Contacts of the helix formed by residues 188 - 194 (chain B) in PDB entry 1GQT
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 GLU 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ASN* 1.3 76.2 - - - +
189B THR* 1.3 64.4 + - - +
191B ALA* 3.5 6.1 + - - +
192B GLU* 3.1 23.2 + - - +
199B VAL* 3.8 43.1 + - + +
200B GLU* 5.0 6.9 - - - +
222B ILE* 4.6 1.8 - - + -
223B THR 3.8 13.2 + - - +
224B LEU* 4.0 27.1 - - + +
225B GLY 5.3 0.4 - - - -
227B ARG* 5.6 4.2 - - - -
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Residues in contact with THR 189 (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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28A GLY 6.1 0.2 - - - +
170B ALA* 4.6 15.0 - - + -
187B ASN* 3.2 13.1 + - - -
188B GLU* 1.3 80.6 - - - +
190B GLU* 1.3 57.2 + - - -
192B GLU* 3.3 9.1 + - - +
193B LYS* 3.0 26.9 + - + +
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Residues in contact with GLU 190 (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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166B ASN* 4.5 2.1 + - - -
167B PRO* 3.1 31.1 - - + +
168B ALA* 3.4 21.7 - - - +
169B PRO* 4.8 0.7 - - - +
170B ALA* 3.9 22.2 + - + +
171B ARG 5.9 0.2 - - - +
185B THR 4.0 2.6 - - - +
186B PRO* 3.3 18.0 - - + +
187B ASN* 2.6 58.4 + - - +
189B THR* 1.3 69.8 - - - +
191B ALA* 1.3 67.0 + - - +
193B LYS* 3.1 7.1 + - - +
194B LEU* 3.0 29.5 + - + +
1310B ACP 4.4 2.6 + - - -
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Residues in contact with ALA 191 (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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186B PRO* 3.5 12.6 - - + +
187B ASN 2.8 22.2 + - - +
188B GLU 3.6 5.2 - - - +
190B GLU* 1.3 72.8 - - - +
192B GLU* 1.3 52.2 + - - +
194B LEU* 3.3 2.8 + - - -
195B THR* 2.5 42.1 + - + +
197B ILE 4.3 0.7 - - - -
199B VAL* 4.0 19.5 - - + -
208B ALA* 4.4 4.0 - - + -
212B LEU* 5.5 1.8 - - + -
222B ILE* 4.0 22.4 - - + -
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Residues in contact with GLU 192 (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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188B GLU 3.1 14.4 + - - +
189B THR* 3.5 12.2 - - - +
190B GLU 3.2 0.2 - - - -
191B ALA* 1.3 72.9 - - - +
193B LYS* 1.3 62.8 + - - +
195B THR* 3.9 0.4 - - - -
196B GLY* 2.8 33.7 + - - +
197B ILE 3.4 25.0 + - - +
198B ARG* 3.8 30.1 + - - +
199B VAL 4.8 0.5 + - - -
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Residues in contact with LYS 193 (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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170B ALA* 4.7 8.5 - - + -
171B ARG* 3.2 33.0 - - - +
172B GLU* 2.9 63.0 + - + +
189B THR* 3.0 17.3 + - + +
190B GLU* 3.1 7.8 + - - +
192B GLU* 1.3 80.3 - - - +
194B LEU* 1.3 58.9 + - - +
196B GLY* 4.6 1.0 + - - -
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Residues in contact with LEU 194 (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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167B PRO* 4.3 17.3 - - + -
171B ARG 3.4 23.6 - - - +
172B GLU* 4.6 1.1 - - - +
173B LEU* 3.8 33.9 - - + +
178B LEU* 4.7 8.7 - - + +
184B ILE* 4.2 24.5 - - + -
186B PRO* 4.5 4.9 - - + -
190B GLU* 3.0 25.2 + - + +
191B ALA* 4.0 2.7 - - - +
193B LYS* 1.3 80.5 - - - +
195B THR* 1.3 60.4 + - + +
211B VAL* 4.9 0.3 - - - +
212B LEU* 4.4 21.1 - - + +
215B LYS* 4.2 16.5 + - - -
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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