Contacts of the helix formed by residues 202 - 208 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A PHE* 4.0 34.4 - - + +
172A HIS* 3.4 9.9 + - - -
176A TYR* 2.9 35.3 + - + +
186A TYR* 4.9 0.7 - - - -
200A LEU* 3.1 16.6 - - - +
201A GLU* 1.3 88.7 + - - +
203A LEU* 1.3 62.7 + - + +
204A ARG 3.1 0.4 - - - -
205A LEU* 3.1 29.4 + - + +
206A MET* 3.5 9.4 + - - +
212A ILE* 3.9 10.6 - - + +
1244A CMK 2.6 36.2 + - - -
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A TYR* 3.6 30.5 - - + +
153A PHE* 3.8 21.5 - - + +
192A SER* 3.2 12.4 + - - +
194A PRO* 3.6 33.6 - - + +
195A GLU 3.9 11.4 - - - +
198A GLU* 3.8 13.0 - - + -
200A LEU* 3.1 37.1 + - + +
201A GLU 2.9 1.4 + - - -
202A GLN* 1.3 75.7 - - + +
204A ARG* 1.3 63.9 + - - +
205A LEU 3.1 0.4 - - - -
206A MET* 3.9 17.0 - - + +
207A ASN* 3.1 18.4 + - - +
151B LEU* 5.7 0.7 - - + -
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU* 4.8 7.1 - - - +
75A SER* 4.5 1.4 + - - -
78A ASP* 2.9 41.8 + - - -
186A TYR* 3.1 46.8 + - + -
187A SER* 3.9 6.3 - - - +
189A LEU* 3.6 30.5 + - + +
190A PRO 3.8 17.2 - - - +
191A GLU* 5.7 1.5 - - - +
192A SER* 3.9 8.1 - - - +
195A GLU* 2.9 45.8 + - - +
196A GLN* 5.7 1.6 - - - +
201A GLU 2.9 10.8 + - - +
203A LEU* 1.3 78.9 - - - +
205A LEU* 1.3 61.8 + - - +
207A ASN* 3.7 3.6 + - - +
208A ALA* 3.4 13.9 + - - +
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A VAL* 3.7 29.6 - - + -
176A TYR* 5.8 1.6 - - + -
178A TYR* 4.8 9.0 - - + -
182A VAL* 3.8 21.3 - - + +
186A TYR* 3.7 32.3 - - + -
189A LEU* 4.2 4.5 - - + -
202A GLN* 3.1 16.9 + - + +
204A ARG* 1.3 76.6 - - - +
206A MET* 1.3 64.3 + - - +
208A ALA* 3.1 7.6 + - - -
210A ILE* 3.0 49.2 + - + +
212A ILE* 3.8 22.9 - - + -
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Residues in contact with MET 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA* 3.2 37.0 - - + +
151A LEU 3.5 18.2 - - - +
152A TYR* 4.0 13.2 - - - +
153A PHE* 3.6 22.9 - - + -
202A GLN 3.5 12.5 + - - +
203A LEU* 3.5 16.8 + - + +
205A LEU* 1.3 73.5 - - - +
207A ASN* 1.3 68.3 + - - +
209A GLY* 2.9 15.3 + - - -
210A ILE 4.3 7.4 - - - +
211A ASN* 6.5 0.2 - - - -
212A ILE* 4.1 16.2 - - + +
145B ASN* 3.6 12.2 + - - +
151B LEU* 4.3 23.5 - - + +
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Residues in contact with ASN 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A PRO* 4.1 12.3 + - - +
191A GLU 3.6 17.8 + - - +
192A SER* 3.7 22.1 + - - +
193A MET 4.9 0.7 + - - -
194A PRO* 4.6 5.9 - - + +
203A LEU 3.1 18.9 + - - +
204A ARG 3.8 6.2 + - - +
206A MET* 1.3 75.9 - - - +
208A ALA* 1.3 57.6 + - - +
144B VAL 3.9 5.7 - - - +
145B ASN* 3.1 26.8 - - - +
146B THR* 2.9 53.7 + - - -
151B LEU* 5.1 3.3 - - + +
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 4.0 19.7 - - + -
190A PRO* 5.2 8.3 - - + -
204A ARG 3.4 10.6 + - - +
205A LEU 3.1 8.1 + - - +
206A MET 3.0 1.0 - - - -
207A ASN* 1.3 79.4 - - - +
209A GLY* 1.3 57.5 + - - +
210A ILE* 3.2 25.0 + - + +
146B THR* 5.4 2.5 - - - -
147B ARG* 5.0 8.8 + - - -
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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