Contacts of the helix formed by residues 202 - 208 (chain B) in PDB entry 1GQC
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 GLN 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B VAL* 4.2 2.8 - - - +
153B PHE* 3.5 36.8 - - + +
172B HIS* 3.2 30.5 + - - -
176B TYR* 3.5 32.8 + - + +
200B LEU* 3.5 33.7 - - - +
201B GLU* 1.3 75.3 + - - +
203B LEU* 1.3 63.7 + - - +
205B LEU* 3.0 28.7 + - + +
206B MET* 3.6 7.2 + - - +
212B ILE* 4.1 9.0 - - + +
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Residues in contact with LEU 203 (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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151A LEU* 5.6 2.2 - - + +
152B TYR* 4.0 14.6 - - + +
153B PHE* 3.6 41.1 - - + +
192B SER* 4.1 2.7 + - - -
194B PRO* 3.6 38.1 - - + +
195B GLU* 3.8 12.8 - - - +
198B GLU* 3.8 21.8 - - + -
200B LEU* 2.9 20.4 + - + +
202B GLN* 1.3 79.8 - - - +
204B ARG* 1.3 60.9 + - - +
206B MET* 3.2 16.7 + - + +
207B ASN* 3.0 23.0 + - - +
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Residues in contact with ARG 204 (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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78B ASP* 4.8 4.4 + - - -
186B TYR* 3.6 40.4 + - + +
187B SER* 6.3 0.2 - - - +
189B LEU* 4.0 29.9 + - + +
190B PRO 3.2 27.7 - - - +
191B GLU* 3.9 22.0 + - - +
192B SER* 4.4 2.0 - - - +
195B GLU* 2.8 38.9 + - - +
201B GLU* 3.0 27.9 + - - +
203B LEU* 1.3 77.6 - - - +
205B LEU* 1.3 62.7 + - + +
207B ASN* 3.6 8.0 + - - +
208B ALA* 3.4 21.0 + - - +
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Residues in contact with LEU 205 (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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122B VAL* 4.4 8.1 - - + -
176B TYR* 5.3 2.5 - - + -
178B TYR* 4.2 26.0 - - + +
182B VAL* 4.4 12.6 - - + -
186B TYR* 3.9 29.6 - - + +
189B LEU* 4.2 3.6 - - + -
201B GLU 5.1 1.6 - - - +
202B GLN* 3.0 19.8 + - + +
204B ARG* 1.3 75.3 - - - +
206B MET* 1.3 63.5 + - - +
208B ALA* 3.3 3.5 + - - +
209B GLY 3.3 3.8 + - - -
210B ILE* 2.9 57.9 + - + +
212B ILE* 3.9 25.8 - - + -
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Residues in contact with MET 206 (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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145A ASN* 3.6 9.7 + - - +
151A LEU* 3.9 26.2 - - + +
150B ALA* 3.2 44.2 - - + +
151B LEU 3.9 7.9 - - - +
152B TYR* 3.9 17.0 - - - -
153B PHE* 3.7 22.0 - - + -
202B GLN 3.9 12.8 - - - +
203B LEU* 3.2 16.3 + - + +
205B LEU* 1.3 73.6 - - - +
207B ASN* 1.3 67.1 + - - +
209B GLY* 3.0 13.9 + - - +
210B ILE 4.2 7.6 - - - +
211B ASN* 5.9 1.1 - - - +
212B ILE* 4.4 18.4 - - + +
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Residues in contact with ASN 207 (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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144A VAL 4.4 3.1 - - - +
145A ASN* 3.0 31.2 - - - +
146A THR* 3.1 50.3 + - - +
147A ARG* 5.8 0.3 + - - -
151A LEU* 4.8 4.0 - - - +
190B PRO* 4.4 18.2 + - - +
191B GLU 5.1 0.2 + - - -
192B SER* 3.3 33.4 - - - +
194B PRO* 5.1 3.4 - - + +
203B LEU 3.0 16.2 + - - +
204B ARG* 3.6 6.9 + - - +
205B LEU 3.2 0.2 - - - -
206B MET* 1.3 76.7 - - - +
208B ALA* 1.3 60.6 + - - +
209B GLY 3.2 2.3 + - - -
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Residues in contact with ALA 208 (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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146A THR* 4.3 5.8 - - - -
147A ARG* 3.9 15.7 + - - -
189B LEU* 3.7 31.4 - - + -
190B PRO* 6.0 2.0 - - + -
204B ARG 3.4 8.0 + - - +
205B LEU 3.3 8.8 + - - +
206B MET 3.2 0.4 - - - -
207B ASN* 1.3 80.5 - - - +
209B GLY* 1.3 61.3 + - - +
210B ILE* 3.6 12.7 + - + +
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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