Contacts of the helix formed by residues 213 - 222 (chain B) 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 LYS 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A GLU* 2.9 37.5 + - - -
462A PRO* 3.9 2.0 - - - -
208B ILE* 3.6 11.4 - - + -
210B ASP 3.0 12.5 + - - +
212B HIS* 1.3 78.4 - - - +
214B PHE* 1.3 62.8 + - - +
215B PRO* 3.4 1.6 - - - -
216B ASP* 3.0 23.7 + - - +
217B PHE* 3.0 22.5 + - - +
242B TYR* 3.3 22.0 - - - +
246B GLN* 3.3 19.1 - - - +
248B GLU* 5.3 2.7 - - - +
497B ARG* 4.2 10.8 - - - +
91C ASP 3.4 3.3 + - - +
92C GLN* 2.8 50.2 + - - +
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Residues in contact with PHE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 4.1 14.4 - - + -
128B HIS* 6.1 0.9 - + - -
169B VAL* 6.1 2.2 - - + -
206B PHE* 3.7 33.0 - + - -
208B ILE* 3.5 11.3 - - + +
211B ALA 3.0 12.9 + - - +
213B LYS* 1.3 77.5 - - - +
215B PRO* 1.3 64.0 - - + +
216B ASP 3.2 0.3 + - - -
217B PHE* 3.2 1.9 + + - -
218B VAL* 2.8 56.9 + - + +
760B HDD 3.4 73.6 - + + -
117C PHE* 3.6 26.0 - + - -
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Residues in contact with PRO 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B HIS 3.6 12.1 - - - +
213B LYS 3.5 2.7 - - - -
214B PHE* 1.3 95.8 - - + +
216B ASP* 1.3 52.9 + - - +
219B HIS* 2.8 49.2 + - + +
113C LYS* 4.0 23.3 - - + +
114C ILE* 3.7 21.8 - - + -
117C PHE* 3.7 40.6 - - + -
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Residues in contact with ASP 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A PHE* 4.4 8.1 - - - +
459A ASN 4.8 0.4 - - - +
460A TYR* 3.2 19.0 - - - +
461A GLU* 3.2 42.2 + - - +
213B LYS* 3.0 25.6 + - - +
215B PRO* 1.3 75.0 - - - +
217B PHE* 1.3 65.3 + - - +
220B ALA* 3.0 20.4 + - - +
242B TYR* 3.7 11.4 - - + +
91C ASP* 3.8 1.8 - - - +
113C LYS* 2.8 33.9 + - - -
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B VAL* 5.8 6.1 - - + -
206B PHE* 4.3 16.6 - + - -
207B PHE* 3.2 54.5 - + + -
208B ILE* 3.9 20.2 - - + -
213B LYS 3.0 15.4 + - - +
214B PHE* 3.8 2.7 - + - +
216B ASP* 1.3 75.6 - - - +
218B VAL* 1.3 75.5 + - + +
220B ALA* 3.1 6.5 + - + +
221B VAL* 3.0 34.4 + - + +
239B PHE* 3.8 28.9 - + - -
242B TYR* 3.8 30.8 + + + -
243B VAL* 5.3 0.9 - - + -
249B THR* 4.7 2.7 - - + -
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ILE 5.2 0.2 - - - +
127B VAL* 3.5 23.3 - - + -
169B VAL* 5.8 2.9 - - + -
214B PHE* 2.8 61.1 + - + +
217B PHE* 1.3 82.2 - - + +
219B HIS* 1.3 63.7 + - + +
221B VAL* 3.3 7.2 + - + +
222B LYS* 3.0 44.7 + - + +
117C PHE* 3.5 24.5 - - + -
120C GLU* 6.1 0.2 - - - +
121C ARG* 5.4 1.1 - - - +
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Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A PHE* 3.2 20.6 + - - +
444A GLN* 4.5 1.8 - - - -
445A ARG* 4.1 16.7 - - + +
459A ASN* 2.7 57.8 + - - +
215B PRO* 2.8 34.6 + - + +
216B ASP 3.9 2.7 - - - +
218B VAL* 1.3 76.0 - - + +
220B ALA* 1.3 63.2 + - - +
222B LYS* 3.6 20.3 + - + +
223B PRO 4.8 1.2 - - - +
224B GLU* 5.6 0.2 - - - -
225B PRO* 5.6 0.9 - - - +
238B THR* 4.5 2.1 + - - -
117C PHE* 4.2 9.6 - + - -
120C GLU* 2.6 38.3 + - - -
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A TYR* 4.1 14.0 - - + +
216B ASP 3.0 14.9 + - - +
217B PHE* 3.1 8.7 + - + +
219B HIS* 1.3 76.6 - - - +
221B VAL* 1.3 56.5 + - - +
236B HIS* 3.1 9.0 - - - -
238B THR* 2.6 45.7 + - - +
239B PHE* 3.1 11.1 + - + -
242B TYR* 3.6 21.5 - - + -
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Residues in contact with VAL 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 6.5 0.2 - - + -
169B VAL* 5.6 6.5 - - + -
170B GLN* 2.9 33.7 + - + -
181B ASP* 5.7 3.1 - - - +
207B PHE* 6.4 0.2 - - + -
217B PHE* 3.0 28.5 + - + +
218B VAL* 3.4 15.9 - - + +
220B ALA* 1.3 73.3 - - - +
222B LYS* 1.3 68.0 + - + +
233B GLN 3.5 0.3 - - - +
234B SER* 3.7 20.2 - - - -
236B HIS* 2.7 22.0 + - - -
239B PHE* 3.5 31.6 - - + -
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Residues in contact with LYS 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLU* 5.1 4.9 + - - -
125B ARG 5.1 1.2 + - - -
126B ILE 3.0 28.8 + - - -
127B VAL* 4.1 14.5 - - - +
129B ALA* 5.6 0.4 - - - +
169B VAL 4.2 3.0 + - - -
170B GLN* 2.8 35.9 + - - +
171B GLY 4.6 5.7 + - - -
172B GLY* 5.2 0.4 - - - +
218B VAL* 3.0 32.8 + - + +
219B HIS* 3.7 15.7 - - + +
220B ALA 3.5 0.2 - - - -
221B VAL* 1.3 85.1 - - + +
223B PRO* 1.3 82.5 - - + +
224B GLU* 3.3 1.0 + - - +
236B HIS* 3.1 13.4 - - - -
121C ARG* 3.4 20.5 - - - +
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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