Contacts of the helix formed by residues 259 - 274 (chain A) in PDB entry 3J2I
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 MET 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A LYS* 1.3 91.7 - - + +
260A LYS* 1.3 66.2 + - + +
261A THR* 3.8 11.4 - - - +
262A SER* 3.1 10.9 + - - +
263A ARG* 3.0 26.6 + - - +
295A GLU* 3.4 20.0 + - + +
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Residues in contact with LYS 260 (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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258A LYS 4.1 0.6 + - - -
259A MET* 1.3 74.5 - - + +
261A THR* 1.3 71.3 + - + +
263A ARG* 3.4 28.0 - - - +
264A ALA* 3.0 30.8 + - - +
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Residues in contact with THR 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 MET* 3.8 13.2 - - - +
260A LYS* 1.3 88.0 - - + +
262A SER* 1.3 61.9 + - - +
264A ALA* 3.5 4.9 + - - +
265A PHE* 2.9 31.3 + - - +
288A LYS* 5.1 8.4 - - + +
291A MET* 4.0 38.1 - - + +
292A GLY* 4.4 2.5 + - - -
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Residues in contact with SER 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.6 16.7 - - - +
259A MET* 3.1 13.3 + - - +
261A THR* 1.3 78.4 + - - +
263A ARG* 1.3 61.7 + - - +
265A PHE* 3.3 1.2 + - - +
266A PHE* 2.9 30.7 + - - +
291A MET 4.3 2.3 + - - -
292A GLY* 4.1 21.7 - - - -
295A GLU* 2.9 42.1 + - - +
296A CYS* 4.0 1.7 - - - -
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Residues in contact with ARG 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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256A GLY 5.7 0.2 - - - -
257A LEU* 3.0 46.1 + - + +
258A LYS* 3.1 24.4 + - - +
259A MET 3.0 11.6 + - - +
260A LYS* 3.4 32.2 - - - +
262A SER* 1.3 78.4 - - - +
264A ALA* 1.3 57.2 + - - +
266A PHE* 3.4 7.1 - - - +
267A SER* 3.0 26.3 + - - -
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Residues in contact with ALA 264 (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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260A LYS 3.0 17.6 + - - +
261A THR* 3.9 5.2 - - - +
263A ARG* 1.3 74.2 - - - +
265A PHE* 1.3 60.2 + - - +
267A SER* 3.2 8.8 + - - -
268A GLU* 3.0 41.6 + - - +
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Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A THR 2.9 18.8 + - - +
262A SER 3.6 3.8 - - - +
264A ALA* 1.3 73.6 - - - +
266A PHE* 1.3 65.5 + - - +
268A GLU* 3.1 10.1 + - - +
269A VAL* 2.9 42.0 + - + +
278A PHE* 4.5 2.5 - + - -
280A LEU* 4.0 8.7 - - + -
283A PHE* 3.6 34.5 - + - -
288A LYS 4.7 3.4 - - - +
289A ALA* 3.8 27.6 - - + -
292A GLY* 3.6 25.4 - - - -
293A VAL* 3.5 31.6 - - + -
296A CYS* 4.1 7.0 - - - -
302A LEU* 3.8 19.1 - - + -
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Residues in contact with PHE 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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249A ARG* 3.8 34.6 - - + -
253A LYS 5.8 0.9 - - - -
254A GLN* 5.0 11.2 - - - -
255A TYR 5.7 1.1 - - - -
257A LEU* 3.8 11.7 - - + -
262A SER 2.9 20.9 + - - +
263A ARG* 3.4 7.9 - - - +
265A PHE* 1.3 72.6 - - - +
267A SER* 1.3 68.0 + - - +
269A VAL* 3.4 7.1 + - - +
270A GLU* 3.0 36.6 + - - +
296A CYS* 4.3 7.9 - - - -
301A LEU* 3.9 37.7 - - + -
302A LEU* 6.6 0.2 - - + -
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Residues in contact with SER 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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263A ARG 3.0 13.6 + - - -
264A ALA* 3.2 11.4 + - - -
266A PHE* 1.3 82.6 - - - +
268A GLU* 1.3 60.4 + - - +
270A GLU* 3.4 4.5 + - - +
271A ARG* 3.0 30.0 + - - +
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Residues in contact with GLU 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 ALA* 3.0 26.5 + - - +
265A PHE* 3.6 10.1 - - - +
267A SER* 1.3 75.8 - - - +
269A VAL* 1.3 59.8 + - - +
271A ARG* 3.4 24.5 + - - +
272A ARG* 2.9 40.8 + - - +
283A PHE* 3.5 30.8 - - + -
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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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249A ARG* 4.0 26.0 - - + -
265A PHE* 2.9 36.2 + - + +
266A PHE* 3.6 7.2 - - - +
268A GLU* 1.3 76.3 - - - +
270A GLU* 1.3 63.0 + - - +
273A PHE* 2.9 28.6 + - + -
274A ASP 3.4 5.1 + - - +
278A PHE* 3.7 38.4 - - + -
283A PHE* 3.8 19.3 - - + -
302A LEU* 4.2 7.2 - - + -
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Residues in contact with GLU 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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249A ARG* 3.6 46.7 + - - +
266A PHE* 3.0 33.9 + - - +
267A SER* 3.8 5.3 - - - +
268A GLU 3.3 0.2 - - - -
269A VAL* 1.3 76.7 - - - +
271A ARG* 1.3 64.6 + - - +
274A ASP* 3.0 28.6 + - - +
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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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71A LYS* 5.2 9.7 + - - -
267A SER 3.0 16.6 + - - +
268A GLU* 3.8 21.3 - - - +
270A GLU* 1.3 81.3 - - - +
272A ARG* 1.3 91.6 + - - +
274A ASP 4.6 0.5 + - - -
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Residues in contact with ARG 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 GLU* 2.9 27.5 + - - +
271A ARG* 1.3 110.9 - - - +
273A PHE* 1.3 98.0 + - + +
282A ALA* 3.0 34.5 + - - +
283A PHE* 4.0 18.8 - - - +
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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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74A ILE 6.1 1.1 - - - -
269A VAL* 2.9 20.0 + - + +
272A ARG* 1.3 121.4 - - + +
274A ASP* 1.3 73.4 + - - +
275A ALA 3.0 0.2 + - - -
276A MET* 2.9 44.6 + - + +
277A PRO 5.4 1.1 - - - -
278A PHE* 3.6 35.2 - + + -
282A ALA* 3.7 19.7 - - + -
283A PHE* 3.6 30.1 - + - -
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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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71A LYS* 2.9 31.7 + - + +
193A HIS* 5.5 11.2 + - - +
249A ARG* 3.4 40.0 + - - +
269A VAL* 3.4 5.0 + - - +
270A GLU* 3.0 25.7 + - - +
271A ARG 4.6 0.6 + - - +
272A ARG 3.8 0.2 - - - -
273A PHE* 1.3 79.7 - - - +
275A ALA* 1.3 68.8 + - - +
276A MET* 3.9 2.8 + - + +
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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