Contacts of the helix formed by residues 249 - 258 (chain C) in PDB entry 1GGE
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 THR 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207C PHE* 3.1 34.6 - - + +
208C ILE* 4.4 1.1 - - + -
217C PHE* 4.6 2.0 - - + -
242C TYR* 3.9 31.6 - - + -
243C VAL* 3.4 25.5 - - + +
246C GLN* 2.8 22.7 + - + +
248C GLU* 1.3 76.9 - - + +
250C LEU* 1.3 65.3 + - - +
251C HIS 3.2 1.4 + - - -
252C ASN* 3.4 4.1 + - - +
253C VAL* 3.0 28.6 + - - +
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Residues in contact with LEU 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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243C VAL* 4.1 20.9 - - + -
247C PRO* 3.0 26.4 + - + +
249C THR* 1.3 77.1 + - - +
251C HIS* 1.3 57.7 + - - +
253C VAL* 3.6 9.8 - - + +
254C MET* 2.9 34.3 + - - +
504C TYR 4.2 0.9 - - - +
505C TYR* 3.4 36.1 - - + -
508C PRO* 4.1 7.0 - - + -
527C PHE* 5.7 2.2 - - + -
543C VAL* 5.7 2.5 - - + +
546C GLN* 3.7 31.2 - - + +
547C LEU* 4.9 9.0 - - + -
550C ILE* 4.1 20.6 - - + -
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Residues in contact with HIS 251 (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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205C ILE* 3.4 26.7 - - + +
248C GLU 4.1 7.6 + - - +
249C THR 3.2 0.8 + - - -
250C LEU* 1.3 77.8 - - - +
252C ASN* 1.3 63.8 + - - +
254C MET* 3.1 13.7 + - + +
255C TRP* 3.2 39.5 + + - -
357C THR* 2.7 27.9 + - - +
359C LEU* 3.6 23.0 - - + +
504C TYR 4.9 1.3 + - - +
507C HIS* 3.5 40.4 + + + +
508C PRO* 3.7 20.9 - - + +
511C PHE* 4.3 4.3 - - + +
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Residues in contact with ASN 252 (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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182C ILE* 3.5 14.1 - - - +
203C THR* 2.8 30.0 + - - -
205C ILE* 3.4 30.3 + - + +
206C PHE* 3.8 20.0 + - - +
207C PHE* 3.2 42.2 + - + -
248C GLU 5.2 0.2 + - - -
249C THR 3.4 3.4 + - - -
251C HIS* 1.3 78.9 - - - +
253C VAL* 1.3 61.6 + - - +
255C TRP* 3.2 3.4 + - - +
256C ALA* 3.0 22.0 + - - +
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Residues in contact with VAL 253 (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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207C PHE* 3.8 19.7 - - + -
239C PHE* 3.9 5.8 - - + -
240C TRP* 3.6 29.4 - - + -
243C VAL* 3.8 31.2 - - + -
249C THR 3.0 23.2 + - - +
250C LEU* 3.6 8.5 - - + +
251C HIS 3.2 0.2 - - - -
252C ASN* 1.3 75.6 - - - +
254C MET* 1.3 63.2 + - - +
256C ALA* 3.2 4.7 + - - +
257C MET* 2.9 27.3 + - + +
527C PHE* 3.6 19.3 - - + -
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Residues in contact with MET 254 (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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250C LEU* 2.9 23.4 + - - +
251C HIS* 3.1 8.3 + - - +
253C VAL* 1.3 77.4 - - - +
255C TRP* 1.3 61.7 + - + +
257C MET* 3.4 2.3 + - - +
258C SER* 3.1 22.7 + - - -
508C PRO* 3.8 24.9 - - + +
511C PHE* 3.6 23.7 - - + -
512C TRP* 3.9 31.4 - - + -
523C ILE* 4.0 15.0 - - + +
527C PHE* 3.7 25.8 - - - -
550C ILE* 4.4 11.0 - - + -
554C LEU* 3.9 26.2 - - + -
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Residues in contact with TRP 255 (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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203C THR* 3.7 25.1 - - + -
204C PRO* 3.3 43.1 - - + -
205C ILE* 3.5 12.2 - - + +
251C HIS* 3.2 44.5 + + - -
252C ASN* 3.2 10.2 + - - +
254C MET* 1.3 79.3 - - - +
256C ALA* 1.3 61.4 + - - +
258C SER* 2.6 26.5 + - - +
260C ARG* 3.4 65.0 - - + +
261C GLY 3.7 0.2 + - - -
270C GLU* 5.1 0.2 - - - -
272C PHE* 4.9 4.0 - + - -
359C LEU* 3.8 2.2 - - + -
511C PHE* 3.3 36.2 - + - -
587C SER 5.6 0.2 - - - -
588C LEU* 3.8 23.1 - - + -
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Residues in contact with ALA 256 (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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180C ARG* 2.8 41.1 + - + +
181C ASP* 5.3 5.6 - - - -
182C ILE* 4.2 19.7 - - + +
207C PHE* 4.6 8.3 - - + -
239C PHE* 6.1 1.6 - - + -
252C ASN 3.0 16.5 + - - +
253C VAL* 3.6 7.9 - - - +
255C TRP* 1.3 77.9 - - - +
257C MET* 1.3 63.2 + - + +
258C SER 3.3 2.4 - - - +
261C GLY* 3.6 9.3 - - - -
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Residues in contact with MET 257 (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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180C ARG* 3.1 40.2 + - + +
234C SER* 3.9 7.4 - - - +
239C PHE* 5.1 2.7 - - + -
240C TRP* 3.9 16.6 - - + -
253C VAL* 2.9 22.1 + - + +
254C MET 3.9 2.2 - - - +
256C ALA* 1.3 82.8 - - + +
258C SER* 1.3 61.4 + - - +
522C HIS 3.6 7.4 - - - +
523C ILE* 3.6 20.1 - - + +
526C GLY* 3.8 25.8 - - - +
527C PHE* 3.9 40.2 - - + -
530C GLU* 3.6 24.5 - - - +
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Residues in contact with SER 258 (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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180C ARG* 2.9 18.2 + - - -
254C MET 3.1 10.0 + - - -
255C TRP 2.6 20.4 + - - -
257C MET* 1.3 77.1 - - - +
259C ASP* 1.3 61.3 + - - +
260C ARG* 3.1 26.3 + - - +
261C GLY 3.1 6.8 + - - -
511C PHE* 3.8 10.0 - - - -
515C GLN* 5.1 2.9 - - - -
519C GLU* 5.3 2.2 - - - -
523C ILE* 3.4 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