Contacts of the helix formed by residues 260 - 273 (chain A) in PDB entry 3CQ6
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PRO* 3.9 1.3 - - - -
96A ASN* 5.1 1.2 + - - -
258A HIS 4.1 1.8 + - - -
259A LEU* 1.3 73.6 - - - +
261A ALA* 1.3 59.3 + - - +
262A LEU* 3.9 4.8 + - - +
263A SER* 2.8 35.2 + - - -
264A GLN* 2.8 32.2 + - - +
96C ASN* 5.7 3.1 + - - -
234C GLY 3.6 11.9 - - - -
235C GLY* 4.2 11.0 - - - -
236C ARG* 3.8 22.3 - - - +
263C SER* 3.9 10.9 + - - -
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Residues in contact with ALA 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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56A ILE* 3.9 9.9 - - + +
59A GLU* 5.9 2.2 - - + +
60A LEU* 3.6 17.9 - - + -
62A ARG 5.6 0.2 - - - +
64A PRO* 3.4 20.8 - - + +
260A SER* 1.3 72.7 - - - +
262A LEU* 1.3 57.4 + - - +
264A GLN* 3.4 5.7 + - - +
265A ALA* 2.9 31.2 + - - +
234C GLY* 3.1 18.6 + - - +
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Residues in contact with LEU 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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53A VAL* 4.6 22.4 - - + -
56A ILE* 3.4 27.8 - - + -
57A ALA* 5.6 0.7 - - - -
60A LEU* 4.4 25.4 - - + -
260A SER* 3.3 6.3 + - - +
261A ALA* 1.3 76.4 - - - +
263A SER* 1.3 66.8 + - - +
265A ALA* 3.9 0.8 - - + +
266A ALA* 2.9 29.1 + - - +
49C LEU* 4.7 7.6 - - + -
53C VAL* 5.8 5.2 - - + -
232C PHE* 5.9 0.2 - - + -
234C GLY 4.5 1.3 + - - +
235C GLY* 5.9 3.4 - - - -
262C LEU* 4.1 29.3 - - + +
263C SER* 5.2 2.2 - - - +
266C ALA* 3.6 31.2 - - + -
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Residues in contact with SER 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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96A ASN* 4.2 10.0 + - - -
232A PHE* 5.6 0.5 - - - -
235A GLY* 4.3 15.8 + - - +
237A LEU* 5.0 5.9 - - - +
259A LEU* 4.7 13.2 - - - -
260A SER* 2.8 33.3 + - - -
262A LEU* 1.3 75.8 - - - +
264A GLN* 1.3 63.7 + - - +
266A ALA* 3.9 3.6 - - - +
267A ALA* 3.0 26.3 + - - +
260C SER* 4.1 14.9 + - - -
262C LEU* 5.6 2.6 - - - +
263C SER* 4.4 1.4 + - - -
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Residues in contact with GLN 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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64A PRO* 3.9 8.3 - - - +
65A GLU* 2.9 32.6 + - - +
68A ALA* 3.3 35.4 - - + +
70A GLU* 5.6 2.2 - - - +
71A LEU* 4.3 20.4 - - + +
259A LEU* 3.2 33.0 - - + +
260A SER 2.8 17.5 + - - +
261A ALA* 3.7 5.2 - - - +
263A SER* 1.3 78.6 - - - +
265A ALA* 1.3 62.2 + - - +
267A ALA* 3.3 2.8 + - - +
268A ILE* 3.0 33.0 + - + +
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Residues in contact with ALA 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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49A LEU* 5.2 1.1 - - + -
52A THR* 4.3 17.2 - - + +
53A VAL* 6.5 1.1 - - + -
56A ILE* 3.8 25.8 - - + -
261A ALA 2.9 17.9 + - - +
262A LEU* 3.9 2.7 - - + +
263A SER 3.3 0.2 - - - -
264A GLN* 1.3 76.9 - - - +
266A ALA* 1.3 56.9 + - - +
268A ILE* 3.4 12.6 + - - +
269A VAL* 3.0 32.7 + - - +
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Residues in contact with ALA 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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45A LEU* 5.7 0.2 - - - +
49A LEU* 3.8 23.4 - - + +
232A PHE* 3.7 20.2 - - + -
235A GLY* 6.1 0.4 - - - -
262A LEU 2.9 17.8 + - - +
263A SER* 4.0 3.1 - - - +
265A ALA* 1.3 74.3 - - - +
267A ALA* 1.3 60.4 + - - +
269A VAL* 3.3 3.5 + - - +
270A ALA* 2.9 27.7 + - - +
262C LEU* 3.7 25.4 - - + -
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Residues in contact with ALA 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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71A LEU* 3.6 20.6 - - + -
226A MET* 4.0 8.7 - - - +
232A PHE* 4.2 6.8 - - + -
237A LEU* 3.8 24.7 - - + -
263A SER 3.0 17.2 + - - +
264A GLN 3.7 1.1 - - - +
266A ALA* 1.3 73.8 - - - +
268A ILE* 1.3 60.7 + - - +
270A ALA* 3.3 7.6 + - - +
271A LEU* 2.9 36.6 + - - +
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Residues in contact with ILE 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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70A GLU* 3.8 31.9 - - + +
71A LEU* 3.7 38.6 - - + +
74A GLU* 4.5 16.4 - - + +
264A GLN* 3.0 26.6 + - + +
265A ALA* 3.5 11.9 - - - +
266A ALA 3.3 0.2 - - - -
267A ALA* 1.3 78.1 - - - +
269A VAL* 1.3 64.8 + - + +
271A LEU* 3.3 8.3 + - - +
272A ARG* 3.3 40.7 + - - +
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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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45A LEU* 3.6 31.4 - - + +
48A ASP* 3.7 16.8 - - + +
49A LEU* 3.7 13.2 - - + +
52A THR* 3.4 32.5 - - + +
265A ALA 3.0 20.8 + - - +
266A ALA* 3.6 8.5 - - - +
268A ILE* 1.3 75.2 - - + +
270A ALA* 1.3 64.6 + - - +
272A ARG* 3.1 30.9 + - - +
273A HIS* 3.2 21.1 + - - +
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Residues in contact with ALA 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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45A LEU* 3.9 17.3 - - + +
226A MET* 3.7 18.2 - - + -
230A PHE* 3.9 11.8 - - + +
232A PHE* 4.2 23.6 - - + -
266A ALA 2.9 16.8 + - - +
267A ALA* 3.5 6.3 - - - +
269A VAL* 1.3 76.6 - - - +
271A LEU* 1.3 64.1 + - - +
273A HIS* 2.9 16.1 + - - +
274A SER 3.5 6.6 + - - -
277A THR* 5.0 0.5 + - - -
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Residues in contact with LEU 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 LEU* 3.9 20.6 - - + -
74A GLU* 3.7 31.9 - - + +
75A LEU* 3.8 25.6 - - + +
78A TYR* 4.0 22.3 - - + +
226A MET* 4.0 9.0 - - + -
230A PHE* 3.5 31.2 - - + -
267A ALA 2.9 24.7 + - - +
268A ILE* 3.6 5.6 - - - +
269A VAL 3.3 0.2 - - - -
270A ALA* 1.3 72.5 - - - +
272A ARG* 1.3 57.1 + - - +
273A HIS 3.1 0.2 - - - -
274A SER* 3.2 26.5 + - - -
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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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48A ASP* 2.9 38.5 + - - +
52A THR* 3.5 16.6 + - - +
55A LYS* 5.6 4.4 - - - +
70A GLU* 5.6 1.2 + - - -
268A ILE* 3.3 28.4 + - - +
269A VAL* 3.1 30.5 + - - +
271A LEU* 1.3 77.0 - - - +
273A HIS* 1.3 64.4 + - + +
274A SER* 3.5 1.3 + - - -
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Residues in contact with HIS 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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42A SER* 4.8 3.1 - - - +
44A ALA* 3.4 24.3 + - + +
45A LEU* 3.8 37.2 - - + -
48A ASP* 2.9 41.5 - - + +
269A VAL* 3.2 18.0 + - - +
270A ALA 2.9 10.7 + - - +
272A ARG* 1.3 86.2 - - + +
274A SER* 1.3 60.6 + - - +
275A ALA 3.4 2.4 + - - -
276A ASP* 3.5 11.5 + - + +
277A THR* 3.1 23.4 + - - +
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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