Contacts of the helix formed by residues 236 - 252 (chain E) in PDB entry 1G3I
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 ASN 236 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115E GLU* 6.4 0.6 - - - +
237E PRO* 1.3 83.2 - - - +
238E GLU* 3.8 16.0 + - - +
239E GLU* 3.1 41.6 + - + +
240E LEU* 3.2 23.0 + - - +
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Residues in contact with PRO 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ASN* 1.3 88.0 - - - +
238E GLU* 1.3 84.1 + - - +
240E LEU* 2.7 19.9 + - + +
241E LYS* 3.1 21.1 + - + +
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Residues in contact with GLU 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ASN* 3.8 13.2 + - - +
237E PRO* 1.3 88.8 - - - +
239E GLU* 1.3 67.0 + - - +
240E LEU 2.9 0.3 + - - -
241E LYS* 3.4 4.6 + - - +
242E GLN* 3.1 24.0 + - - +
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Residues in contact with GLU 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ASN* 3.1 31.0 + - + +
237E PRO 3.2 0.2 + - - -
238E GLU* 1.3 78.6 - - - +
240E LEU* 1.3 52.0 + - - +
242E GLN* 3.7 7.4 - - - +
243E LYS* 2.7 47.6 + - + +
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Residues in contact with LEU 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E MET* 3.9 26.5 - - + -
111E VAL* 3.3 41.3 - - + +
112E ARG* 4.3 26.0 - - - +
115E GLU* 4.3 18.6 - - + -
236E ASN 3.2 13.9 + - - +
237E PRO* 2.7 17.7 + - + +
239E GLU* 1.3 69.8 - - - +
241E LYS* 1.3 55.1 + - + +
242E GLN 3.0 0.2 - - - -
243E LYS* 2.5 29.5 + - + -
244E ALA* 2.5 17.1 + - - -
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Residues in contact with LYS 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E MET* 4.4 7.4 - - + -
237E PRO* 3.1 15.9 + - + +
238E GLU* 4.1 6.1 - - - +
240E LEU* 1.3 76.2 - - + +
242E GLN* 1.3 63.5 + - - +
244E ALA* 3.4 8.3 + - - +
245E ILE* 2.9 30.4 + - - +
294E LYS 3.4 15.2 + - - -
295E HIS* 3.5 54.7 - - + +
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Residues in contact with GLN 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E GLU 3.1 16.3 + - - +
239E GLU* 3.7 8.1 - - - +
240E LEU 2.7 3.4 + - - -
241E LYS* 1.3 73.0 - - - +
243E LYS* 1.3 61.2 + - - +
245E ILE* 2.7 30.7 + - - +
246E ASP* 2.7 47.0 + - - +
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Residues in contact with LYS 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E VAL* 4.2 16.5 - - + +
114E GLN* 5.6 7.2 - - - +
115E GLU* 3.3 30.8 + - + +
239E GLU* 2.7 30.2 + - + +
240E LEU* 2.5 12.8 + - + +
242E GLN* 1.3 74.0 - - - +
244E ALA* 1.3 64.0 + - - +
246E ASP* 3.1 13.5 + - + +
247E ALA* 3.4 14.7 + - - +
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Residues in contact with ALA 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E THR* 5.1 3.6 - - + +
107E ALA* 3.9 5.5 - - + +
108E MET* 3.6 41.5 - - + +
111E VAL* 3.4 24.5 - - + +
240E LEU 2.5 11.9 + - - +
241E LYS 3.6 7.6 - - - +
243E LYS* 1.3 70.7 - - - +
245E ILE* 1.3 56.2 + - + +
247E ALA* 2.7 35.2 + - - +
248E VAL* 3.2 3.9 + - - -
295E HIS* 5.8 0.7 - - + -
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Residues in contact with ILE 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E THR* 4.5 10.0 - - + +
241E LYS 2.9 15.6 + - - +
242E GLN* 2.7 29.2 + - - +
244E ALA* 1.3 68.5 - - - +
246E ASP* 1.3 66.7 + - - +
248E VAL* 3.1 9.5 + - - +
249E GLU* 2.8 44.8 + - + +
295E HIS* 3.4 27.8 - - + +
296E GLY* 3.8 15.5 - - - -
297E MET 4.0 17.0 - - - +
298E VAL* 3.9 13.5 - - + -
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Residues in contact with ASP 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E GLN* 2.7 49.9 + - - +
243E LYS* 3.1 18.2 - - + +
244E ALA 3.3 0.2 - - - -
245E ILE* 1.3 77.5 - - - +
247E ALA* 1.3 55.9 + - - +
249E GLU* 4.4 6.0 - - - +
250E GLN* 2.6 49.4 + - + +
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Residues in contact with ALA 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E PRO* 3.9 19.7 - - + -
107E ALA* 4.0 5.6 - - + -
110E LEU* 6.3 0.9 - - + -
111E VAL* 4.2 10.8 - - + -
243E LYS 3.4 6.3 + - - +
244E ALA 2.7 17.8 + - - +
246E ASP* 1.3 77.8 - - - +
248E VAL* 1.3 54.1 + - - +
250E GLN* 4.8 1.1 - - - -
251E ASN* 2.7 47.3 + - - +
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Residues in contact with VAL 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E PRO* 4.0 7.2 - - - +
100E ILE* 4.9 1.3 - - + -
103E LEU* 3.5 29.6 - - + +
104E THR* 3.3 46.7 - - + +
107E ALA* 3.6 17.5 - - + -
244E ALA 3.2 3.3 + - - +
245E ILE* 3.1 7.6 + - - +
247E ALA* 1.3 82.4 - - - +
249E GLU* 1.3 68.0 + - - +
250E GLN 3.0 0.2 + - - -
252E GLY 3.2 9.5 + - - +
298E VAL* 4.6 15.3 - - + -
299E LYS 5.7 0.2 - - - +
303E ILE* 3.0 24.5 - - + +
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Residues in contact with GLU 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E ILE* 2.8 28.7 + - + +
246E ASP* 3.6 6.8 - - - +
248E VAL* 1.3 77.9 - - - +
250E GLN* 1.3 64.4 + - + +
297E MET 3.4 6.9 - - - +
298E VAL* 3.4 13.6 - - + -
299E LYS* 3.0 66.1 + - + +
302E HIS* 3.5 30.8 - - - +
303E ILE* 4.2 2.0 + - - -
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Residues in contact with GLN 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ARG* 3.3 26.2 + - - +
37E ARG* 3.2 42.1 + - - +
38E MET* 3.4 19.5 - - + +
45E ARG* 4.5 12.9 + - - -
46E HIS* 5.3 5.5 - - - -
246E ASP* 2.6 34.3 + - + +
247E ALA* 4.0 0.9 - - - +
249E GLU* 1.3 82.6 + - + +
251E ASN* 1.3 73.6 + - - +
252E GLY 3.8 0.7 - - - -
302E HIS* 4.3 3.4 - - - +
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Residues in contact with ASN 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU* 5.9 3.4 - - + -
34E ARG* 2.9 25.3 - - + +
38E MET* 4.6 9.9 - - - +
74E ALA* 5.2 3.4 + - + +
75E ASN 4.6 9.5 + - - -
76E ALA* 3.1 17.6 - - + +
77E PRO* 3.0 23.1 - - - +
247E ALA* 2.7 27.0 + - - +
250E GLN* 1.3 90.0 - - - +
252E GLY* 1.3 55.7 + - - +
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Residues in contact with GLY 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ARG* 3.1 8.9 + - - +
77E PRO* 3.3 12.8 - - - -
103E LEU* 4.4 6.3 - - - -
248E VAL 3.2 16.9 + - - -
250E GLN 3.8 0.8 - - - -
251E ASN* 1.3 78.4 - - - +
253E ILE* 1.3 55.0 + - - -
303E ILE* 3.6 13.4 - - - +
304E LEU 2.7 32.3 + - - -
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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