Contacts of the helix formed by residues 295 - 311 (chain B) in PDB entry 1B3U
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 ALA 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B CYS 3.9 3.0 + - - -
294B GLU* 1.3 72.0 + - - +
296B GLU* 1.3 60.5 + - + +
298B ARG* 3.1 29.5 + - - +
299B ALA* 2.7 37.8 + - - +
337B ASN* 3.8 33.2 - - + +
340B VAL* 3.8 1.0 - - - +
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Residues in contact with GLU 296 (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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256B TRP* 3.4 47.0 - - + -
260B TYR* 3.5 21.2 - - + -
294B GLU* 3.2 23.9 - - - +
295B ALA* 1.3 79.3 + - + +
297B VAL* 1.3 60.6 + - - +
299B ALA* 3.7 6.7 - - - +
300B ALA 3.2 16.1 + - - -
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TRP* 3.9 35.9 - - + +
259B ARG* 4.5 6.3 - - + +
260B TYR* 4.3 13.7 - - - +
263B ALA* 4.6 3.1 - - + +
289B LEU* 3.7 30.3 - - + +
292B ASP* 3.4 38.1 - - + +
294B GLU* 2.9 10.3 + - + +
296B GLU* 1.3 75.6 - - - +
298B ARG* 1.3 67.0 + - - +
300B ALA* 3.0 5.7 + - - +
301B ALA* 2.9 19.8 + - - +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU 3.9 7.0 - - - -
290B MET* 3.3 25.5 - - - +
291B LYS* 4.2 3.1 - - - +
292B ASP 3.1 34.9 + - - +
293B CYS 4.8 4.6 + - - -
294B GLU 3.2 3.3 + - - +
295B ALA* 3.1 26.0 + - - +
297B VAL* 1.3 77.1 - - - +
299B ALA* 1.3 56.2 + - - +
301B ALA* 3.2 3.5 + - - +
302B SER* 2.9 34.9 + - - -
332B LEU* 4.7 3.2 - - + +
335B ASP* 2.8 41.2 + - - -
336B ALA* 5.5 3.6 - - - +
337B ASN* 4.7 2.8 - - - +
340B VAL* 3.1 19.8 - - + +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 2.7 20.5 + - - +
296B GLU* 3.7 8.7 - - - +
298B ARG* 1.3 73.8 - - - +
300B ALA* 1.3 61.3 + - - +
302B SER* 3.3 4.7 + - - -
303B HIS* 3.2 19.4 + - - +
339B HIS* 4.3 15.0 - - + +
340B VAL* 4.0 27.9 - - + +
343B ALA* 3.6 9.3 - - + +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B TYR* 3.7 25.1 - - + +
263B ALA* 3.8 18.5 - - + +
264B ASP* 4.6 7.7 - - - +
296B GLU 3.2 10.8 + - - +
297B VAL 3.0 9.7 + - - +
299B ALA* 1.3 75.5 - - - +
301B ALA* 1.3 67.7 + - - +
303B HIS* 3.4 17.1 + - - +
304B LYS* 3.7 15.1 + - - +
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ALA* 4.2 7.7 - - + +
286B PHE* 3.4 29.7 - - + -
289B LEU* 4.1 12.8 - - + -
290B MET* 3.9 34.8 - - + +
297B VAL 2.9 12.1 + - - +
298B ARG 3.6 7.0 - - - +
300B ALA* 1.3 73.5 - - - +
302B SER* 1.3 59.0 + - - +
304B LYS* 2.8 23.1 + - - +
305B VAL* 3.4 0.9 + - - -
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B MET* 5.0 0.4 - - - +
298B ARG 2.9 15.7 + - - -
299B ALA* 3.4 10.1 - - - -
301B ALA* 1.3 76.5 - - - +
303B HIS* 1.3 58.0 + - - +
304B LYS 3.0 5.0 + - - -
305B VAL* 3.1 29.0 + - - +
332B LEU* 3.3 23.9 - - - +
340B VAL* 3.5 14.5 + - - +
343B ALA* 4.1 14.6 - - - -
344B LEU* 4.1 14.4 - - - +
347B VAL* 3.6 9.9 - - - +
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Residues in contact with HIS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ALA 3.2 10.0 + - - +
300B ALA* 3.7 11.7 - - - +
301B ALA 3.2 0.4 - - - -
302B SER* 1.3 78.0 - - - +
304B LYS* 1.3 74.9 + - + +
305B VAL 3.6 0.2 - - - -
306B LYS 5.2 0.3 + - - -
307B GLU* 5.1 5.0 + - - +
343B ALA* 4.3 18.4 - - + +
346B SER* 5.8 2.7 - - - -
347B VAL* 4.2 24.9 - - + +
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Residues in contact with LYS 304 (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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263B ALA 3.9 14.1 - - - +
264B ASP* 2.8 38.5 + - - +
266B PHE* 4.7 4.7 - - + -
267B THR* 3.7 30.7 - - - +
268B GLU* 4.8 3.8 - - - -
286B PHE* 4.1 14.8 - - + -
300B ALA 3.7 13.1 + - - +
301B ALA* 2.8 10.7 + - - +
303B HIS* 1.3 97.7 + - + +
305B VAL* 1.3 65.1 + - - +
306B LYS 3.3 2.5 - - - -
307B GLU* 3.1 15.6 + - + +
308B PHE* 2.8 25.7 + - + +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PHE* 4.2 9.4 - - + -
290B MET* 4.6 10.8 - - - -
301B ALA 3.4 3.8 + - - +
302B SER* 3.1 30.2 + - - +
303B HIS 3.6 0.4 - - - -
304B LYS* 1.3 75.2 - - - +
306B LYS* 1.3 63.6 + - - +
308B PHE* 3.9 1.6 - - - +
309B CYS* 3.1 29.0 + - - -
325B ILE* 4.4 9.0 - - + -
329B ILE* 3.7 33.7 - - + -
332B LEU* 5.2 0.7 - - + -
344B LEU* 4.4 8.1 - - + -
347B VAL* 4.5 7.4 - - + -
348B ILE* 5.8 1.3 - - - -
351B LEU* 3.7 25.1 - - + -
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Residues in contact with LYS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B HIS 5.9 0.4 - - - +
304B LYS 3.3 0.4 - - - -
305B VAL* 1.3 75.8 - - - +
307B GLU* 1.3 58.5 + - + +
309B CYS* 3.1 2.6 + - - +
310B GLU* 2.7 69.8 + - + +
346B SER 4.3 5.5 + - - -
347B VAL* 3.1 52.9 + - + +
350B GLY* 3.2 30.8 - - - +
351B LEU* 3.7 11.4 - - + -
386B ASN* 5.6 3.6 + - - +
389B CYS* 5.1 5.4 - - - -
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Residues in contact with GLU 307 (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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267B THR* 3.5 33.3 + - - +
270B GLN* 4.7 0.2 - - - -
271B LYS* 5.9 0.5 + - - -
303B HIS 5.1 3.7 + - - +
304B LYS* 3.1 23.3 + - + +
306B LYS* 1.3 80.7 - - + +
308B PHE* 1.3 62.8 + - - +
310B GLU* 3.2 19.0 + - - +
311B ASN* 2.6 37.3 + - - -
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Residues in contact with PHE 308 (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 PHE* 3.8 24.9 - + + -
267B THR* 4.6 1.7 + - - +
270B GLN* 3.1 57.7 - - + +
278B THR* 4.9 2.0 - - - -
282B LEU* 4.1 23.8 - - + -
283B VAL* 4.1 19.5 - - + -
286B PHE* 3.9 36.1 - + + -
304B LYS* 2.8 21.4 + - + +
305B VAL 3.9 2.9 - - - +
307B GLU* 1.3 74.3 - - - +
309B CYS* 1.3 63.3 + - - +
311B ASN 3.3 3.8 + - - -
312B LEU* 3.5 26.1 + - + +
325B ILE* 4.5 17.5 - - + -
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Residues in contact with CYS 309 (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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286B PHE* 6.3 0.2 - - - -
305B VAL* 3.1 24.2 + - - +
306B LYS 3.6 2.5 - - - +
308B PHE* 1.3 74.9 - - - +
310B GLU* 1.3 58.6 + - - +
311B ASN 2.8 10.7 + - - -
312B LEU* 3.1 23.9 + - + +
317B ARG* 3.9 11.1 + - - +
321B ILE* 4.1 22.0 - - + -
325B ILE* 3.2 40.6 - - - -
351B LEU* 3.7 22.7 - - + -
354B ILE* 4.2 4.6 - - + +
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Residues in contact with GLU 310 (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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306B LYS* 2.7 62.0 + - + +
307B GLU* 3.5 16.3 + - - +
309B CYS* 1.3 69.2 - - - +
311B ASN* 1.3 64.8 + - - +
312B LEU 3.7 0.4 - - - -
317B ARG* 3.2 28.5 + - - +
350B GLY 4.6 3.1 - - - +
354B ILE* 3.3 21.0 - - + +
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Residues in contact with ASN 311 (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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267B THR* 4.1 13.7 - - - +
270B GLN* 3.5 26.7 - - + +
271B LYS* 4.9 15.9 - - + +
275B PRO* 6.0 1.7 - - - +
307B GLU* 2.6 41.0 + - - +
308B PHE 3.3 0.2 + - - -
309B CYS 2.8 3.6 + - - -
310B GLU* 1.3 85.8 - - - +
312B LEU* 1.3 63.1 + - - +
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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