Contacts of the helix formed by residues 313 - 327 (chain B) in PDB entry 1R6U
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 GLN 313 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B CYS* 5.2 0.4 - - + -
310B ALA* 2.9 32.2 + - + +
312B ASP* 1.3 111.7 + - - +
314B ASP* 1.3 65.9 + - - +
315B PRO* 3.2 4.5 - - - -
316B TYR* 3.0 50.0 + - + +
317B PHE* 3.1 32.7 + - + -
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Residues in contact with ASP 314 (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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107B PHE* 3.5 23.1 - - + +
109B SER* 5.1 1.1 - - - -
141B ARG* 2.6 46.3 + - - -
310B ALA 4.0 1.6 + - - -
311B ILE* 3.1 16.8 + - + +
313B GLN* 1.3 77.9 - - - +
315B PRO* 1.3 68.2 - - + +
317B PHE* 3.3 7.3 + - - +
318B ARG* 3.0 24.4 + - - +
334B LEU* 3.6 4.0 - - - +
336B HIS* 3.1 27.1 - - + -
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Residues in contact with PRO 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 3.4 32.8 - - + -
266B ILE* 4.0 13.9 - - + +
312B ASP 4.0 5.2 - - - +
313B GLN* 3.2 10.1 - - - +
314B ASP* 1.3 96.3 - - + +
316B TYR* 1.3 71.3 + - + +
318B ARG* 3.1 25.7 + - + +
319B MSE 3.8 2.3 + - - -
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Residues in contact with TYR 316 (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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266B ILE* 3.1 41.1 + - + -
267B PHE* 3.5 31.4 - + + -
284B GLN* 5.5 9.4 - - - +
312B ASP 4.7 5.2 - - - -
313B GLN* 3.0 44.5 + - + +
315B PRO* 1.3 83.5 - - + +
317B PHE* 1.3 67.5 + + + +
318B ARG 3.1 1.2 + - - -
319B MSE 3.2 21.3 + - - +
320B THR* 4.0 3.1 + - - -
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Residues in contact with PHE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TYR* 4.7 11.2 - + - -
284B GLN* 5.0 17.5 - - + -
307B ILE* 3.8 42.6 - - + -
309B CYS* 3.8 33.2 - - + -
313B GLN* 3.1 30.4 + - + +
314B ASP 3.3 6.5 + - - +
316B TYR* 1.3 79.5 - + + +
318B ARG* 1.3 64.4 + - - +
319B MSE 3.2 0.7 - - - -
320B THR* 3.4 16.9 + - + +
321B ARG* 3.0 27.0 + - + +
332B PRO* 5.7 0.9 - - + -
334B LEU* 4.0 22.2 - - + -
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE 5.7 2.0 + - - -
141B ARG* 5.7 10.8 - - - +
266B ILE* 6.2 0.4 - - + -
314B ASP* 3.0 16.8 + - - +
315B PRO* 3.1 19.7 - - - +
316B TYR 3.1 0.6 - - - -
317B PHE* 1.3 75.2 - - - +
319B MSE 1.3 55.3 + - - +
321B ARG* 3.1 9.2 + - + +
322B ASP* 2.7 85.3 + - - +
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Residues in contact with MSE 319 (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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275A ILE* 5.9 0.2 - - + -
254B ILE* 4.3 6.7 - - + -
258B VAL* 4.1 38.8 - - + -
262B GLN* 5.9 3.6 - - + +
263B VAL* 4.4 3.4 - - - -
266B ILE* 3.9 24.1 - - + +
267B PHE* 4.3 12.6 - - - -
281B PRO* 3.7 45.8 - - + +
282B ALA 4.5 0.2 - - - +
285B ALA* 4.0 16.4 - - + -
315B PRO 3.8 1.4 + - - -
316B TYR* 3.2 13.3 + - - +
318B ARG* 1.3 80.2 - - - +
320B THR* 1.3 69.3 + - - +
322B ASP* 3.3 6.4 + - - +
323B VAL* 3.1 29.5 + - + +
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Residues in contact with THR 320 (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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285B ALA* 3.2 33.3 - - + +
288B SER* 3.7 32.3 + - - +
289B PHE* 4.0 13.1 - - + -
316B TYR 4.6 3.8 + - - -
317B PHE* 3.4 19.9 + - + -
318B ARG 3.2 0.4 - - - -
319B MSE 1.3 82.3 - - - +
321B ARG* 1.3 63.2 + - - +
323B VAL* 3.3 6.3 + - - +
324B ALA* 3.2 21.3 + - - +
332B PRO* 4.1 10.1 - - + -
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG* 3.0 51.9 - - - +
142B ASP* 2.5 43.8 + - - +
317B PHE* 3.0 20.6 + - + +
318B ARG* 3.7 8.5 - - + +
320B THR* 1.3 75.5 - - - +
322B ASP* 1.3 63.0 + - - +
324B ALA* 3.4 2.8 + - - +
325B PRO* 3.2 12.5 - - - +
331B LYS* 3.0 50.7 - - + +
332B PRO* 3.4 36.9 + - + +
334B LEU* 4.0 9.4 - - + -
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Residues in contact with ASP 322 (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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262B GLN* 6.3 0.9 - - - +
318B ARG* 2.7 62.5 + - - +
319B MSE 3.6 6.8 + - - +
321B ARG* 1.3 74.2 - - - +
323B VAL* 1.3 62.2 + - + +
325B PRO* 3.5 10.1 - - - +
326B ARG* 3.2 24.4 + - - +
331B LYS* 4.4 10.4 + - - +
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 4.3 17.5 - - + -
257B HIS* 4.2 19.1 - - + +
258B VAL* 3.7 27.8 - - + -
289B PHE* 5.7 1.6 - - + -
319B MSE 3.1 19.8 + - + +
320B THR* 3.3 6.3 + - - +
322B ASP* 1.3 76.8 - - + +
324B ALA* 1.3 66.5 + - - +
326B ARG* 3.0 26.1 + - + +
327B ILE* 3.1 34.3 + - + +
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Residues in contact with ALA 324 (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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289B PHE* 3.9 16.2 - - + -
320B THR 3.2 12.4 + - - +
321B ARG 3.5 9.4 - - - +
323B VAL* 1.3 76.8 - - - +
325B PRO* 1.3 68.9 - - + +
327B ILE* 3.2 6.7 + - - +
328B GLY 3.1 5.2 + - - -
329B TYR 2.8 38.4 + - - +
330B PRO 3.8 4.0 - - - +
331B LYS* 3.8 20.2 - - - -
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Residues in contact with PRO 325 (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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321B ARG 3.2 16.4 - - - +
322B ASP* 3.5 11.0 - - - +
324B ALA* 1.3 91.3 - - + +
326B ARG* 1.3 64.3 + - + +
328B GLY* 3.2 12.7 + - - +
329B TYR 3.6 6.9 - - - +
331B LYS* 4.3 15.0 - - + +
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Residues in contact with ARG 326 (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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601A GOL 6.0 0.3 - - - -
257B HIS* 3.1 59.6 + - - +
262B GLN* 5.2 10.1 + - - +
322B ASP* 3.2 28.6 + - - +
323B VAL* 3.0 19.7 + - + +
325B PRO* 1.3 81.1 - - + +
327B ILE* 1.3 59.6 - - + +
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Residues in contact with ILE 327 (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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601A GOL 5.3 8.0 - - - +
250B ASN* 5.2 0.7 - - - +
253B LYS* 4.1 36.6 + - + +
254B ILE* 4.0 18.8 - - + -
257B HIS* 3.4 38.4 - - + +
289B PHE* 4.2 9.0 - - + -
323B VAL* 3.1 28.5 + - + +
324B ALA 3.5 7.4 - - - +
326B ARG* 1.3 77.7 - - - +
328B GLY* 1.3 59.4 + - - +
329B TYR* 3.8 31.0 - - + -
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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