Contacts of the helix formed by residues 304 - 321 (chain K) in PDB entry 6R1U
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 PRO 304 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287K ASP 5.5 2.9 - - - +
288K VAL* 6.1 0.2 - - - -
289K MET* 3.6 27.1 - - + +
294K LEU* 6.3 0.4 - - + -
300K TYR* 3.1 22.4 - - + +
301K SER* 4.6 5.6 - - - +
302K ARG 4.1 4.5 - - - +
303K ASP* 1.3 87.7 - - - +
305K THR* 1.3 66.3 + - - +
306K MET 3.4 2.2 - - - -
307K TYR* 3.2 4.5 + - - +
308K LEU* 2.9 37.3 + - + +
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Residues in contact with THR 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208K PRO* 3.6 20.6 - - + +
209K PRO 3.6 22.4 - - - +
210K LEU* 4.0 9.2 - - + -
226K ASP 4.9 6.3 + - - +
229K GLY* 3.8 19.5 - - - +
303K ASP* 2.5 25.9 + - - -
304K PRO* 1.3 80.8 - - - +
306K MET* 1.3 64.0 + - - +
308K LEU* 3.4 7.0 + - - +
309K ALA* 3.1 20.8 + - - +
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Residues in contact with MET 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202K TYR* 3.6 27.2 + - + +
209K PRO* 4.0 24.5 - - + -
300K TYR* 3.2 35.0 - - + +
303K ASP 4.7 2.0 + - - -
304K PRO 3.4 0.4 - - - -
305K THR* 1.3 81.2 - - - +
307K TYR* 1.3 63.4 + - - +
309K ALA* 3.5 5.4 + - - +
310K LEU* 3.2 30.7 + - + +
344K ARG* 3.9 33.4 - - + +
345K CYS* 3.9 34.8 - - - -
348K GLU* 4.2 3.8 - - + -
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Residues in contact with TYR 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289K MET* 3.8 20.4 - - + -
293K GLU* 2.8 49.2 + - + +
297K PHE* 3.5 27.8 - + - -
300K TYR* 3.9 31.0 - + + -
304K PRO 3.2 8.3 + - - +
306K MET* 1.3 79.3 - - - +
308K LEU* 1.3 66.7 + - + +
310K LEU* 3.0 3.3 + - - +
311K ARG* 2.7 50.1 + - + +
352K ILE* 3.6 36.3 - - + +
355K PHE* 3.9 14.7 - - - -
356K MET* 5.0 0.7 - - - +
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Residues in contact with LEU 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227K CYS 4.7 6.7 - - - +
228K VAL* 4.6 6.5 - - - +
286K PRO 3.2 22.2 - - - +
287K ASP* 3.4 32.3 - - - +
288K VAL* 3.9 0.9 - - - +
289K MET* 3.4 33.2 - - + +
304K PRO* 2.9 32.1 + - + +
305K THR* 3.8 5.4 - - - +
307K TYR* 1.3 82.9 - - + +
309K ALA* 1.3 58.3 + - - +
311K ARG* 4.0 17.0 - - - +
312K ASN* 2.8 39.7 + - - +
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Residues in contact with ALA 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209K PRO 5.4 2.2 - - - +
211K LEU* 3.8 22.2 - - + +
214K SER* 4.9 1.9 + - - -
228K VAL 3.9 8.9 + - - -
229K GLY* 3.4 27.8 - - - +
230K MET* 5.7 1.8 - - + -
305K THR 3.1 15.0 + - - +
306K MET* 3.7 7.4 - - + +
307K TYR 3.2 0.2 - - - -
308K LEU* 1.3 77.9 - - - +
310K LEU* 1.3 59.0 + - + +
312K ASN* 4.1 2.4 - - - +
313K LEU* 3.0 29.3 + - - +
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Residues in contact with LEU 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211K LEU* 4.4 12.1 - - + -
306K MET* 3.2 26.4 + - + +
307K TYR 3.0 7.0 + - - +
309K ALA* 1.3 75.2 - - + +
311K ARG* 1.3 60.1 - - - +
313K LEU* 3.4 4.5 + - + +
314K ILE* 2.9 40.1 + - + +
335K ILE* 3.9 32.5 - - + -
345K CYS* 3.7 28.7 - - + +
348K GLU* 3.8 19.7 - - + -
349K VAL* 4.2 9.2 - - + +
352K ILE* 3.7 17.7 - - + -
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Residues in contact with ARG 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284K VAL* 3.7 17.1 - - - +
285K ARG 2.8 20.0 + - - -
286K PRO* 3.8 4.4 + - - +
288K VAL 2.8 28.9 + - - -
289K MET* 3.8 2.0 - - - +
290K GLU* 4.2 4.9 - - - +
293K GLU* 2.9 40.4 + - - +
307K TYR* 2.7 35.1 + - + +
308K LEU* 4.0 9.7 - - - +
310K LEU* 1.3 73.8 - - - +
312K ASN* 1.3 82.6 + - - +
314K ILE* 3.2 5.3 + - - +
315K LEU* 3.0 37.7 + - + +
352K ILE* 4.3 10.4 - - + +
356K MET* 3.6 20.9 - - - -
222L LEU* 5.6 0.4 - - - +
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Residues in contact with ASN 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214K SER* 5.7 0.2 - - - +
216K ALA* 3.6 14.3 - - + +
220K LEU* 4.3 4.2 - - + +
228K VAL* 3.7 15.9 + - - +
230K MET* 6.4 0.2 - - - -
272K PHE* 3.1 32.4 - - + -
286K PRO* 3.1 30.8 + - - +
308K LEU 2.8 32.8 + - - +
309K ALA* 4.1 3.1 - - - +
311K ARG* 1.3 97.7 + - - +
313K LEU* 1.3 61.0 + - - +
315K LEU 3.4 0.2 + - - -
316K ALA* 3.0 25.1 + - - +
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Residues in contact with LEU 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211K LEU* 4.4 9.4 - - + -
214K SER* 3.7 13.5 - - - +
215K VAL* 3.6 41.1 - - + +
216K ALA* 4.2 2.4 - - - +
309K ALA 3.0 19.6 + - - +
310K LEU* 3.6 8.7 - - + +
312K ASN* 1.3 76.2 - - - +
314K ILE* 1.3 59.2 + - + +
316K ALA* 3.3 2.8 + - - +
317K LEU* 2.9 44.3 + - + +
331K CYS* 4.4 6.7 - - + +
334K HIS* 3.7 29.2 - - + +
335K ILE* 3.8 24.0 - - + -
349K VAL* 5.8 0.7 - - + -
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Residues in contact with ILE 314 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310K LEU 2.9 22.1 + - - +
311K ARG* 3.5 4.3 - - - +
313K LEU* 1.3 78.9 - - + +
315K LEU* 1.3 57.7 + - - +
317K LEU* 3.3 2.9 + - - -
318K TRP* 3.0 24.8 + - - +
326K LEU* 3.3 10.5 - - + +
331K CYS* 4.3 12.1 - - + -
349K VAL* 4.0 20.9 - - + +
352K ILE* 3.9 26.5 - - + -
353K LEU* 3.7 28.3 - - + +
356K MET* 4.4 9.9 - - + -
362K ILE* 3.6 35.0 - - + -
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Residues in contact with LEU 315 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271K PRO* 4.9 6.7 - - + -
272K PHE* 4.2 14.4 - - + -
284K VAL* 4.0 25.1 - - + -
311K ARG* 3.0 38.7 + - + +
312K ASN 3.9 3.6 - - - +
314K ILE* 1.3 73.8 - - - +
316K ALA* 1.3 66.5 + - - +
318K TRP* 3.3 3.3 + - - +
319K TYR* 3.0 53.3 + - + +
356K MET* 4.6 9.2 - - + -
361K LEU* 4.1 22.9 - - + +
362K ILE* 3.8 21.3 - - + -
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Residues in contact with ALA 316 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K VAL* 3.7 10.1 - - + +
216K ALA* 3.5 33.4 - - + +
219K LEU* 4.7 15.9 - - + -
265K MET* 5.2 1.2 - - - +
271K PRO* 6.1 0.2 - - - -
272K PHE* 4.7 2.2 - - + -
312K ASN 3.0 19.0 + - - +
313K LEU 3.5 4.3 - - - +
315K LEU* 1.3 76.5 - - - +
317K LEU* 1.3 54.2 + - - +
319K TYR* 3.4 3.2 + - - +
320K THR* 2.6 38.5 + - - +
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Residues in contact with LEU 317 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215K VAL* 3.5 28.9 - - + -
313K LEU* 2.9 37.9 + - + +
314K ILE 3.6 4.0 - - - +
316K ALA* 1.3 74.9 - - - +
318K TRP* 1.3 65.4 + - - +
320K THR* 3.3 8.0 + - + +
321K ASN* 3.1 21.7 + - - +
326K LEU* 3.9 18.9 - - + +
330K LYS 4.4 0.4 - - - +
331K CYS* 3.9 38.8 - - - -
334K HIS* 3.8 22.9 - - + +
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Residues in contact with TRP 318 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314K ILE 3.0 16.5 + - - +
315K LEU 3.6 3.4 - - - +
317K LEU* 1.3 77.8 - - - +
319K TYR* 1.3 86.5 + + - +
321K ASN 3.0 29.2 - - - +
322K CYS* 3.1 40.9 + - + -
324K GLU 3.4 24.0 - - - -
326K LEU* 4.0 10.7 - - + +
361K LEU 3.6 22.1 + - - -
362K ILE* 3.6 16.1 - - + +
363K ASN* 3.4 38.6 - - - -
364K THR* 3.5 21.9 - - + +
367K LEU* 4.3 4.9 - - + -
449K LEU* 4.1 12.6 - - + +
453K GLN* 3.6 15.7 - - - -
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Residues in contact with TYR 319 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K LEU* 6.1 0.4 - - + -
265K MET* 3.9 21.7 - - - +
269K PHE* 3.5 61.7 - + + -
271K PRO* 3.4 37.8 - - + +
282K LEU 5.6 1.7 + - - -
315K LEU* 3.0 41.2 + - + +
316K ALA* 4.1 2.9 - - - +
318K TRP* 1.3 99.5 + + - +
320K THR* 1.3 64.2 + - - +
321K ASN* 4.5 0.5 - - - -
322K CYS* 4.7 1.9 + - - -
361K LEU* 4.0 13.0 + - - +
444K ASN* 5.6 9.4 + - - +
449K LEU* 4.8 8.3 - - + -
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Residues in contact with THR 320 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215K VAL* 3.6 18.7 - - + +
265K MET* 4.6 15.5 - - - +
316K ALA* 2.6 23.6 + - - -
317K LEU* 3.5 12.3 - - + -
318K TRP 3.2 0.2 - - - -
319K TYR* 1.3 79.2 - - - +
321K ASN* 1.3 61.8 + - + +
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Residues in contact with ASN 321 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317K LEU 3.1 12.8 + - - +
318K TRP* 3.0 9.3 - - - +
320K THR* 1.3 84.0 - - + +
322K CYS* 1.3 58.6 + - - +
323K LYS* 3.3 27.6 + - - +
324K GLU* 3.1 47.6 + - - +
326K LEU* 6.0 0.7 - - - +
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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