Contacts of the helix formed by residues 324 - 346 (chain A) in PDB entry 3K5N
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 324 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.2 10.5 - - - +
186A GLY* 4.7 9.6 - - - -
187A ASP 5.1 1.6 + - - +
319A ARG* 5.6 6.2 + - - +
320A ARG* 2.8 25.1 + - + +
323A GLU* 1.3 77.9 - - - +
325A LYS* 1.3 64.4 + - - +
326A PRO* 3.3 10.0 - - - +
327A ALA* 2.4 38.7 + - - +
328A LEU 3.5 3.8 + - - -
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A MET* 3.8 17.0 - - + +
181A LEU 3.0 24.5 - - - -
183A PRO* 2.7 33.7 + - - +
185A ASN* 2.6 25.6 + - - +
195A LEU* 5.6 0.2 - - - -
197A TYR* 3.3 22.4 - - + +
320A ARG 3.1 4.2 + - - -
321A PHE* 3.3 44.3 + - - +
322A ALA* 5.3 0.4 + - - +
324A ASP* 1.3 72.2 - - - +
326A PRO* 1.3 59.9 - - + +
328A LEU* 2.7 28.0 + - - +
329A ALA* 2.8 12.6 + - - +
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Residues in contact with PRO 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASN* 2.9 23.1 - - - +
186A GLY* 4.2 0.7 - - - -
187A ASP 3.7 34.3 - - - +
188A ALA* 4.4 7.9 - - + -
191A LEU* 4.3 18.1 - - + +
195A LEU* 4.6 3.6 - - + -
197A TYR* 3.8 7.2 - - - +
324A ASP* 3.4 9.2 - - - +
325A LYS* 1.3 89.4 - - + +
327A ALA* 1.3 55.2 + - - +
329A ALA* 3.5 10.0 + - + +
330A THR* 2.6 35.8 + - - +
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Residues in contact with ALA 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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320A ARG* 3.8 22.3 + - - +
324A ASP* 2.4 29.0 + - - +
326A PRO* 1.3 75.5 - - - +
328A LEU* 1.3 68.5 + - - +
330A THR* 3.5 8.5 - - - +
331A TYR* 2.7 24.9 + - - +
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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
----------------------------------------------------------
158A GLU* 4.5 8.1 - - + -
166A TYR* 4.1 18.4 - - + -
167A CYS* 4.4 5.4 - - - -
180A MET* 3.4 21.5 - - + -
317A ILE* 4.0 25.4 - - + +
320A ARG* 4.1 18.3 - - + +
321A PHE* 3.7 31.2 - - + -
324A ASP 3.5 1.4 + - - -
325A LYS* 2.7 20.1 + - - +
327A ALA* 1.3 81.1 - - - +
329A ALA* 1.3 61.8 + - - +
331A TYR* 2.8 29.6 + - + +
332A ASN* 2.9 13.9 + - - +
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 3.5 21.7 - - + +
180A MET* 3.8 4.2 - - + +
193A PHE* 3.6 18.2 - - + -
195A LEU* 3.4 33.4 - - + -
325A LYS 2.8 8.7 + - - +
326A PRO* 3.7 7.0 - - + +
327A ALA 3.2 0.2 - - - -
328A LEU* 1.3 76.1 - - - +
330A THR* 1.3 59.3 + - - +
332A ASN* 3.2 5.5 - - - +
333A LEU* 2.9 23.7 + - - +
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Residues in contact with THR 330 (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 LEU* 4.0 11.9 - - + -
193A PHE* 3.5 25.3 - - + -
326A PRO 2.6 28.9 - - - +
327A ALA* 3.5 12.8 - - - +
329A ALA* 1.3 72.9 - - - +
331A TYR* 1.3 67.7 + - - +
332A ASN 3.0 0.9 - - - -
333A LEU* 3.8 4.0 - - - +
334A LYS* 3.2 20.6 + - - +
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Residues in contact with TYR 331 (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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158A GLU* 3.6 34.0 + - + -
317A ILE* 4.2 18.7 - - + +
320A ARG* 3.7 29.6 - - - +
327A ALA 2.7 20.9 + - - +
328A LEU* 3.4 13.2 - - + +
330A THR* 1.3 76.8 + - - +
332A ASN* 1.3 66.4 + - - +
334A LYS* 3.4 4.5 + - - +
335A ASN* 2.9 47.3 + - - +
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Residues in contact with ASN 332 (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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156A ASP* 3.7 12.3 + - - +
158A GLU* 3.9 24.0 - - + +
167A CYS* 3.0 29.0 - - - -
168A ILE 4.0 0.6 - - - -
169A GLY* 3.5 24.4 - - - +
178A VAL* 4.3 3.7 - - - +
328A LEU 2.9 10.2 + - - +
329A ALA 3.2 10.5 - - - +
331A TYR* 1.3 82.5 - - - +
333A LEU* 1.3 59.1 + - - +
335A ASN* 2.8 24.9 + - - +
336A CYS* 3.3 17.8 + - - -
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Residues in contact with LEU 333 (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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170A LEU 4.8 2.7 - - - +
171A GLU* 4.1 22.7 - - + -
176A ARG* 4.0 24.5 - - + +
177A ILE 5.1 0.4 - - - +
178A VAL* 4.1 12.8 - - + -
193A PHE* 2.9 52.0 - - + -
329A ALA 2.9 18.3 + - - +
330A THR* 3.7 6.0 + - - -
331A TYR 3.5 0.2 - - - -
332A ASN* 1.3 73.0 + - - +
334A LYS* 1.3 67.6 + - - +
336A CYS* 3.1 14.5 + - + -
337A GLU* 2.9 35.5 + - + +
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Residues in contact with LYS 334 (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 GLU* 3.6 34.0 + - - +
330A THR* 3.2 17.7 + - - +
331A TYR* 3.7 5.8 - - - +
332A ASN 3.1 1.0 - - - -
333A LEU* 1.3 79.1 - - - +
335A ASN* 1.3 65.3 + - - +
337A GLU* 3.1 15.6 + - + +
338A LEU* 2.9 36.9 + - + +
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Residues in contact with ASN 335 (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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156A ASP* 3.5 31.0 + - - +
158A GLU* 3.5 9.5 + - - -
293A LEU* 3.9 16.9 - - + +
331A TYR* 2.9 41.4 + - - +
332A ASN 2.8 12.2 + - - +
334A LYS* 1.3 79.6 - - - +
336A CYS* 1.3 60.2 + - - +
338A LEU* 3.1 19.5 + - - +
339A VAL* 3.2 17.8 + - - +
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Residues in contact with CYS 336 (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 SER* 2.8 20.9 + - - +
155A ILE 5.2 0.4 - - - -
156A ASP* 3.8 14.1 - - - -
169A GLY 3.7 27.4 - - - -
170A LEU 4.5 0.4 - - - -
171A GLU* 3.7 18.6 - - + -
332A ASN* 3.6 23.8 - - - -
333A LEU* 3.1 13.4 + - - +
335A ASN* 1.3 76.2 - - - +
337A GLU* 1.3 54.7 + - - +
339A VAL* 3.3 2.8 + - - -
340A THR* 2.5 36.2 + - - +
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Residues in contact with GLU 337 (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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171A GLU* 3.6 20.4 - - - +
176A ARG* 2.8 39.6 + - - -
333A LEU* 2.9 31.4 + - + +
334A LYS* 3.5 14.9 - - + +
336A CYS* 1.3 74.0 - - - +
338A LEU* 1.3 52.2 - - + +
340A THR* 3.3 1.8 + - - +
341A GLN* 2.5 56.8 + - + +
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Residues in contact with LEU 338 (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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293A LEU* 4.0 27.4 - - + +
294A GLU* 5.8 1.6 - - - +
297A ALA* 3.8 28.5 - - + -
301A LEU* 4.1 10.0 - - + +
303A GLU* 3.9 24.2 - - + +
334A LYS* 2.9 35.1 + - + +
335A ASN* 3.5 12.6 - - - +
337A GLU* 1.3 74.0 - - + +
339A VAL* 1.3 69.1 + - - +
341A GLN* 3.2 9.5 + - - +
342A ILE* 2.9 30.3 + - + +
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER* 3.8 9.2 - - - +
155A ILE 5.5 2.0 - - - +
156A ASP* 5.6 2.9 - - - +
221A ILE* 4.2 3.1 - - + -
222A GLY* 3.9 21.8 - - - +
223A TRP* 3.9 31.4 - - + +
293A LEU* 4.0 12.3 - - + -
335A ASN 3.2 14.4 + - - +
336A CYS* 3.7 7.0 - - - +
338A LEU* 1.3 79.1 - - - +
340A THR* 1.3 61.0 + - - +
342A ILE* 3.1 9.9 - - - +
343A PHE* 2.9 56.8 + - + -
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Residues in contact with THR 340 (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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152A TRP* 4.6 5.6 - - - -
154A SER* 3.3 14.6 - - - -
171A GLU* 2.7 29.4 + - - +
221A ILE* 3.8 20.0 - - - -
336A CYS 2.5 33.4 - - - +
337A GLU 3.6 3.3 + - - +
339A VAL* 1.3 74.2 - - - +
341A GLN* 1.3 66.4 + - - +
343A PHE* 3.1 11.1 + - - +
344A HIS* 3.1 27.4 + - - -
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Residues in contact with GLN 341 (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 LEU* 3.6 30.3 - - + +
303A GLU* 4.7 8.3 + - - -
337A GLU* 2.5 51.7 + - + +
338A LEU* 3.7 10.4 - - - +
340A THR* 1.3 74.8 - - - +
342A ILE* 1.3 57.2 + - - +
344A HIS* 3.1 9.3 + - - +
345A LYS* 2.8 29.9 + - - +
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Residues in contact with ILE 342 (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 TRP* 4.0 28.9 - - + -
281A LEU* 4.2 13.7 - - + -
293A LEU* 3.7 27.1 - - + -
296A VAL* 4.6 4.7 - - + -
297A ALA* 4.1 19.5 - - + +
300A LEU* 4.1 12.3 - - + -
301A LEU* 4.1 12.1 - - + -
338A LEU 2.9 19.7 + - - +
339A VAL 3.1 8.7 - - - +
341A GLN* 1.3 77.6 - - - +
343A PHE* 1.3 61.2 + - + +
345A LYS* 4.4 4.5 - - - +
346A THR* 2.3 43.5 + - + +
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Residues in contact with PHE 343 (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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152A TRP* 3.6 18.8 - + + -
221A ILE* 3.7 27.1 - - + -
223A TRP* 4.6 1.8 - + - -
275A ILE* 3.4 34.1 - - + -
277A GLY* 3.9 25.1 - - - -
280A ALA* 4.8 1.3 - - + -
281A LEU* 6.3 0.7 - - + -
339A VAL* 2.9 47.9 + - + -
340A THR 3.1 9.8 + - - +
342A ILE* 1.3 82.2 - - + +
344A HIS* 1.3 57.5 + - - +
346A THR* 3.2 4.9 + - - -
347A GLU* 3.2 18.9 + - - -
348A ILE* 3.2 37.4 + - + +
349A MET* 3.8 15.1 + - + -
350A PRO* 5.5 0.7 - - - +
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Residues in contact with HIS 344 (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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152A TRP* 3.7 31.2 - + - -
340A THR* 3.1 26.3 + - - -
341A GLN* 3.1 11.2 + - - +
342A ILE 3.0 0.6 - - - -
343A PHE* 1.3 79.1 - - - +
345A LYS* 1.3 65.4 + - - +
347A GLU* 3.1 18.6 + - - +
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Residues in contact with LYS 345 (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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286A TRP* 5.4 2.2 - - + -
300A LEU* 3.3 52.4 + - + -
301A LEU* 4.0 14.7 - - + +
341A GLN 2.8 15.7 + - - +
342A ILE 4.0 0.4 - - - +
344A HIS* 1.3 78.4 - - - +
346A THR* 1.3 62.5 + - + +
347A GLU* 3.3 7.3 + - - +
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Residues in contact with THR 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 4.3 15.8 - - + +
286A TRP* 3.9 40.6 + - + -
300A LEU* 3.9 29.4 - - + -
342A ILE* 2.3 36.9 + - + +
343A PHE* 3.2 10.4 + - - -
345A LYS* 1.3 72.4 - - - +
347A GLU* 1.3 72.2 + - - +
348A ILE* 3.0 11.3 + - - +
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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