Contacts of the helix formed by residues 259 - 279 (chain A) in PDB entry 3M4A
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 SER 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU* 3.8 3.9 - - - +
258A SER* 1.3 82.2 + - - +
260A GLU* 1.3 61.2 + - - +
261A ARG* 4.2 7.0 - - - +
262A GLN* 3.1 32.4 + - - +
263A ALA* 3.0 26.4 + - - +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER 4.2 0.4 + - - -
259A SER* 1.3 72.5 - - - +
261A ARG* 1.3 56.9 + - - +
263A ALA* 3.4 7.5 + - - +
264A LYS* 3.0 57.5 + - - +
299A LEU* 4.1 32.6 - - + +
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Residues in contact with ARG 261 (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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259A SER* 3.2 6.1 - - - +
260A GLU* 1.3 79.6 - - - +
262A GLN* 1.3 80.2 + - + +
264A LYS* 3.4 18.6 + - + +
265A LYS* 3.4 11.6 + - - +
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Residues in contact with GLN 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU* 3.9 25.8 + - + +
259A SER* 3.1 26.7 + - - +
261A ARG* 1.3 96.6 + - + +
263A ALA* 1.3 64.7 + - - +
265A LYS* 3.3 35.9 + - - +
266A VAL* 3.3 16.3 + - - +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU* 3.6 19.6 - - + +
259A SER 3.0 14.6 + - - +
260A GLU* 3.5 11.7 - - - +
261A ARG 3.3 0.2 - - - -
262A GLN* 1.3 76.6 - - - +
264A LYS* 1.3 61.9 + - - +
266A VAL* 3.1 6.8 + - - +
267A LEU* 3.1 24.8 + - - +
298A TYR* 3.6 17.8 - - + +
299A LEU* 3.7 22.2 - - + +
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLU* 3.0 46.9 + - + +
261A ARG* 3.7 10.3 - - + +
262A GLN 3.3 0.6 - - - -
263A ALA* 1.3 75.9 - - - +
265A LYS* 1.3 62.2 + - - +
267A LEU* 3.3 15.8 + - + +
268A VAL* 3.1 26.1 + - - +
286A ARG* 5.3 2.9 + - - +
299A LEU* 4.1 17.9 - - + -
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU* 6.0 1.1 - - - -
261A ARG 3.4 9.6 + - - +
262A GLN* 3.3 30.4 + - - +
263A ALA 3.2 0.2 - - - -
264A LYS* 1.3 76.4 - - - +
266A VAL* 1.3 76.8 + - - +
268A VAL* 3.3 11.7 + - + +
269A ASP* 2.6 53.9 + - - +
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Residues in contact with VAL 266 (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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250A TYR* 4.7 2.7 - - + -
251A LEU* 3.7 17.7 - - + -
254A GLN* 4.1 24.2 - - + -
255A GLY 5.0 0.7 - - - +
257A GLU* 3.8 18.6 - - + +
262A GLN 3.3 13.7 + - - +
263A ALA 3.1 7.1 + - - +
265A LYS* 1.3 91.9 - - - +
267A LEU* 1.3 58.6 + - - +
269A ASP* 3.2 6.7 + - + +
270A CYS* 2.9 26.9 + - - +
298A TYR* 3.4 26.9 - - + +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 3.8 12.8 - - + -
263A ALA 3.1 14.8 + - - +
264A LYS* 3.5 13.9 - - + +
265A LYS 3.2 0.2 - - - -
266A VAL* 1.3 77.8 - - - +
268A VAL* 1.3 60.7 + - - +
270A CYS* 3.3 3.5 + - - +
271A VAL* 3.0 29.5 + - - +
286A ARG* 3.9 26.7 - - - +
295A PHE* 3.6 39.0 - - + -
298A TYR* 3.7 22.7 - - + -
299A LEU* 4.0 34.5 - - + -
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Residues in contact with VAL 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 LYS 3.1 17.1 + - - +
265A LYS* 3.5 11.9 - - + +
266A VAL 3.2 0.2 - - - -
267A LEU* 1.3 76.7 - - - +
269A ASP* 1.3 63.8 + - - +
271A VAL* 3.3 4.2 + - - +
272A LYS* 3.1 49.1 + - + +
286A ARG* 4.5 14.6 - - - +
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Residues in contact with ASP 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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250A TYR* 3.6 19.6 + - + +
265A LYS* 2.6 37.9 + - - +
266A VAL* 3.2 10.8 + - + +
268A VAL* 1.3 79.2 - - - +
270A CYS* 1.3 58.1 + - - +
272A LYS* 3.4 19.7 + - - +
273A PHE* 3.0 29.1 + - - +
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Residues in contact with CYS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ALA* 3.6 45.3 - - - -
250A TYR* 3.5 25.1 - - + -
251A LEU* 4.0 14.4 - - + -
266A VAL 2.9 13.0 + - - +
267A LEU* 3.5 10.5 - - - +
268A VAL 3.2 0.2 - - - -
269A ASP* 1.3 74.4 - - - +
271A VAL* 1.3 65.0 + - - +
273A PHE* 3.1 3.5 + - - +
274A VAL* 3.0 28.5 + - - +
290A ILE* 4.9 0.2 - - - -
295A PHE* 4.0 10.8 - - + -
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Residues in contact with VAL 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 LEU 3.0 20.3 + - - +
268A VAL* 3.3 5.8 + - - +
270A CYS* 1.3 75.3 - - - +
272A LYS* 1.3 59.1 + - + +
274A VAL 3.5 0.3 + - - -
275A ALA* 2.8 30.8 + - - +
282A PRO* 3.3 40.2 - - + +
285A THR* 4.0 4.6 - - + +
286A ARG* 3.9 30.3 - - + +
290A ILE* 4.2 11.4 - - + -
295A PHE* 3.6 29.2 - - + -
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 3.1 38.1 + - + +
269A ASP* 3.8 17.1 + - - +
271A VAL* 1.3 77.7 - - + +
273A PHE* 1.3 61.1 + - - +
275A ALA* 3.5 7.3 + - - +
276A ASP* 3.1 23.6 + - - +
282A PRO* 4.2 22.2 - - + -
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Residues in contact with PHE 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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246A LEU* 4.4 27.4 - - + -
250A TYR* 3.6 38.8 - + + -
269A ASP 3.0 16.6 + - - +
270A CYS 3.1 4.7 + - - +
272A LYS* 1.3 74.3 - - - +
274A VAL* 1.3 67.3 + - + +
276A ASP* 3.3 8.1 + - - +
277A ASP* 3.1 20.2 + - + +
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Residues in contact with VAL 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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243A GLY* 3.7 20.4 - - - +
246A LEU* 4.2 15.5 - - + -
247A ALA* 3.7 35.7 - - + +
250A TYR* 5.6 1.6 - - + -
270A CYS* 3.0 16.6 + - - +
271A VAL 4.1 2.2 - - - +
273A PHE* 1.3 74.9 - - + +
275A ALA* 1.3 60.1 + - - +
277A ASP* 3.2 7.9 + - - +
278A LEU* 2.9 50.8 + - + +
285A THR* 3.8 12.1 - - + -
290A ILE* 4.2 6.3 - - + -
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Residues in contact with ALA 275 (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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271A VAL 2.8 19.5 + - - +
272A LYS* 3.6 8.3 - - - +
273A PHE 3.3 0.2 - - - -
274A VAL* 1.3 76.3 - - - +
276A ASP* 1.3 57.1 + - - +
278A LEU* 3.4 1.1 + - - +
279A GLY* 2.9 25.1 + - - -
280A ASN 3.1 25.5 + - - +
282A PRO* 3.8 19.1 - - + -
285A THR* 3.3 24.1 - - - +
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Residues in contact with ASP 276 (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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177A VAL* 5.6 2.9 - - - +
178A SER 5.5 4.1 - - - +
179A GLN* 4.3 5.0 + - - -
180A HIS* 5.5 8.7 + - - +
272A LYS 3.1 14.1 + - - +
273A PHE* 3.5 10.5 - - - +
274A VAL 3.2 0.2 - - - -
275A ALA* 1.3 74.5 - - - +
277A ASP* 1.3 67.7 + - - +
279A GLY* 3.4 10.4 + - - -
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Residues in contact with ASP 277 (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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134A ALA 5.1 0.3 - - - +
135A ARG* 2.9 50.8 + - - +
179A GLN* 3.7 4.7 + - - -
180A HIS 5.0 10.2 - - - +
181A LYS* 3.1 30.1 + - - +
246A LEU* 3.6 21.1 - - + +
273A PHE* 3.1 13.0 + - + +
274A VAL 3.2 8.0 + - - +
276A ASP* 1.3 80.3 + - - +
278A LEU* 1.3 65.7 + - - +
279A GLY 3.5 0.2 + - - -
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Residues in contact with LEU 278 (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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135A ARG* 4.0 19.5 - - + -
137A ARG* 3.3 10.2 + - - -
179A GLN* 3.9 3.0 + - - +
181A LYS* 4.9 0.2 - - - +
239A ARG* 3.1 54.1 + - + +
243A GLY* 4.4 4.7 - - - -
274A VAL* 2.9 40.2 + - + +
275A ALA* 4.1 2.7 - - - +
277A ASP* 1.3 84.0 - - - +
279A GLY* 1.3 61.0 + - - +
280A ASN* 3.6 12.6 - - + +
285A THR* 4.2 7.4 - - + +
289A TYR* 3.8 36.8 - - + -
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Residues in contact with GLY 279 (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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137A ARG* 3.2 16.6 + - - -
174A LYS 4.6 2.8 - - - +
175A HIS* 5.5 2.9 - - - -
177A VAL* 4.1 29.7 - - - +
179A GLN* 3.7 21.0 - - - +
275A ALA 2.9 7.0 + - - -
276A ASP* 3.4 5.5 + - - -
277A ASP 3.3 3.6 + - - -
278A LEU* 1.3 78.4 - - - +
280A ASN* 1.3 57.9 + - - +
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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