Contacts of the helix formed by residues 299 - 316 (chain D) in PDB entry 6R7H
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 ILE 299 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199D ARG* 4.3 15.0 - - + +
201D PHE* 3.6 39.9 - - + -
235D LEU* 3.8 16.3 - - + +
288D HIS 5.5 0.9 - - - +
289D GLN* 3.3 25.9 + - - +
290D LYS* 4.1 1.8 - - - +
291D ALA* 3.4 27.8 - - + +
293D THR* 3.8 17.0 - - + -
298D SER* 1.3 70.9 - - - +
300D LEU* 1.3 62.2 + - - +
301D ASP 3.1 6.4 + - - -
302D ARG* 3.2 16.3 + - + +
303D ALA* 3.7 7.3 + - - +
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Residues in contact with LEU 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ILE* 3.8 34.5 - - + +
235D LEU* 3.5 29.8 - - + +
278D LEU* 3.9 36.1 - - + +
281D PHE* 3.6 26.5 - - + -
282D ALA* 4.8 6.1 - - + +
285D LEU* 5.0 4.7 - - + -
298D SER* 3.2 10.6 - - - +
299D ILE* 1.3 77.7 - - - +
301D ASP* 1.3 62.6 + - - +
302D ARG 3.2 0.4 - - - -
303D ALA* 3.9 4.9 - - + +
304D VAL* 3.2 34.4 + - + +
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Residues in contact with ASP 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D LEU* 5.5 10.3 - - - +
293D THR* 4.1 1.1 - - - +
295D ASP* 3.4 41.2 - - - +
296D GLY* 3.6 15.6 + - - -
297D SER 4.1 1.7 + - - -
298D SER* 2.6 38.0 + - - +
299D ILE 3.1 1.0 - - - -
300D LEU* 1.3 78.2 - - - +
302D ARG* 1.3 56.7 + - - +
304D VAL* 4.5 3.7 - - - +
305D ILE* 3.4 30.7 + - - +
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Residues in contact with ARG 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D THR* 4.4 19.6 + - + +
294D ALA* 6.1 2.2 - - - +
295D ASP* 5.3 1.6 - - - +
299D ILE* 3.2 11.0 + - + +
300D LEU 3.2 0.6 - - - -
301D ASP* 1.3 78.4 - - - +
303D ALA* 1.3 63.8 + - - +
304D VAL 3.3 1.8 - - - -
305D ILE* 3.5 6.7 + - - +
306D GLU* 3.2 45.9 + - - +
334D LYS* 6.2 3.3 - - - +
338D ILE* 5.5 20.3 - - + +
341D GLN* 4.1 22.4 + - - +
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Residues in contact with ALA 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ILE 3.3 25.4 - - - +
235D LEU* 3.4 24.2 - - - +
236D ALA 3.6 8.1 - - - +
242D ARG* 3.8 5.5 + - - -
299D ILE 3.7 5.5 + - - +
300D LEU* 3.4 10.1 + - + +
302D ARG* 1.3 76.3 - - - +
304D VAL* 1.3 60.3 + - - +
306D GLU* 3.6 8.1 + - - +
307D HIS* 3.0 29.5 + - - +
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Residues in contact with VAL 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ILE* 6.2 2.0 - - + -
267D MET* 6.4 2.7 - - + -
273D ILE* 3.8 28.7 - - + +
278D LEU* 4.4 22.9 - - + -
300D LEU* 3.2 34.5 + - + +
301D ASP* 4.5 4.7 - - - +
303D ALA* 1.3 75.2 - - - +
305D ILE* 1.3 68.3 - - + +
307D HIS* 3.3 6.0 + - - +
308D ASN* 3.0 41.8 + - - +
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Residues in contact with ILE 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D ASP* 4.1 10.3 - - - +
301D ASP 3.4 20.4 - - - +
302D ARG* 3.5 8.0 + - - +
303D ALA 3.4 0.4 - - - -
304D VAL* 1.3 80.5 - - + +
306D GLU* 1.3 59.9 + - - +
308D ASN* 3.4 7.6 + - - +
309D LEU* 3.3 28.4 + - + +
328D LEU* 4.3 14.2 - - + +
330D ILE* 3.7 44.4 - - + -
334D LYS* 4.5 7.6 - - - -
335D ALA* 6.1 0.7 - - - -
338D ILE* 3.8 37.5 - - + -
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Residues in contact with GLU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D SER* 3.3 26.5 - - - -
238D ALA* 3.4 22.9 - - - +
302D ARG* 3.2 44.7 + - - +
303D ALA* 4.1 4.5 - - - +
305D ILE* 1.3 79.1 - - - +
307D HIS* 1.3 61.2 + - - +
309D LEU* 3.7 5.5 + - - +
310D LEU 3.5 12.3 + - - -
338D ILE* 4.0 22.0 - - + +
342D MET* 3.6 23.7 - - + +
347D ARG* 3.7 14.7 + - - -
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Residues in contact with HIS 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ALA* 4.0 10.9 - - - +
242D ARG* 4.0 18.9 + - - +
246D LEU* 5.7 1.8 - - + -
266D LYS 4.7 0.6 + - - -
267D MET* 3.5 54.8 + - + +
270D ASP* 4.5 14.4 - - - -
271D ARG 4.5 10.0 + - - -
273D ILE* 3.9 11.5 - - + +
303D ALA 3.0 19.7 + - - +
304D VAL* 3.8 5.2 - - - +
305D ILE 3.2 0.2 - - - -
306D GLU* 1.3 75.9 - - - +
308D ASN* 1.3 75.9 + - - +
310D LEU* 3.4 6.3 + - - +
311D SER* 3.3 26.1 + - - -
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Residues in contact with ASN 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D ARG 5.2 1.6 - - - +
272D ILE* 5.7 0.2 - - - -
273D ILE* 3.5 35.4 + - - +
304D VAL* 3.0 33.9 + - - +
305D ILE* 3.4 4.6 + - - +
306D GLU 3.4 0.2 - - - -
307D HIS* 1.3 80.6 - - - +
309D LEU* 1.3 59.1 + - - +
311D SER* 3.7 5.4 + - - +
312D ALA* 3.2 28.2 + - - +
328D LEU* 3.4 36.6 - - + +
126G ARG* 5.0 9.2 + - - +
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D ILE* 3.3 23.0 + - + +
306D GLU* 4.0 6.3 - - - +
307D HIS 3.2 0.6 - - - -
308D ASN* 1.3 78.3 - - - +
310D LEU* 1.3 62.4 + - - +
312D ALA* 3.6 4.6 + - + +
313D SER* 3.5 15.4 + - - -
324D LEU* 3.9 33.2 - - + -
328D LEU* 5.1 7.6 - - + -
335D ALA* 5.1 6.1 - - + +
338D ILE* 3.8 28.5 - - + +
339D ALA* 4.0 28.3 - - + +
342D MET* 5.2 4.5 - - + -
348D MET* 3.4 26.5 - - - +
361D PHE* 4.7 8.2 - - + -
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ALA* 3.8 22.9 - - + -
239D GLY 4.3 17.5 - - - +
243D SER* 6.4 1.1 - - - -
306D GLU 3.5 10.9 + - - +
307D HIS* 3.4 11.1 + - - +
308D ASN 3.3 0.8 - - - -
309D LEU* 1.3 76.9 - - - +
311D SER* 1.3 63.0 + - - +
313D SER* 2.7 28.7 + - - +
314D LYS* 3.3 25.7 + - - +
342D MET* 4.6 3.6 - - + +
347D ARG 3.4 24.2 - - - +
348D MET* 4.3 10.5 - - - -
349D ASN* 5.8 1.8 - - - +
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Residues in contact with SER 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ASP* 3.6 41.7 + - - +
271D ARG 5.3 1.8 - - - -
307D HIS* 3.3 20.4 + - - -
308D ASN* 4.2 5.6 - - - -
310D LEU* 1.3 78.6 - - - +
312D ALA* 1.3 61.5 + - - +
313D SER 3.4 0.5 + - - -
314D LYS* 3.5 7.5 + - - +
315D LEU* 3.3 33.7 + - - +
126G ARG* 4.3 11.1 + - - -
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Residues in contact with ALA 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D ASN 3.2 17.6 + - - +
309D LEU* 4.0 8.1 - - + +
310D LEU 3.3 0.4 - - - -
311D SER* 1.3 74.1 - - - +
313D SER* 1.3 59.1 + - - +
314D LYS 3.2 1.3 - - - -
316D TYR* 3.1 42.0 + - + +
324D LEU* 5.6 4.3 - - + -
361D PHE* 3.5 16.2 - - + -
126G ARG* 3.8 28.9 - - - +
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Residues in contact with SER 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D LEU 3.5 10.2 + - - -
310D LEU* 2.7 24.4 + - - +
311D SER 3.2 0.2 - - - -
312D ALA* 1.3 77.7 - - - +
314D LYS* 1.3 71.8 + - - +
348D MET* 4.2 8.3 - - - -
349D ASN* 4.1 29.1 + - - -
361D PHE* 3.6 18.6 - - - +
362D GLU 3.0 25.3 - - - +
363D THR* 3.3 8.1 - - - +
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Residues in contact with LYS 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ASP* 5.2 9.9 - - - +
310D LEU* 3.3 43.2 + - - +
311D SER* 3.5 7.4 + - - +
313D SER* 1.3 83.4 + - - +
315D LEU* 1.3 72.0 + - + +
349D ASN* 5.5 6.0 - - - +
362D GLU 5.0 1.8 - - - +
363D THR* 3.8 17.6 - - - +
145G LEU* 4.9 5.4 - - - +
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Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ASP* 4.2 5.6 - - + +
311D SER* 3.3 25.6 + - - +
314D LYS* 1.3 91.3 - - + +
316D TYR* 1.3 69.4 + - + +
363D THR* 5.5 0.7 - - - -
126G ARG* 3.4 29.2 - - - +
129G GLU* 3.4 9.0 - - - +
133G ILE* 3.7 36.9 - - + +
137G TYR* 3.8 23.1 - - + +
145G LEU* 3.4 24.4 - - + +
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Residues in contact with TYR 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D ILE* 5.1 1.7 - - - +
312D ALA* 3.1 33.7 + - + +
313D SER 4.6 1.4 - - - +
315D LEU* 1.3 83.6 + - + +
317D ASN* 1.3 68.2 + - - +
318D ASN 5.1 0.2 - - - +
319D ILE* 4.5 13.5 - - + -
324D LEU* 4.6 11.2 - - + -
327D LEU* 3.9 26.1 - - + +
361D PHE* 3.3 16.4 - - + +
363D THR* 4.8 3.4 - - - +
126G ARG* 2.4 104.7 + - + -
127G GLU* 5.5 0.9 - - - -
129G GLU* 4.3 4.5 - - + -
130G ASP* 3.2 27.9 + - + +
133G ILE* 5.6 0.9 - - + -
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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