Contacts of the helix formed by residues 301 - 321 (chain A) in PDB entry 4BU2
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 THR 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A PRO* 6.4 1.6 - - + -
294A LEU* 4.7 14.6 - - + -
297A GLN* 6.5 0.2 - - + -
299A GLU 4.9 1.6 - - - +
300A SER* 1.3 77.5 - - - +
302A THR* 1.3 68.4 + - - +
303A VAL* 3.0 30.5 + - + +
304A ALA* 3.0 28.9 + - + +
305A THR* 3.2 13.8 + - - +
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Residues in contact with THR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A SER 4.5 0.2 + - - -
301A THR* 1.3 72.9 + - - +
303A VAL* 1.3 67.9 + - - +
305A THR* 2.8 12.1 + - - -
306A ARG* 2.7 33.4 + - - +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PRO* 6.3 3.6 - - + -
301A THR* 3.0 27.1 - - + +
302A THR* 1.3 85.8 + - - +
304A ALA* 1.3 61.4 + - - +
306A ARG* 2.9 9.6 + - - +
307A ARG* 2.6 39.2 + - - +
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PRO* 6.4 2.0 - - + -
294A LEU* 4.9 16.2 - - + -
300A SER* 5.6 2.7 - - - -
301A THR* 3.0 27.7 + - + +
303A VAL* 1.3 81.8 - - + +
305A THR* 1.3 58.0 + - + +
307A ARG* 3.3 7.6 + - - +
308A LEU* 2.9 41.4 + - + +
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A SER* 4.5 16.4 - - - -
301A THR 3.3 18.2 - - - +
302A THR* 2.8 13.9 + - - -
303A VAL 3.2 0.2 - - - -
304A ALA* 1.3 72.3 - - + +
306A ARG* 1.3 77.1 + - - +
308A LEU* 3.2 11.0 + - + +
309A SER* 2.8 29.1 + - - -
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Residues in contact with ARG 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR 2.7 16.8 + - - +
303A VAL* 3.3 8.5 - - - +
305A THR* 1.3 78.8 + - - +
307A ARG* 1.3 63.2 + - - +
309A SER* 3.2 17.4 + - - -
310A GLY* 3.2 10.0 + - - -
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU* 2.7 43.9 + - - +
288A THR* 4.9 8.5 - - - +
303A VAL* 2.6 17.0 + - - +
304A ALA* 3.4 13.7 - - - +
306A ARG* 1.3 73.1 - - - +
308A LEU* 1.3 62.0 + - + +
310A GLY* 3.1 12.9 + - - -
311A PHE* 3.0 64.5 + - + -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA* 2.9 28.4 + - + +
305A THR* 3.2 9.4 + - + +
307A ARG* 1.3 73.1 - - + +
309A SER* 1.3 64.8 + - - +
311A PHE* 3.4 17.4 + - + +
312A LEU* 3.0 37.0 + - + +
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR* 2.8 17.9 + - - -
306A ARG* 3.2 13.9 - - - -
308A LEU* 1.3 74.7 - - - +
310A GLY* 1.3 65.8 + - - +
312A LEU* 3.2 11.5 + - - +
313A ARG* 3.0 49.6 + - - +
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Residues in contact with GLY 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ARG 3.2 5.7 + - - -
307A ARG 3.1 7.7 + - - -
309A SER* 1.3 79.4 - - - +
311A PHE* 1.3 58.4 + - - +
313A ARG* 3.1 13.5 + - - +
314A THR* 2.9 33.4 + - - -
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Residues in contact with PHE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASP* 5.0 4.5 - - - -
285A GLU* 3.8 23.1 - - + -
286A LEU* 3.4 49.8 - - + +
307A ARG* 3.0 73.3 + - + -
308A LEU* 3.7 19.7 - - + +
309A SER 3.2 0.2 - - - -
310A GLY* 1.3 78.3 - - - +
312A LEU* 1.3 63.0 + - + +
314A THR* 3.3 8.7 + - + -
315A LEU* 3.0 32.5 + - + +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 5.3 7.4 - - + -
308A LEU* 3.0 29.1 + - + +
309A SER* 3.6 8.7 - - - +
311A PHE* 1.3 76.3 - - + +
313A ARG* 1.3 59.8 + - + +
315A LEU* 3.2 19.6 + - + +
316A ALA* 2.8 28.7 + - - +
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A SER* 3.0 51.5 + - - +
310A GLY* 3.1 11.1 + - - +
312A LEU* 1.3 78.0 - - + +
314A THR* 1.3 60.1 + - - +
316A ALA* 3.1 9.0 - - - +
317A ASP* 2.9 32.7 + - - +
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Residues in contact with THR 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR* 4.4 17.3 - - + -
283A ASP* 3.9 21.5 + - + +
286A LEU* 5.8 2.0 - - + -
310A GLY 2.9 17.0 + - - -
311A PHE* 3.5 14.7 - - + +
313A ARG* 1.3 72.0 - - - +
315A LEU* 1.3 68.4 + - + +
317A ASP* 3.3 10.7 + - - +
318A ARG* 2.9 23.4 + - + +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 4.0 15.5 - - + -
275A LEU* 4.0 25.7 - - + +
276A VAL* 3.8 31.2 - - + -
279A THR* 3.7 32.8 - - + +
286A LEU* 4.8 7.6 - - + -
311A PHE* 3.0 23.5 + - + +
312A LEU* 3.4 22.9 - - + +
314A THR* 1.3 77.0 - - - +
316A ALA* 1.3 64.7 + - - +
318A ARG* 3.2 5.9 + - - +
319A LEU* 2.9 25.3 + - - +
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU 2.8 13.6 + - - +
313A ARG* 3.1 15.7 - - - +
315A LEU* 1.3 75.1 - - - +
317A ASP* 1.3 66.4 + - - +
319A LEU* 2.8 28.9 + - - +
320A GLU* 3.3 9.8 + - - +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ARG* 2.9 21.9 + - - +
314A THR* 3.6 9.1 - - - +
316A ALA* 1.3 79.7 - - - +
318A ARG* 1.3 65.3 + - - +
320A GLU* 3.1 37.4 + - - +
321A GLY 3.8 2.4 + - - -
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 5.1 3.0 - - + +
278A ASP* 2.6 37.9 + - - -
279A THR* 2.7 39.7 + - + +
282A GLU* 2.7 36.9 + - - -
314A THR* 2.9 19.3 + - + +
315A LEU* 3.6 4.7 - - - +
317A ASP* 1.3 75.9 - - - +
319A LEU* 1.3 57.1 + - - +
321A GLY* 3.2 13.0 + - - -
322A THR* 2.7 25.9 + - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 6.0 5.6 - - + -
275A LEU* 3.5 34.3 - - + +
315A LEU 2.9 8.7 + - - +
316A ALA* 2.8 19.3 + - - +
318A ARG* 1.3 76.1 - - - +
320A GLU* 1.3 51.7 + - + +
322A THR* 2.5 50.4 + - + +
325A LEU* 4.3 27.1 - - + -
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A ALA 3.5 10.5 - - - +
317A ASP* 3.1 28.9 + - - +
319A LEU* 1.3 74.2 - - - +
321A GLY* 1.3 57.8 + - - +
322A THR 3.3 6.4 + - - +
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Residues in contact with GLY 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ASP 3.8 3.0 + - - -
318A ARG 3.2 10.7 + - - -
319A LEU 3.1 1.0 - - - -
320A GLU* 1.3 77.2 - - - +
322A THR* 1.3 57.3 + - - +
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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