Contacts of the helix formed by residues 261 - 274 (chain A) in PDB entry 4BM9
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 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A VAL* 4.1 30.1 - - + -
229A ILE* 4.0 20.4 - - + -
247A PRO* 3.9 36.4 + - + +
248A VAL 4.4 1.1 - - - -
249A LEU* 4.2 26.2 - - + +
260A CYS* 1.3 72.9 - - - +
262A ASP* 1.3 63.1 + - - +
264A PHE* 3.8 4.6 - - + +
265A HIS* 2.8 31.2 + - - +
306A ILE* 4.4 16.6 - - + +
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Residues in contact with ASP 262 (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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245A ARG* 5.3 11.7 + - - +
260A CYS* 3.3 12.2 - - - -
261A LEU* 1.3 78.5 - - - +
263A CYS* 1.3 65.1 + - - +
265A HIS* 3.4 9.2 + - - +
266A LEU* 3.2 21.5 + - - +
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Residues in contact with CYS 263 (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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238A CYS* 3.8 2.9 - - - -
240A THR* 4.0 17.9 - - + -
241A CYS* 3.7 15.9 - - - -
259A ILE* 3.7 22.2 - - + +
260A CYS* 3.2 3.6 + - - +
262A ASP* 1.3 79.7 - - - +
264A PHE* 1.3 65.9 + - - +
266A LEU* 3.3 7.1 + - - +
267A TYR* 2.9 24.1 + - - +
1470A ZN 2.3 36.1 - - - -
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Residues in contact with PHE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 3.8 24.2 - - + -
251A PHE* 4.1 21.3 - + - -
259A ILE* 3.8 17.4 - - + +
260A CYS 2.9 16.8 + - - +
261A LEU* 3.8 9.0 - - + +
263A CYS* 1.3 75.0 - - - +
265A HIS* 1.3 59.4 + - - +
267A TYR* 3.3 13.5 + + - +
268A CYS* 2.9 54.2 + - - -
298A ILE* 3.6 33.4 - - + -
303A HIS* 3.6 23.6 - - + -
304A PHE* 4.2 6.7 - + - -
306A ILE* 3.7 22.0 - - + -
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Residues in contact with HIS 265 (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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261A LEU 2.8 17.7 + - - +
262A ASP* 3.5 8.1 - - - +
263A CYS 3.2 0.2 - - - -
264A PHE* 1.3 77.7 - - - +
266A LEU* 1.3 69.4 + - + +
268A CYS* 3.3 4.8 + - - +
269A VAL* 3.0 46.5 + - + +
306A ILE* 2.6 36.0 + - + +
307A LEU* 3.2 25.0 - - - -
308A GLY* 5.3 0.4 - - - -
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASP 3.2 13.0 + - - +
263A CYS* 3.3 7.8 + - - +
265A HIS* 1.3 84.2 - - + +
267A TYR* 1.3 65.9 + - - +
269A VAL* 4.5 8.5 - - + -
270A THR* 3.0 47.3 + - + +
380A VAL* 4.4 26.5 - - + -
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Residues in contact with TYR 267 (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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251A PHE* 4.2 5.4 - + - -
259A ILE* 4.8 0.7 - - + -
263A CYS 2.9 13.6 + - - +
264A PHE* 3.3 27.4 - + - +
266A LEU* 1.3 76.7 - - - +
268A CYS* 1.3 62.2 + - - +
270A THR* 3.1 6.9 + - - -
271A ARG* 3.1 65.6 + - + +
287A LEU* 3.7 24.8 - - + +
288A PRO* 2.8 42.5 + - - +
289A CYS 3.9 1.4 + - - -
290A VAL* 3.5 43.5 + - + -
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Residues in contact with CYS 268 (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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264A PHE* 2.9 59.4 + - - +
265A HIS* 3.8 4.5 - - - +
267A TYR* 1.3 76.4 - - - +
269A VAL* 1.3 58.8 + - - +
272A LEU* 2.9 31.2 + - - +
277A PHE* 3.7 5.7 - - + -
287A LEU* 4.0 13.0 - - + -
304A PHE* 3.7 22.2 - - + -
306A ILE* 5.8 1.8 - - - -
307A LEU* 3.6 23.7 - - + +
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Residues in contact with VAL 269 (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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265A HIS* 3.0 46.7 + - + +
266A LEU* 3.9 11.7 - - + +
268A CYS* 1.3 76.9 - - - +
270A THR* 1.3 59.7 + - + +
272A LEU* 3.5 3.1 + - - +
273A ASN* 3.0 27.9 + - - +
307A LEU* 3.8 20.9 - - + +
311A GLN* 3.8 18.5 - - + +
380A VAL* 5.7 0.2 - - + -
381A PHE* 3.6 28.0 - - + -
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Residues in contact with THR 270 (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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266A LEU* 3.0 41.4 + - + +
267A TYR* 3.1 6.9 + - - -
269A VAL* 1.3 76.8 - - - +
271A ARG* 1.3 79.1 + - - +
273A ASN 3.5 0.5 + - - -
274A ASP* 2.9 45.3 + - - +
380A VAL* 3.8 26.5 - - + +
381A PHE* 4.1 9.9 - - + -
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Residues in contact with ARG 271 (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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267A TYR* 3.1 43.3 + - + +
268A CYS 3.9 0.7 - - - +
270A THR* 1.3 95.4 + - - +
272A LEU* 1.3 65.5 + - - +
274A ASP* 4.8 1.3 - - - -
275A ARG 3.0 2.6 + - - -
276A GLN* 2.7 52.5 + - + +
277A PHE* 3.8 5.4 - - + -
287A LEU* 3.6 39.0 - - + -
290A VAL* 5.2 4.9 + - - +
391A TYR* 3.3 38.1 - - - +
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Residues in contact with LEU 272 (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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268A CYS 2.9 18.6 + - - +
269A VAL 3.7 4.3 - - - +
271A ARG* 1.3 77.3 - - - +
273A ASN* 1.3 63.3 + - - +
275A ARG* 3.1 46.9 + - - +
277A PHE* 3.5 13.9 - - + -
307A LEU* 4.1 13.5 - - + -
311A GLN* 3.4 46.2 - - + +
314A ARG* 4.2 20.9 - - + +
315A TYR* 4.1 14.8 - - + -
318A TYR* 3.8 17.9 - - + -
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Residues in contact with ASN 273 (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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269A VAL 3.0 14.4 + - - +
270A THR 4.0 0.7 - - - +
272A LEU* 1.3 80.4 - - - +
274A ASP* 1.3 68.6 + - - +
275A ARG* 3.2 11.5 + - - +
311A GLN* 5.7 2.8 + - - +
314A ARG* 3.8 21.9 + - - +
367A GLU 3.7 19.2 + - - +
368A CYS* 3.3 25.1 + - - +
381A PHE* 3.4 49.0 - - + +
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Residues in contact with ASP 274 (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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270A THR* 2.9 31.5 + - - +
271A ARG* 4.8 0.9 - - - -
273A ASN* 1.3 89.3 - - - +
275A ARG* 1.3 72.5 + - - +
276A GLN* 3.4 25.6 + - + -
380A VAL 4.5 5.4 - - - +
381A PHE* 3.7 15.9 - - - +
382A GLU 4.8 0.2 - - - +
383A ALA* 3.3 34.3 + - - -
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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
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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