Contacts of the helix formed by residues 301 - 314 (chain B) in PDB entry 2BAP
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 LEU 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B PRO* 5.0 9.4 - - + +
244B PRO* 4.6 16.4 - - + +
247B MET* 3.9 37.7 - - + -
248B ILE* 3.8 25.1 - - + +
292B GLY* 3.4 27.8 - - - +
297B THR* 3.9 15.0 - - - +
298B SER* 2.8 24.7 + - - +
300B ALA* 1.3 76.0 - - - +
302B LYS* 1.3 55.1 + - - +
303B VAL 3.0 5.6 - - - -
304B GLY* 2.9 20.4 + - - +
305B CYS* 3.0 15.9 + - - +
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Residues in contact with LYS 302 (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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292B GLY 3.5 9.4 - - - +
293B LEU* 3.7 33.5 - - + +
294B LYS 3.3 21.2 + - - -
296B GLY* 4.1 6.9 - - - +
297B THR* 3.0 50.6 + - - +
298B SER 3.2 6.3 + - - +
299B ILE* 3.5 11.8 + - - +
301B LEU* 1.3 73.1 - - - +
303B VAL* 1.3 59.0 + - - +
305B CYS 4.2 1.3 - - - -
306B LEU* 4.1 7.6 + - - +
341B LEU* 4.6 7.1 - - + +
344B ILE* 4.4 19.9 - - + +
349B MET* 3.3 34.5 - - + +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 3.3 20.6 - - + +
300B ALA* 4.2 9.9 - - - +
301B LEU 3.0 0.8 - - - -
302B LYS* 1.3 78.3 - - - +
304B GLY* 1.3 53.8 + - - +
305B CYS 3.2 1.6 - - - -
307B GLN* 2.8 36.8 + - - +
346B ASN* 4.8 7.4 - - - +
348B ASP* 4.0 23.1 - - + +
349B MET* 4.0 26.5 - - + +
352B GLN* 3.8 21.9 - - + +
1190D GLN* 4.3 20.4 - - + +
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Residues in contact with GLY 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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248B ILE* 5.2 9.9 - - - -
251B ALA* 3.4 27.3 - - - +
252B LYS* 5.4 4.3 - - - -
255B SER* 5.2 0.2 + - - -
300B ALA 3.9 5.9 + - - -
301B LEU* 2.9 11.5 + - - -
303B VAL* 1.3 80.3 - - - +
305B CYS* 1.3 59.9 + - - +
307B GLN* 3.9 12.4 - - - +
308B LEU* 3.3 14.2 + - - +
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Residues in contact with CYS 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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247B MET* 3.7 29.4 - - - -
289B LEU* 3.7 25.6 - - + +
292B GLY 3.5 22.4 - - - -
293B LEU* 3.7 24.0 - - + -
301B LEU* 3.0 14.5 + - - +
302B LYS* 4.5 0.2 - - - -
303B VAL 3.2 0.2 - - - -
304B GLY* 1.3 74.7 - - - +
306B LEU* 1.3 67.1 + - - +
307B GLN 3.0 0.9 - - - -
308B LEU* 3.0 6.6 + - - +
309B ILE* 2.9 27.4 + - - +
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Residues in contact with LEU 306 (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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293B LEU* 4.6 5.3 - - + +
302B LYS 4.1 12.9 + - - +
303B VAL 4.1 1.2 + - - -
305B CYS* 1.3 79.0 - - - +
307B GLN* 1.3 56.7 + - - +
309B ILE* 4.0 18.1 - - + +
310B ASN* 2.9 51.0 + - - +
334B LEU* 6.2 1.1 - - + -
338B LEU* 5.1 4.7 - - + -
341B LEU* 4.4 9.0 - - + -
349B MET* 4.7 2.0 - - - +
352B GLN* 3.5 17.3 - - + -
353B LEU* 3.4 50.9 - - + +
356B PHE* 3.9 25.1 - - + -
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Residues in contact with GLN 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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252B LYS* 3.6 31.9 - - - +
255B SER* 4.1 7.8 + - - +
303B VAL 2.8 23.3 + - - +
304B GLY* 3.9 7.5 + - - +
305B CYS 3.0 0.6 - - - -
306B LEU* 1.3 78.1 - - - +
308B LEU* 1.3 63.6 + - - +
310B ASN* 3.4 4.2 + - - +
311B ALA* 3.1 21.0 + - - +
352B GLN* 3.1 18.9 + - - +
1186D LEU* 4.9 1.2 - - - +
1189D LEU* 3.3 58.1 - - + +
1190D GLN* 3.4 19.6 + - - +
1195D PHE* 4.6 1.6 - - - -
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Residues in contact with LEU 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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239B MET* 3.5 38.6 - - + -
251B ALA* 3.9 5.6 - - + +
254B LEU* 3.6 17.0 - - + -
255B SER* 3.5 38.3 - - - +
258B CYS* 5.1 0.9 - - - -
270B VAL* 5.1 4.7 - - + -
274B MET* 4.8 5.8 - - + -
289B LEU* 3.7 19.1 - - + -
304B GLY 3.3 11.2 + - - +
305B CYS 3.0 8.1 + - - +
307B GLN* 1.3 75.2 - - - +
309B ILE* 1.3 54.6 + - - +
311B ALA* 2.9 4.2 + - - +
312B LEU* 2.7 54.2 + - + +
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Residues in contact with ILE 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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289B LEU* 4.0 20.2 - - + -
293B LEU* 4.7 9.2 - - + -
305B CYS 2.9 20.3 + - - +
306B LEU* 3.5 20.4 - - + +
308B LEU* 1.3 75.4 - - - +
310B ASN* 1.3 64.0 + - - +
312B LEU* 2.9 21.6 + - + +
313B ILE* 3.0 31.8 + - + +
325B ILE* 5.9 0.4 - - + -
329B LEU* 3.9 24.7 - - + -
334B LEU* 4.0 26.5 - - + -
356B PHE* 3.9 19.7 - - + -
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Residues in contact with ASN 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 LEU* 2.9 20.7 + - - +
307B GLN 3.6 5.6 - - - +
309B ILE* 1.3 73.0 - - - +
311B ALA* 1.3 57.1 + - - +
313B ILE* 4.6 3.8 - - - +
314B THR* 2.8 39.0 + - - +
352B GLN* 2.8 37.6 + - - -
355B VAL* 3.0 27.5 - - + +
356B PHE* 3.2 31.6 - - - +
1195D PHE* 3.7 17.3 - - + -
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Residues in contact with ALA 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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255B SER* 3.7 33.9 - - - +
258B CYS* 3.0 24.2 - - + +
259B ILE* 4.9 3.6 - - + -
267B ASN* 3.8 1.0 - - - +
307B GLN 3.1 13.3 + - - +
308B LEU 2.9 8.8 + - - +
310B ASN* 1.3 74.0 - - - +
312B LEU* 1.3 59.6 + - - +
313B ILE 3.3 0.7 - - - -
315B PRO* 3.0 23.0 - - - +
1189D LEU* 4.7 8.7 - - + -
1195D PHE* 4.3 5.6 - - + -
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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
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258B CYS* 4.6 4.3 - - - -
267B ASN* 2.8 35.4 + - - +
270B VAL* 3.8 27.8 - - + -
271B LEU* 3.9 25.6 - - + +
274B MET* 4.0 21.3 - - - -
286B PHE* 4.2 15.5 - - + -
289B LEU* 4.5 6.3 - - + -
308B LEU* 2.7 35.9 + - + +
309B ILE* 2.9 13.4 + - + +
311B ALA* 1.3 75.1 - - - +
313B ILE* 1.3 62.8 + - + +
321B PHE* 4.2 9.4 - - - -
325B ILE* 5.3 5.3 - - + +
329B LEU* 6.5 0.2 - - + -
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Residues in contact with ILE 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 ILE* 3.0 32.6 + - + +
310B ASN* 4.0 2.9 - - - +
312B LEU* 1.3 76.5 - - - +
314B THR* 1.3 60.2 + - - +
315B PRO* 3.2 3.1 - - - -
316B ALA* 2.8 37.7 + - - +
321B PHE* 5.7 0.9 - - - -
322B ARG* 3.8 31.6 - - + +
325B ILE* 3.8 28.3 - - + -
326B ARG* 4.3 24.2 - - - +
329B LEU* 4.9 3.1 - - + -
356B PHE* 4.0 17.7 - - + -
359B GLN* 4.6 10.8 - - + -
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Residues in contact with THR 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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310B ASN* 2.8 27.2 + - - +
313B ILE* 1.3 74.4 - - - +
315B PRO* 1.3 64.6 - - - +
316B ALA 4.3 4.0 - - - +
322B ARG* 5.7 1.8 + - - +
355B VAL* 5.1 4.9 + - - +
359B GLN* 4.7 28.0 - - - +
1194D ALA 4.7 2.0 - - - +
1195D PHE* 3.5 46.4 - - + +
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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