Contacts of the helix formed by residues 247 - 265 (chain A) in PDB entry 1K7E
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ASN* 2.9 17.7 + - - +
246A ALA* 1.3 78.8 + - - +
248A PRO* 1.3 75.7 - - - +
249A LYS* 3.2 2.4 + - - -
250A GLN* 3.3 28.7 + - - +
251A MET 2.8 20.1 + - - -
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Residues in contact with PRO 248 (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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32A GLN* 3.6 32.0 + - - +
244A ASN 4.6 0.9 - - - +
245A LEU 4.2 7.6 - - - +
246A ALA 3.3 11.4 - - - +
247A SER* 1.3 89.2 - - - +
249A LYS* 1.3 60.7 + - + +
251A MET* 3.0 25.9 + - + +
252A LEU* 3.2 9.1 + - - +
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Residues in contact with LYS 249 (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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247A SER* 3.3 1.5 - - - -
248A PRO* 1.3 78.7 - - + +
250A GLN* 1.3 57.7 + - - +
252A LEU* 3.2 14.1 + - + +
253A ALA* 3.0 26.9 + - - +
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Residues in contact with GLN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASN* 3.0 24.6 + - - +
247A SER* 3.3 28.3 + - - +
249A LYS* 1.3 73.8 - - - +
251A MET* 1.3 65.6 - - - +
253A ALA* 4.2 8.3 - - + -
254A GLU* 2.9 40.6 + - + +
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Residues in contact with MET 251 (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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28A PRO* 4.3 7.4 - - + -
32A GLN* 3.2 23.1 - - - +
36A ILE* 3.9 14.6 - - - -
240A ILE* 4.2 2.3 - - - +
241A ILE* 3.6 46.9 - - + +
244A ASN* 3.5 36.4 - - + +
245A LEU* 3.8 14.1 - - + +
247A SER 2.8 13.1 + - - +
248A PRO* 3.0 18.1 + - + +
250A GLN* 1.3 73.2 - - - +
252A LEU* 1.3 62.1 + - - +
254A GLU* 3.2 1.4 + - - +
255A LEU* 3.0 33.5 + - + +
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Residues in contact with LEU 252 (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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32A GLN* 4.0 9.9 - - - +
35A LYS* 3.9 22.9 - - + +
36A ILE* 3.6 39.0 - - + +
39A THR* 3.4 29.2 - - + +
248A PRO* 3.2 14.1 + - + +
249A LYS* 3.2 12.8 + - + +
251A MET* 1.3 77.1 - - - +
253A ALA* 1.4 57.4 + - - +
255A LEU* 3.3 7.7 - - + +
256A ARG* 2.8 30.2 + - - +
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Residues in contact with ALA 253 (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 LYS 3.0 16.6 + - - +
250A GLN* 3.8 11.0 - - + +
251A MET 3.2 0.2 - - - -
252A LEU* 1.4 76.9 - - - +
254A GLU* 1.3 63.9 + - + +
256A ARG* 3.2 10.1 + - - +
257A SER* 3.1 24.9 + - - -
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Residues in contact with GLU 254 (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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240A ILE* 3.8 26.6 - - + +
243A LYS* 5.6 4.5 - - - +
244A ASN* 3.2 27.3 + - - +
250A GLN* 2.9 35.7 + - + +
253A ALA* 1.3 74.6 - - + +
255A LEU* 1.3 62.7 + - - +
257A SER* 3.9 6.9 - - - +
258A PHE* 3.0 24.3 + - - +
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Residues in contact with LEU 255 (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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36A ILE* 3.7 41.3 - - + +
39A THR* 4.1 7.9 - - + -
40A LEU* 4.5 9.9 - - + -
237A ILE* 4.0 27.1 - - + +
240A ILE* 3.7 32.1 - - + -
241A ILE* 4.2 6.1 - - + -
251A MET* 3.0 28.7 + - + +
252A LEU* 3.3 15.5 - - + +
254A GLU* 1.3 72.0 - - - +
256A ARG* 1.3 69.2 + - - +
258A PHE* 4.6 2.2 - - - -
259A VAL* 2.8 31.2 + - - +
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Residues in contact with ARG 256 (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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39A THR* 4.0 20.5 + - + +
42A ASP* 2.9 51.5 + - - +
43A ALA* 3.6 17.0 - - + +
252A LEU 2.8 14.4 + - - +
253A ALA* 3.2 13.4 - - - +
255A LEU* 1.3 80.7 - - - +
257A SER* 1.3 66.2 + - - +
260A SER* 2.8 27.3 + - - -
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Residues in contact with SER 257 (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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253A ALA 3.1 10.5 + - - -
254A GLU* 3.9 8.1 - - - -
256A ARG* 1.3 79.7 - - - +
258A PHE* 1.4 64.7 + - - +
260A SER* 3.3 5.9 + - - -
261A ALA* 3.0 23.6 + - - +
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Residues in contact with PHE 258 (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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19A PHE* 4.7 1.8 - + - -
215A SER 3.3 24.7 - - - -
216A SER* 5.0 0.2 - - - -
217A PRO* 5.3 2.2 - - + -
233A SER* 4.1 7.0 - - - -
236A ALA* 3.8 19.7 - - + -
237A ILE* 3.7 33.0 - - + -
240A ILE* 3.6 24.0 - - + -
254A GLU 3.0 17.1 + - - +
255A LEU* 3.9 2.7 - - - +
257A SER* 1.4 73.3 - - - +
259A VAL* 1.3 71.5 + - + +
261A ALA* 3.1 7.6 + - + +
262A MET* 2.8 61.4 + - + +
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Residues in contact with VAL 259 (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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19A PHE* 4.1 18.4 - - + -
21A PRO* 4.9 0.9 - - + -
40A LEU* 3.6 41.1 - - + +
43A ALA* 3.6 27.1 - - + +
44A GLY 4.3 0.9 - - - -
45A ALA* 3.9 12.1 - - + +
237A ILE* 3.9 20.4 - - + -
255A LEU* 2.8 26.8 + - - +
258A PHE* 1.3 77.2 - - + +
260A SER* 1.3 65.6 + - - +
262A MET* 3.1 2.0 + - - +
263A LYS* 2.8 22.0 + - - +
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Residues in contact with SER 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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43A ALA* 3.7 17.9 + - - -
256A ARG* 2.8 19.1 + - - -
257A SER* 3.4 7.4 - - - -
259A VAL* 1.3 82.0 - - - +
261A ALA* 1.3 57.1 + - - +
263A LYS* 3.9 1.7 - - - +
264A ALA* 2.8 33.6 + - - +
267A ARG* 5.2 0.3 + - - -
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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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217A PRO* 4.0 22.6 - - + +
257A SER 3.0 13.5 + - - +
258A PHE* 3.3 14.1 - - + +
260A SER* 1.3 80.7 - - - +
262A MET* 1.4 63.2 + - + +
264A ALA* 3.9 5.1 - - - +
265A ALA* 3.3 18.7 + - - +
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Residues in contact with MET 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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19A PHE* 3.5 36.5 - - + +
214A ILE* 3.7 17.0 - - + +
215A SER* 3.9 4.3 - - - -
216A SER 3.4 20.9 - - - +
217A PRO* 3.2 33.7 - - - -
220A VAL* 3.4 41.5 - - + +
233A SER* 4.4 0.4 - - - +
258A PHE* 2.8 47.4 + - + +
259A VAL 3.7 0.2 - - - +
261A ALA* 1.4 73.8 - - - +
263A LYS* 1.3 61.2 + - - +
265A ALA* 3.1 16.6 + - - +
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Residues in contact with LYS 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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11A LEU* 3.9 0.6 - - - +
14A ARG* 5.4 0.2 - - - +
16A GLU* 3.2 29.6 + - - +
17A GLY 2.9 10.7 + - - -
19A PHE* 4.2 12.8 - - + -
43A ALA 4.4 6.1 - - - +
44A GLY* 3.4 32.3 - - - +
46A ASP* 2.7 33.3 + - - +
259A VAL 2.8 20.3 + - - +
260A SER* 3.9 3.1 - - - +
262A MET* 1.3 69.3 - - - +
264A ALA* 1.3 72.7 + - - +
265A ALA 3.0 1.8 - - - -
266A SER* 2.6 47.1 + - - +
267A ARG* 3.4 30.3 + - - +
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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 SER 2.8 19.7 + - - +
261A ALA* 3.9 5.2 - - - +
263A LYS* 1.3 82.5 - - - +
265A ALA* 1.3 62.2 + - - +
266A SER 3.0 1.7 + - - -
267A ARG* 3.1 41.5 - - - +
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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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217A PRO* 3.5 34.8 - - + +
220A VAL* 4.2 3.8 - - + -
221A SER* 3.7 24.1 - - - +
224A VAL* 4.9 0.5 - - - +
261A ALA 3.3 11.2 + - - +
262A MET 3.1 11.5 + - - +
263A LYS 3.0 1.2 - - - -
264A ALA* 1.3 78.4 - - - +
266A SER* 1.3 57.6 + - - +
267A ARG 3.2 5.8 + - - +
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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