Contacts of the helix formed by residues 301 - 317 (chain B) in PDB entry 5T0H
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 GLY 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A GLY* 6.3 0.6 - - - -
300B GLY* 1.3 77.1 + - - -
302B GLU* 1.3 66.9 + - - -
303B ARG* 3.3 7.7 - - - +
304B GLU* 3.7 6.3 + - - +
305B ILE* 3.3 22.6 + - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ILE* 3.9 26.2 - - + +
301B GLY* 1.3 71.2 - - - -
303B ARG* 1.3 53.8 + - - +
305B ILE* 3.0 9.4 + - + +
306B GLN* 2.4 50.7 + - + +
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Residues in contact with ARG 303 (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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246A VAL* 4.3 3.2 - - - +
279A ALA 4.3 0.8 + - - -
282A GLY* 5.6 8.2 - - - -
291A GLY 4.3 2.2 - - - -
292A ASP* 2.6 45.6 + - - +
295A VAL* 3.3 44.5 - - - +
301B GLY* 5.0 4.7 - - - +
302B GLU* 1.3 80.4 - - - +
304B GLU* 1.3 61.1 + - + +
306B GLN* 3.4 21.7 - - - +
307B ARG* 2.5 77.4 + - - +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A SER* 5.7 0.7 - - - +
246A VAL* 4.5 21.4 - - + +
247A GLN 4.9 1.7 + - - +
256B ILE* 5.2 4.2 - - + +
260B LEU* 4.0 9.0 - - - +
261B GLY* 2.9 40.2 + - - +
263B GLY* 6.3 1.6 - - - -
300B GLY 2.8 28.7 - - - +
301B GLY 3.7 3.9 + - - +
302B GLU 3.3 0.2 - - - -
303B ARG* 1.3 87.0 - - + +
305B ILE* 1.3 59.9 + - + +
307B ARG* 3.4 18.2 - - + +
308B THR* 3.1 26.7 + - - +
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Residues in contact with ILE 305 (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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253B SER* 6.0 3.8 - - - -
256B ILE* 6.1 2.9 - - + -
257B GLN* 5.2 15.9 - - + +
289B ALA* 4.6 24.5 - - + +
293B LYS 5.5 6.1 - - - +
295B TYR* 5.3 8.3 - - + -
299B SER* 3.2 29.6 - - - +
300B GLY* 4.6 3.1 - - - +
301B GLY 3.3 17.9 + - - +
302B GLU* 3.0 8.8 + - - +
304B GLU* 1.3 76.9 - - + +
306B GLN* 1.3 64.2 + - - +
308B THR* 3.2 25.7 - - + +
309B MET* 3.4 9.9 + - - +
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Residues in contact with GLN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ALA* 6.5 0.4 - - - -
323A ARG* 4.2 21.6 - - - +
290B ILE* 6.5 0.9 - - + -
302B GLU* 2.4 43.9 + - + +
303B ARG* 3.4 21.6 + - - +
305B ILE* 1.3 70.1 - - - +
307B ARG* 1.3 59.3 + - - +
309B MET* 3.4 14.5 + - + +
310B LEU* 2.8 34.4 + - + +
338B ASP* 4.9 12.6 + - - +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A SER* 4.0 13.5 - - - +
246A VAL* 3.2 43.9 - - + +
276A GLU* 4.5 4.4 - - - +
279A ALA* 2.4 62.2 + - + +
280A ILE* 3.4 11.1 - - - +
303B ARG* 2.5 65.1 + - - +
304B GLU* 3.4 14.1 - - + +
306B GLN* 1.3 70.7 - - + +
308B THR* 1.3 59.1 + - - +
309B MET 3.1 1.8 - - - -
310B LEU* 3.5 12.5 - - + +
311B GLU* 2.3 40.1 + - - +
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Residues in contact with THR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A SER* 4.4 8.5 - - - -
253B SER* 5.0 11.6 + - - -
256B ILE* 3.4 40.0 - - + +
263B GLY 3.4 11.3 + - - -
264B PRO* 3.5 10.7 - - - +
267B VAL* 5.7 2.3 - - - +
304B GLU 3.1 17.3 + - - +
305B ILE* 3.2 24.7 - - + +
307B ARG* 1.3 77.5 - - - +
309B MET* 1.3 60.6 + - + +
311B GLU* 4.1 3.8 - - - +
312B LEU* 3.2 22.2 + - - +
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Residues in contact with MET 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B SER* 5.3 4.0 - - - +
287B ILE* 4.9 4.0 - - + -
289B ALA* 4.0 28.0 - - + -
290B ILE* 5.4 12.1 - - + -
305B ILE 3.4 7.9 + - - +
306B GLN* 3.7 17.7 - - + +
307B ARG 3.1 0.4 - - - -
308B THR* 1.3 81.4 - - + +
310B LEU* 1.3 63.4 + - - +
311B GLU 3.3 0.2 - - - -
312B LEU* 3.1 25.9 + - + +
313B LEU* 3.2 13.2 + - - +
337B LEU* 4.4 22.0 - - - -
338B ASP* 3.3 37.0 - - + +
341B LEU* 4.8 17.3 - - + +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU* 3.1 37.0 - - + +
278A ASP* 4.9 9.4 - - - +
279A ALA* 4.2 18.6 - - + -
306B GLN* 2.8 33.6 + - + +
307B ARG* 3.5 7.0 - - - +
309B MET* 1.3 77.6 - - - +
311B GLU* 1.3 55.8 + - - +
313B LEU* 3.6 7.5 + - + +
314B ASN* 3.0 24.6 + - + +
338B ASP* 5.7 5.2 - - - +
341B LEU* 5.9 1.6 - - - -
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ILE* 3.4 17.2 - - - +
242A GLY 3.3 4.9 + - - -
243A SER* 3.1 22.1 + - - -
276A GLU* 2.8 34.3 + - - +
264B PRO* 3.6 18.4 - - + -
268B ARG* 2.6 39.8 + - - +
307B ARG 2.3 31.0 + - - +
308B THR* 4.3 2.2 - - - +
310B LEU* 1.3 66.2 - - - +
312B LEU* 1.3 57.8 + - - +
314B ASN* 4.0 5.8 + - - -
315B GLN* 2.6 38.7 + - + +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B SER* 5.0 10.3 - - - +
264B PRO* 5.2 1.8 - - - +
267B VAL* 3.6 33.0 - - + -
271B PHE* 5.5 4.5 - - + -
284B ILE* 4.6 22.0 - - + -
287B ILE* 5.4 7.0 - - + -
308B THR 3.2 18.7 + - - +
309B MET* 3.1 23.5 + - + +
311B GLU* 1.3 76.9 - - - +
313B LEU* 1.3 61.7 + - + +
315B GLN* 4.2 5.0 - - - +
316B LEU* 3.2 32.4 + - + +
329B MET* 4.6 21.1 - - + -
341B LEU* 6.5 0.7 - - + -
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Residues in contact with LEU 313 (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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309B MET 3.2 3.8 + - - +
310B LEU* 4.1 9.4 - - + +
312B LEU* 1.3 79.4 - - + +
314B ASN* 1.3 56.1 + - - +
316B LEU* 2.9 21.2 + - + -
317B ASP* 2.4 40.7 + - + +
329B MET* 6.2 4.5 - - + -
340B ALA* 3.9 10.5 - - + +
341B LEU* 3.6 48.5 - - + +
344B PRO* 4.1 23.8 - - + -
345B GLY 4.0 19.7 - - - +
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Residues in contact with ASN 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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222A LYS* 3.8 5.2 - - - -
241A ILE* 5.6 5.0 - - - +
242A GLY 5.2 1.2 - - - +
275A ASP* 2.7 41.8 + - - +
276A GLU* 3.2 36.3 + - - +
310B LEU* 3.0 13.7 + - + +
311B GLU* 3.9 10.2 + - - +
313B LEU* 1.3 76.1 - - - +
315B GLN* 1.3 60.4 + - - +
317B ASP* 3.2 31.9 - - - +
318B GLY* 4.0 3.6 - - - -
319B PHE 4.7 1.4 + - - -
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Residues in contact with GLN 315 (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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164A MET* 5.3 7.5 - - + +
241A ILE* 6.0 3.1 - - + -
264B PRO* 4.8 3.1 - - - +
267B VAL* 4.4 6.6 - - - +
268B ARG* 3.3 71.1 + - - +
271B PHE* 3.3 41.2 - - + +
272B ARG* 4.6 4.9 - - - +
311B GLU* 2.6 27.1 + - + +
312B LEU* 4.2 4.3 - - - +
314B ASN* 1.3 72.2 - - - +
316B LEU* 1.3 60.4 + - - +
317B ASP 3.1 1.8 + - - -
318B GLY* 3.6 10.7 - - - -
319B PHE 4.7 1.0 + - - -
321B SER* 5.0 2.8 - - - -
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Residues in contact with LEU 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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271B PHE* 3.6 31.2 - - + -
312B LEU* 3.2 26.4 + - + +
313B LEU* 2.9 23.0 + - + +
315B GLN* 1.3 78.2 - - - +
317B ASP* 1.3 65.9 + - - +
318B GLY* 3.4 1.4 + - - -
321B SER* 5.7 1.6 - - - +
327B VAL* 3.6 45.1 - - + -
329B MET* 5.0 7.9 - - + -
344B PRO* 6.2 0.7 - - + -
345B GLY* 4.7 12.6 - - - +
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLY 5.3 2.5 - - - +
222A LYS* 3.5 18.1 + - - +
313B LEU* 2.4 26.9 + - - +
314B ASN* 3.2 34.2 - - - +
315B GLN 3.1 2.2 - - - -
316B LEU* 1.3 72.8 - - - +
318B GLY* 1.3 51.8 + - - +
344B PRO* 3.9 29.7 - - - +
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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
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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