Contacts of the helix formed by residues 241 - 250 (chain C) in PDB entry 1GZU
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 PRO 241 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C ILE* 4.9 1.1 - - + +
21C THR* 4.5 2.9 - - - +
22C ASN* 3.4 19.7 - - - +
25C LEU* 5.2 11.7 - - + -
72C LEU 5.8 0.4 - - - +
73C ALA* 4.5 23.3 - - + +
240C VAL* 1.3 92.0 - - + +
242C ASP* 1.3 58.4 + - - +
243C LEU* 3.4 3.4 - - + +
244C VAL* 2.7 57.5 + - + +
245C GLN 2.9 4.4 + - - -
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Residues in contact with ASP 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ARG* 3.4 30.0 + - - +
238C TYR* 5.8 0.9 - - - -
240C VAL 3.6 2.9 + - - +
241C PRO* 1.3 67.6 - - - +
243C LEU* 1.3 74.5 + - + +
244C VAL 2.8 2.0 - - - -
245C GLN* 2.6 23.5 + - - +
246C GLU* 2.6 31.4 + - + +
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Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LEU* 4.2 35.7 - - + +
75C LYS* 4.2 36.3 - - + +
76C ASN* 5.4 7.2 - - - +
241C PRO* 3.2 3.6 + - + +
242C ASP* 1.3 79.7 - - + +
244C VAL* 1.3 53.8 + - + +
246C GLU* 3.5 17.5 - - - +
247C TYR* 2.6 37.4 + - - +
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 4.3 18.4 - - + +
69C MSE 3.5 35.0 - - + +
72C LEU* 4.8 2.4 - - - +
73C ALA* 4.0 23.8 - - + +
240C VAL* 4.3 6.7 - - + -
241C PRO* 2.7 48.0 + - + +
243C LEU* 1.3 73.9 - - - +
245C GLN* 1.3 67.1 + - - +
247C TYR* 2.8 17.0 + - - +
248C ILE* 2.8 20.2 + - + +
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Residues in contact with GLN 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C SER 4.8 5.4 + - - +
236C ILE* 4.2 22.9 - - + -
237C ARG* 3.1 48.9 + - - +
240C VAL* 5.0 5.9 - - + +
241C PRO 2.9 7.3 + - - +
242C ASP* 2.6 19.5 + - - +
244C VAL* 1.3 71.0 - - - +
246C GLU* 1.3 57.1 - - - +
248C ILE* 2.6 32.2 + - + +
249C GLU* 2.7 43.4 + - + +
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ARG* 5.8 3.1 - - - +
242C ASP* 2.6 47.1 + - + +
243C LEU* 3.3 15.9 + - - +
245C GLN* 1.3 78.1 - - + +
247C TYR* 1.3 66.3 + - - +
248C ILE 3.0 0.7 + - - -
249C GLU* 4.1 9.8 - - + +
250C LYS* 3.0 38.2 + - + +
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Residues in contact with TYR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C TYR* 5.1 1.2 - - - -
65C HIS* 3.4 22.4 + - + -
68C ILE* 3.4 46.0 - - + +
69C MSE 4.3 13.0 - - + -
72C LEU* 4.0 15.3 - - + -
243C LEU 2.6 18.6 + - - +
244C VAL* 2.8 10.9 + - - +
246C GLU* 1.3 73.2 - - - +
248C ILE* 1.3 59.9 + - - +
250C LYS* 3.0 22.0 - - - +
251C HIS* 3.2 33.3 + + - +
253C LEU* 3.0 32.1 - - + -
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PRO* 4.6 7.2 - - + -
69C MSE 4.0 21.3 - - - -
230C LEU* 3.4 35.9 - - + -
236C ILE* 4.5 10.3 - - + -
240C VAL* 6.0 1.8 - - + -
244C VAL* 2.8 22.9 + - + +
245C GLN* 2.6 21.4 + - + +
247C TYR* 1.3 76.3 - - + +
249C GLU* 1.3 64.7 + - + +
250C LYS 3.3 0.5 + - - -
251C HIS 3.4 1.9 + - - -
252C ASN* 3.1 21.4 + - - -
253C LEU* 3.7 11.4 + - + +
254C TYR* 3.6 30.7 - - + +
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Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C LEU* 6.6 0.2 - - + -
245C GLN* 2.7 41.6 + - + +
246C GLU* 3.2 13.2 + - + +
248C ILE* 1.3 76.8 - - + +
250C LYS* 1.3 69.1 + - + +
251C HIS 3.1 0.2 + - - -
252C ASN* 2.9 26.9 + - - +
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Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLU* 3.0 23.1 + - + +
247C TYR* 3.0 3.0 - - - +
249C GLU* 1.3 83.8 - - + +
251C HIS* 1.3 95.8 + - + +
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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