0.7 + - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.5 25.6 - - + +
309A LEU* 2.9 23.8 + - + +
310A PHE* 3.2 11.6 + - + +
312A ILE* 1.3 76.0 - - + +
314A GLY* 1.3 57.5 + - - +
315A HIS 3.0 10.6 + - - -
316A MET* 3.5 21.0 + - - +
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Residues in contact with GLY 314 (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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204A ASN* 3.1 40.8 + - - +
207A LEU* 3.6 20.6 - - - +
208A ALA* 3.8 11.7 - - - +
310A PHE 2.9 9.9 + - - -
311A LEU 3.5 0.6 + - - -
312A ILE 3.2 0.6 - - - -
313A ALA* 1.3 74.9 - - - +
315A HIS* 1.3 66.6 + - - +
316A MET 3.5 1.1 - - - -
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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
------------------------------------------------------------
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