Contacts of the helix formed by residues 247 - 259 (chain A) in PDB entry 3E6G
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 GLY 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ASN* 5.1 1.1 - - - -
245A VAL* 3.8 2.9 + - - -
246A GLN* 1.3 78.1 - - - +
248A PRO* 1.4 76.6 - - - +
249A PHE 3.4 2.2 - - - -
250A ASP* 3.4 12.5 + - - -
251A SER* 2.9 25.9 + - - -
250B ASP* 4.4 11.2 - - - -
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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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39A ILE* 3.8 17.9 - - + -
40A TYR 3.2 28.9 - - - +
41A ALA* 4.4 7.2 - - + -
42A THR 5.0 2.9 - - - +
63A ASN* 3.4 26.2 - - - +
65A THR* 3.5 7.9 - - - +
247A GLY* 1.4 80.6 - - - +
249A PHE* 1.3 62.9 + - + +
251A SER* 3.4 4.3 - - - -
252A PHE* 2.8 28.2 + - - +
217B ASP 5.9 0.7 - - - +
218B MET* 6.2 3.6 - - - -
219B VAL 6.2 2.2 - - - +
250B ASP* 4.5 13.9 - - - +
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Residues in contact with PHE 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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39A ILE* 4.2 15.5 - - + -
41A ALA* 4.5 11.4 - - + -
247A GLY 3.4 0.4 - - - -
248A PRO* 1.3 76.3 - - + +
250A ASP* 1.3 62.7 + - - +
252A PHE* 3.0 9.0 + + - +
253A LEU* 2.8 33.2 + - + +
217B ASP 5.7 0.2 - - - -
249B PHE* 3.4 57.2 - + + -
250B ASP* 4.0 13.0 - - - -
253B LEU* 4.1 28.9 - - + -
39C ILE* 3.9 21.1 - - + -
249C PHE* 3.5 36.6 - + - -
252C PHE* 5.2 2.5 - + - -
249D PHE* 5.9 1.6 - + - -
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Residues in contact with ASP 250 (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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218A MET* 3.9 20.6 - - - +
219A VAL 4.7 5.0 + - - +
246A GLN* 3.5 28.3 - - - +
247A GLY* 3.4 10.6 + - - +
248A PRO 3.4 0.4 - - - -
249A PHE* 1.3 76.7 - - - +
251A SER* 1.3 59.2 + - - +
253A LEU* 3.1 8.7 + - - +
254A ALA* 2.8 31.7 + - - +
247B GLY* 4.6 9.8 - - - -
248B PRO* 4.3 9.4 - - - +
249B PHE* 3.2 29.4 - - - -
250B ASP* 4.3 12.8 - - - +
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Residues in contact with SER 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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65A THR* 4.2 3.1 - - - -
66A ARG* 3.4 40.7 - - - +
69A TYR* 3.9 20.0 - - - +
246A GLN* 3.2 15.8 - - - +
247A GLY 2.9 22.7 + - - -
248A PRO 3.4 4.5 - - - -
250A ASP* 1.3 76.9 - - - +
252A PHE* 1.3 57.0 + - - -
254A ALA 3.8 0.2 - - - -
255A LEU* 2.9 33.5 + - - +
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Residues in contact with PHE 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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36A MET* 4.9 8.3 - - + -
37A PRO* 4.0 27.8 - - + -
39A ILE* 3.5 38.1 - - + -
65A THR* 3.9 11.4 - - + +
248A PRO 2.8 16.9 + - - +
249A PHE* 3.0 4.4 + - - +
251A SER* 1.3 78.5 - - - +
253A LEU* 1.3 73.4 + - + +
255A LEU* 4.0 5.3 - - + +
256A ARG* 3.1 32.0 + - + +
41C ALA* 4.2 14.1 - - + -
249C PHE* 5.1 2.0 - + - -
217D ASP* 3.5 39.0 - - + -
253D LEU* 4.7 11.9 - - + -
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Residues in contact with LEU 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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213A ASN* 3.3 11.8 + - - +
217A ASP* 5.0 3.8 - - - +
218A MET* 4.5 13.0 - - + -
249A PHE* 2.8 19.1 + - + +
250A ASP* 3.1 6.0 + - - +
252A PHE* 1.3 90.9 - - + +
254A ALA* 1.3 60.3 + - - +
256A ARG* 3.3 6.6 + - - +
257A GLY 2.8 23.6 + - - -
249B PHE* 3.1 40.8 - - + -
249C PHE* 6.5 0.4 - - + -
252D PHE* 4.3 13.9 - - + -
253D LEU* 4.3 21.1 - - + -
256D ARG* 3.4 29.4 + - - +
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Residues in contact with ALA 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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69A TYR* 3.3 37.2 - - + +
208A ALA* 4.9 0.4 - - + -
212A LEU 4.1 4.2 - - - +
213A ASN* 3.5 12.9 - - + +
218A MET* 4.0 18.8 - - + -
250A ASP 2.8 17.1 + - - +
253A LEU* 1.3 75.4 - - - +
255A LEU* 1.3 59.8 + - - +
257A GLY* 3.1 1.9 + - - -
258A LEU* 2.8 30.7 + - - +
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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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21A ALA 5.7 1.1 - - - +
26A GLN* 3.8 18.2 - - + +
37A PRO* 3.9 15.3 - - + -
65A THR* 4.5 5.4 - - + +
68A ALA* 3.7 16.8 - - + -
69A TYR* 3.6 32.3 - - + +
72A CYS* 3.9 30.7 - - + -
251A SER 2.9 19.1 + - - +
252A PHE* 4.0 6.7 - - + +
254A ALA* 1.3 75.5 - - - +
256A ARG* 1.3 65.3 + - - +
258A LEU* 3.2 22.6 - - + +
259A LYS* 3.6 20.6 + - - +
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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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36A MET* 6.5 0.4 - - - -
215A HIS* 5.9 1.0 - - - -
252A PHE* 3.1 29.6 + - + +
253A LEU* 3.5 8.3 - - - +
254A ALA 3.2 0.2 - - - -
255A LEU* 1.3 76.5 - - - +
257A GLY* 1.3 63.0 + - - +
259A LYS* 3.1 30.6 + - + +
213D ASN* 2.6 32.5 + - - +
215D HIS* 3.5 42.5 + - + +
217D ASP* 2.6 36.4 + - - +
253D LEU* 3.2 32.0 + - - +
256D ARG* 3.3 27.8 - - - +
257D GLY* 3.8 10.7 - - - +
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Residues in contact with GLY 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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212A LEU 3.6 0.9 - - - -
213A ASN 3.3 22.7 - - - -
215A HIS* 4.4 10.1 - - - -
253A LEU 2.8 17.0 + - - -
254A ALA 3.1 3.3 + - - -
256A ARG* 1.3 72.2 - - - +
258A LEU* 1.3 60.1 + - - +
260A THR* 2.9 14.2 + - - -
264A ARG* 2.7 25.1 + - - -
215D HIS* 5.8 1.1 - - - -
256D ARG* 4.1 2.8 - - - +
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Residues in contact with LEU 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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21A ALA* 3.6 18.3 - - - +
69A TYR* 4.1 9.6 - - + -
72A CYS* 3.5 34.1 - - + -
73A VAL* 3.9 23.1 - - + +
76A LEU* 4.0 18.2 - - + -
212A LEU* 3.5 43.8 + - + +
254A ALA 2.8 9.7 + - - +
255A LEU* 3.2 20.6 - - + +
257A GLY* 1.3 76.1 - - - +
259A LYS* 1.3 60.5 + - - +
261A LEU* 3.1 21.8 + - + +
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Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ALA 5.6 0.2 - - - +
21A ALA* 3.6 18.4 + - - +
22A ILE* 4.0 30.4 + - + +
26A GLN* 4.9 6.3 - - - +
36A MET* 3.6 39.1 - - + -
37A PRO* 5.4 2.8 - - - +
255A LEU* 3.6 32.1 + - - +
256A ARG* 3.1 20.2 + - + +
257A GLY 2.9 0.6 + - - -
258A LEU* 1.3 78.0 - - - +
260A THR* 1.3 58.5 + - - +
261A LEU 3.3 1.1 + - - -
262A PRO* 4.1 5.9 - - - +
215D HIS* 4.1 15.3 - - + +
343D VAL* 3.7 22.9 - - + -
379D ILE* 3.8 17.0 - - - +
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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