Contacts of the helix formed by residues 299 - 321 (chain A) in PDB entry 5JNQ
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 SER 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A GLY 3.7 3.0 + - - -
298A TRP* 1.3 75.8 - - - +
300A GLU* 1.4 65.8 + - - +
301A THR* 3.6 18.2 - - - -
302A ARG* 3.0 35.8 + - - +
303A VAL* 3.1 13.2 + - - +
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Residues in contact with GLU 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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177A LEU* 3.4 39.1 - - + +
178A ASP* 3.6 26.2 + - + +
223A TYR* 3.9 33.6 - - + -
294A GLU* 4.4 14.9 + - - +
298A TRP 3.9 1.2 + - - -
299A SER* 1.4 70.2 - - - +
301A THR* 1.4 57.7 + - + +
303A VAL* 3.5 5.1 + - - +
304A VAL* 3.2 33.2 + - + +
401A TUM 4.5 3.8 - - - +
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Residues in contact with THR 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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223A TYR* 4.7 23.1 - - + -
299A SER* 3.6 12.8 - - - -
300A GLU* 1.4 74.8 - - + +
302A ARG* 1.4 58.5 + - - -
304A VAL* 3.4 9.0 + - + +
305A ALA* 2.9 30.2 + - - +
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Residues in contact with ARG 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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298A TRP* 4.3 17.7 - - + -
299A SER* 3.0 35.2 + - - +
301A THR* 1.4 75.0 + - - +
303A VAL* 1.4 58.6 + - - +
305A ALA* 3.3 6.1 + - - +
306A VAL* 2.8 53.1 + - - +
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Residues in contact with VAL 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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177A LEU* 3.8 10.1 - - + -
180A LEU* 4.7 2.5 - - + -
290A HIS* 3.7 31.4 - - + +
293A PHE* 4.0 9.2 - - + -
294A GLU* 4.2 10.3 - - + -
298A TRP* 3.8 30.7 - - + -
299A SER 3.1 13.1 + - - +
300A GLU 3.7 7.0 - - - +
302A ARG* 1.4 73.0 - - - +
304A VAL* 1.4 61.9 + - - +
307A PHE* 3.0 56.3 + - + +
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Residues in contact with VAL 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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177A LEU* 4.4 7.6 - - + -
178A ASP 3.1 23.1 - - - +
179A GLY* 3.8 24.9 - - - +
180A LEU* 4.0 23.2 - - + +
183A SER* 3.9 12.6 - - - +
184A VAL* 5.3 0.2 - - - +
222A VAL* 6.1 4.0 - - + -
300A GLU* 3.2 19.8 + - + +
301A THR* 3.7 10.1 - - + +
302A ARG 3.3 0.2 - - - -
303A VAL* 1.4 75.0 - - - +
305A ALA* 1.3 60.3 + - - +
307A PHE* 4.1 1.6 - - - +
308A ALA* 3.2 23.8 + - - +
402A PLM 5.8 2.9 - - + -
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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
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301A THR 2.9 18.7 + - - +
302A ARG* 3.3 7.6 + - - +
304A VAL* 1.3 73.5 - - - +
306A VAL* 1.3 61.1 + - + +
308A ALA* 3.3 5.3 + - - +
309A ILE* 2.9 47.4 + - + +
402A PLM 4.7 10.8 - - + -
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Residues in contact with VAL 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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298A TRP* 3.7 35.9 - - + -
302A ARG* 2.8 36.4 + - - +
303A VAL 4.1 1.6 - - - +
305A ALA* 1.3 72.7 - - + +
307A PHE* 1.3 60.8 + - + +
309A ILE* 4.0 7.8 - - + +
310A VAL* 3.0 35.4 + - + +
403A PLM 4.3 23.1 - - + -
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Residues in contact with PHE 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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180A LEU* 3.7 25.1 - - + -
184A VAL* 4.1 6.5 - - + -
260A ILE* 3.6 36.3 - - + +
264A GLU* 3.4 22.4 - - + -
289A ILE* 3.9 22.0 - - + -
290A HIS* 4.0 15.3 - - + -
293A PHE* 3.9 20.2 - + - -
298A TRP* 5.1 1.1 - + - -
303A VAL* 3.0 38.8 + - + +
304A VAL 4.1 0.4 - - - +
306A VAL* 1.3 86.1 - - + +
308A ALA* 1.3 51.2 + - - +
310A VAL* 3.9 0.8 - - - +
311A THR* 2.7 36.3 + - - -
403A PLM 4.3 13.0 - - + -
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Residues in contact with ALA 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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183A SER* 4.3 13.7 - - - -
184A VAL* 4.2 4.7 - - + +
187A LEU* 3.3 26.3 - - + +
304A VAL 3.2 18.1 + - - +
305A ALA 3.3 3.8 + - - +
307A PHE* 1.3 73.3 - - - +
309A ILE* 1.4 59.1 + - - +
311A THR* 3.3 4.6 + - - -
312A ALA* 3.0 25.2 + - - +
402A PLM 3.8 26.7 - - + -
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Residues in contact with ILE 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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305A ALA* 2.9 33.4 + - + +
306A VAL* 4.0 8.5 - - + +
308A ALA* 1.4 71.3 - - - +
310A VAL* 1.4 67.2 + - + +
312A ALA* 3.3 8.1 + - - +
313A ILE* 3.1 33.7 + - + +
402A PLM 4.5 18.2 - - + -
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Residues in contact with VAL 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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259A LEU* 4.9 4.9 - - + -
260A ILE* 3.7 23.1 - - + -
306A VAL* 3.0 25.1 + - + +
307A PHE 3.9 2.9 - - - +
309A ILE* 1.4 73.9 - - + +
311A THR* 1.4 66.2 + - - +
313A ILE* 3.2 8.2 + - - +
314A LEU* 3.0 44.3 + - + +
403A PLM 4.2 24.2 - - + -
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Residues in contact with THR 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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184A VAL* 3.5 32.0 - - + +
187A LEU* 3.9 12.6 - - + -
188A VAL* 3.9 8.3 - - + -
257A ILE 3.9 20.8 + - - +
260A ILE* 3.5 15.9 - - - +
307A PHE 2.7 21.6 + - - -
308A ALA* 3.4 11.0 - - - -
310A VAL* 1.4 75.1 - - - +
312A ALA* 1.3 56.2 + - - +
314A LEU* 3.4 7.9 + - - +
315A CYS* 2.9 37.4 + - - -
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Residues in contact with ALA 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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187A LEU* 4.2 21.5 - - + +
308A ALA 3.0 13.8 + - - +
309A ILE* 3.3 12.8 + - - +
311A THR* 1.3 75.5 - - - +
313A ILE* 1.4 61.3 + - + +
315A CYS* 3.3 8.4 + - - +
316A MET* 3.2 40.4 + - + +
402A PLM 4.2 19.2 - - + +
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Residues in contact with ILE 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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309A ILE* 3.1 31.5 + - + +
310A VAL* 3.7 6.3 - - - +
312A ALA* 1.4 73.6 - - + +
314A LEU* 1.3 61.5 + - + +
316A MET* 3.3 29.1 + - + +
317A VAL* 3.0 35.0 + - + +
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Residues in contact with LEU 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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256A VAL* 3.4 43.1 - - + +
257A ILE* 5.2 0.4 - - - -
259A LEU* 3.7 28.9 - - + -
260A ILE* 5.8 0.7 - - + +
310A VAL* 3.0 39.2 + - + +
311A THR* 3.9 7.0 - - - +
313A ILE* 1.3 77.1 - - + +
315A CYS* 1.4 54.2 + - - +
317A VAL* 3.6 13.4 - - + +
318A ALA* 2.8 33.5 + - - +
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Residues in contact with CYS 315 (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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187A LEU 3.9 22.2 - - - -
188A VAL* 4.5 1.8 - - - -
191A PHE* 3.4 31.6 - - + -
257A ILE* 4.1 16.8 - - - -
311A THR* 2.9 38.1 + - - +
312A ALA* 3.3 6.9 + - - +
314A LEU* 1.4 74.3 - - - +
316A MET* 1.3 58.9 + - - +
318A ALA* 3.5 3.5 + - - -
319A TYR* 3.0 24.1 + - - +
402A PLM 3.8 19.5 - - + -
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Residues in contact with MET 316 (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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312A ALA* 3.2 29.5 + - + +
313A ILE* 3.3 28.5 + - + +
315A CYS* 1.3 75.2 - - - +
317A VAL* 1.3 63.6 + - + +
319A TYR* 3.4 6.2 + - - +
320A LEU* 3.2 28.1 + - + +
402A PLM 3.8 45.1 - - + -
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Residues in contact with VAL 317 (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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140A PHE* 3.2 37.9 - - + -
256A VAL* 4.7 8.5 - - + -
313A ILE* 3.0 29.3 + - + +
314A LEU* 3.3 19.0 + - + +
316A MET* 1.3 73.7 - - + +
318A ALA* 1.3 64.0 + - - +
320A LEU* 3.2 24.0 + - + +
321A GLY 3.4 0.3 + - - -
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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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139A PRO* 6.4 0.2 - - - -
140A PHE* 5.0 3.6 - - - -
191A PHE* 3.9 3.1 - - + -
253A PHE* 3.4 21.9 - - + -
256A VAL* 3.8 12.6 - - + -
257A ILE* 3.0 37.0 - - + -
314A LEU 2.8 16.1 + - - +
315A CYS 3.5 4.9 - - - +
316A MET 3.4 0.2 - - - -
317A VAL* 1.3 76.3 - - - +
319A TYR* 1.4 56.2 + - - +
321A GLY* 2.9 22.6 + - - +
322A LEU* 4.1 0.7 - - - +
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Residues in contact with TYR 319 (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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191A PHE* 3.8 3.3 - + + -
194A ILE* 4.0 26.3 - - + +
195A VAL* 4.4 15.5 - - + -
315A CYS 3.0 14.5 + - - +
316A MET* 3.5 10.8 - - - +
317A VAL 3.3 0.2 - - - -
318A ALA* 1.4 68.9 - - - +
320A LEU* 1.4 61.8 + - + +
321A GLY 3.0 8.5 + - - -
322A LEU* 3.0 41.4 + - + +
323A GLY 4.2 1.7 + - - -
402A PLM 4.0 21.1 - - + -
404A BOG 5.4 8.8 + - - +
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Residues in contact with LEU 320 (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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140A PHE* 3.8 15.7 - - + -
316A MET* 3.2 16.1 + - + +
317A VAL* 3.2 21.1 + - + +
319A TYR* 1.4 79.1 - - + +
321A GLY* 1.3 54.9 - - - +
322A LEU 3.2 4.7 + - - -
323A GLY* 3.8 9.7 + - - +
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Residues in contact with GLY 321 (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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137A LEU* 5.0 1.2 - - - +
139A PRO 2.6 31.4 - - - +
140A PHE* 3.7 22.0 - - - -
143A GLY 5.1 1.1 + - - -
253A PHE* 3.2 19.9 - - - -
317A VAL 3.4 4.4 + - - -
318A ALA 2.9 14.2 + - - -
320A LEU* 1.3 74.7 - - - +
322A LEU* 1.4 56.6 + - - +
323A GLY 3.9 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
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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