Contacts of the helix formed by residues 211 - 231 (chain B) in PDB entry 5KJH
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 GLU 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B SER 3.7 13.1 + - - +
208B VAL* 3.3 33.2 + - - +
209B LEU 3.1 1.2 - - - -
210B ALA* 1.3 76.1 - - - +
212B GLU* 1.4 60.1 + - - +
213B VAL 3.3 0.2 - - - -
214B PRO* 3.4 15.6 - - + +
215B GLN* 3.1 38.3 + - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B VAL 4.5 0.6 + - - +
209B LEU* 3.0 31.8 + - - +
211B GLU* 1.4 75.6 - - - +
213B VAL* 1.4 55.6 + - - +
215B GLN* 3.6 11.8 + - - +
216B ASN* 2.8 52.6 + - - +
380B TYR* 4.0 13.4 - - + -
383B PRO* 5.9 1.6 - - - +
384B TRP* 3.0 17.9 + - - -
387B LYS* 2.8 30.7 + - - -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA* 3.1 15.6 + - + +
212B GLU* 1.4 75.4 - - - +
214B PRO* 1.4 61.3 - - + +
216B ASN* 4.0 1.2 - - - +
217B HIS* 3.0 31.3 + - + +
373B TYR* 5.2 6.3 - - + +
376B THR* 3.8 28.5 - - + -
377B LEU* 3.8 16.8 - - + -
380B TYR* 3.9 20.6 + - + -
384B TRP* 3.8 29.8 - - + -
448B PHE* 5.6 0.4 - - + -
455B ARG* 5.5 6.3 - - - +
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Residues in contact with PRO 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A SER* 3.1 54.0 - - - +
506A ASN* 6.1 0.7 - - + -
210B ALA 3.3 13.9 - - - +
211B GLU* 3.4 13.2 - - + +
213B VAL* 1.4 91.8 - - + +
215B GLN* 1.3 58.7 + - + +
216B ASN 3.5 0.2 - - - -
218B SER* 3.1 17.5 + - - -
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Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A LYS* 3.7 33.8 + - + +
211B GLU* 3.1 36.4 + - - +
212B GLU* 3.6 12.4 - - - +
213B VAL 3.2 0.6 - - - -
214B PRO* 1.3 78.4 - - + +
216B ASN* 1.4 66.6 + - - +
218B SER* 3.6 4.9 + - - -
219B ARG* 3.2 48.8 + - - +
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Residues in contact with ASN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLU* 2.8 30.3 + - - +
213B VAL 4.0 0.2 - - - +
215B GLN* 1.4 70.8 - - - +
217B HIS* 1.4 60.1 + - - +
219B ARG* 3.2 16.5 + - - +
220B LEU* 2.9 30.2 + - - +
380B TYR* 2.8 39.4 + - - +
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Residues in contact with HIS 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A THR* 4.7 7.6 - - + +
314A ARG 3.5 22.0 - - - -
315A LEU* 2.8 30.4 + - + -
504A LEU 3.3 24.7 - - - -
505A SER 3.5 21.3 - - - +
507A PRO* 3.8 21.0 - - + +
213B VAL* 3.0 20.3 + - + +
214B PRO 3.9 0.4 - - - +
216B ASN* 1.4 76.3 - - - +
218B SER* 1.3 55.6 + - - +
220B LEU* 3.2 12.0 + - + +
221B VAL* 3.0 44.3 + - + +
376B THR* 6.0 4.2 - - + +
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A ALA* 4.7 6.2 - - - +
503A ASP* 5.3 2.1 + - - -
504A LEU* 3.5 16.1 + - - +
505A SER* 3.8 16.8 + - - -
214B PRO 3.1 18.8 + - - -
215B GLN* 3.8 5.6 - - - -
217B HIS* 1.3 75.2 - - - +
219B ARG* 1.4 57.6 + - - +
221B VAL* 4.2 0.2 - - - -
222B ASN* 2.9 50.3 + - - +
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Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ALA* 4.8 17.0 - - - +
371A LYS* 6.3 0.6 - - - +
215B GLN* 3.2 38.2 + - - +
216B ASN* 3.2 19.3 + - - +
218B SER* 1.4 73.0 - - - +
220B LEU* 1.3 65.6 + - - +
222B ASN* 3.9 2.9 - - - +
223B PHE* 3.0 25.9 + - - +
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ARG* 3.5 32.3 - - - +
313A THR* 4.8 9.6 - - + -
315A LEU* 3.9 20.6 - - + -
216B ASN 2.9 16.7 + - - +
217B HIS* 3.6 12.8 - - - +
219B ARG* 1.3 76.4 - - - +
221B VAL* 1.3 63.2 + - - +
223B PHE* 3.1 9.3 + - + +
224B LEU* 2.9 44.5 + - + +
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Residues in contact with VAL 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LEU* 4.2 16.6 - - + -
315A LEU* 3.5 35.9 - - + +
316A ALA* 4.5 4.0 - - + -
504A LEU* 3.8 28.3 - - + +
217B HIS* 3.0 46.3 + - + +
218B SER 4.3 1.8 - - - +
220B LEU* 1.3 71.1 - - - +
222B ASN* 1.3 56.6 + - - +
224B LEU* 3.2 9.3 + - - +
225B LEU* 2.9 35.4 + - + +
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Residues in contact with ASN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A PHE* 3.3 33.2 + - - +
361A GLY* 3.4 7.9 + - - -
364A ALA* 3.6 23.6 - - + +
502A TYR 5.7 0.6 + - - -
504A LEU* 3.8 17.8 - - - +
218B SER* 2.9 40.3 + - - +
219B ARG* 4.1 3.6 - - - +
221B VAL* 1.3 70.4 - - - +
223B PHE* 1.3 65.7 + - - +
225B LEU* 3.4 6.9 + - - +
226B GLU* 3.1 33.9 + - - +
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ARG 3.0 18.9 + - - +
220B LEU* 3.5 9.2 - - + +
222B ASN* 1.3 75.6 - - - +
224B LEU* 1.4 75.8 + - + +
226B GLU* 3.4 11.8 + - + +
227B GLU* 3.0 64.0 + - + +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LEU* 4.0 24.0 - - + -
269A ARG* 3.8 26.2 - - - +
315A LEU* 3.8 28.9 - - + -
220B LEU* 2.9 41.2 + - + +
221B VAL* 3.6 7.0 - - + +
223B PHE* 1.4 90.6 - - + +
225B LEU* 1.4 55.9 + - - +
227B GLU* 3.5 5.5 + - + +
228B THR* 2.8 36.8 + - - -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A TYR* 4.1 12.8 + - + +
254A LEU* 4.3 4.7 - - + -
267A LEU* 3.8 27.1 - - + -
318A PHE* 6.2 0.7 - - + -
357A LEU* 4.1 31.0 - - + +
360A PHE* 3.8 26.0 - - + -
504A LEU* 3.6 31.2 - - + -
221B VAL* 2.9 22.2 + - + +
222B ASN* 3.8 8.1 - - - +
223B PHE 3.4 0.2 - - - -
224B LEU* 1.4 73.3 - - - +
226B GLU* 1.3 55.4 + - + +
228B THR* 3.3 5.2 + - - -
229B GLU* 2.8 35.5 + - - +
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A GLY* 3.9 27.6 - - - +
365A ARG* 4.6 14.5 + - - -
222B ASN* 3.1 22.6 + - - +
223B PHE* 3.8 8.2 - - + +
224B LEU 3.4 0.2 - - - -
225B LEU* 1.3 74.4 - - + +
227B GLU* 1.3 59.3 - - - +
229B GLU* 3.4 13.4 + - - +
230B LYS* 3.1 40.4 + - + +
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 3.0 56.9 + - + +
224B LEU* 3.9 7.6 - - + +
226B GLU* 1.3 73.4 - - - +
228B THR* 1.4 64.6 + - - +
230B LYS* 3.2 33.6 + - - +
231B ARG* 3.2 41.0 + - - +
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Residues in contact with THR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A TYR* 3.5 55.8 + - + +
252A GLY* 3.7 11.9 - - - +
253A ASP 4.9 2.1 + - - -
254A LEU* 3.6 16.3 - - - +
335A HIS* 3.5 6.5 + - + -
224B LEU 2.8 22.9 + - - -
225B LEU 3.3 4.7 + - - -
227B GLU* 1.4 73.2 - - - +
229B GLU* 1.4 64.8 + - - +
231B ARG* 3.1 15.5 + - - +
232B ALA 3.4 8.7 + - - -
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A TYR* 4.2 6.2 + - - -
335A HIS* 4.3 4.3 - - + -
336A VAL 5.5 0.3 - - - +
337A PRO* 5.3 2.1 - - - +
339A LYS 4.1 7.9 - - - +
340A HIS* 3.9 11.1 - - - -
341A PRO* 3.3 38.4 - - + +
358A ALA* 3.9 20.3 - - - +
225B LEU 2.8 20.8 + - - +
226B GLU* 3.8 15.1 - - - +
228B THR* 1.4 72.7 - - - +
230B LYS* 1.3 62.2 + - + +
231B ARG 3.4 0.2 + - - -
232B ALA* 3.4 17.7 + - - +
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A PRO* 6.0 1.6 - - - +
226B GLU* 3.1 25.6 + - + +
227B GLU* 3.2 35.2 + - - +
228B THR 3.3 0.2 - - - -
229B GLU* 1.3 76.5 - - + +
231B ARG* 1.3 61.4 + - + +
232B ALA 3.3 4.7 + - - +
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Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ASP* 5.4 1.2 - - - +
253A ASP* 5.9 1.0 + - - -
275A SER* 5.6 2.0 + - - -
276A ASP* 2.8 43.1 + - - -
335A HIS* 5.2 1.1 - - - -
227B GLU* 3.2 27.3 + - - +
228B THR* 3.1 10.1 + - - +
230B LYS* 1.3 82.3 - - + +
232B ALA* 1.4 63.7 + - - +
233B PRO* 3.5 5.2 - - - +
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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
------------------------------------------------------------
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