Contacts of the helix formed by residues 176 - 191 (chain A) in PDB entry 1GUD
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 ASP 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ALA 3.0 13.2 + - - +
174A ASP* 3.9 8.3 - - + +
175A TRP* 1.3 78.8 - - - +
177A ARG* 1.3 59.3 + - - +
178A ILE* 3.1 16.7 + - - +
179A LYS* 2.9 32.0 + - + +
180A ALA* 2.9 30.5 + - - +
203A THR* 4.7 0.2 - - - -
204A MET* 3.7 3.7 - - - +
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Residues in contact with ARG 177 (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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176A ASP* 1.3 74.6 + - - +
178A ILE* 1.3 63.6 + - + +
180A ALA* 3.4 2.3 + - - -
181A LEU* 3.0 27.9 + - - +
203A THR* 3.6 38.4 - - + +
206A MET* 3.4 23.9 + - - +
207A GLY* 3.7 13.5 - - - +
231A GLU* 3.1 39.8 + - - -
235A MET* 3.7 21.0 - - - +
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Residues in contact with ILE 178 (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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176A ASP* 3.1 10.3 + - - +
177A ARG* 1.3 79.8 - - + +
179A LYS* 1.3 65.0 + - - +
181A LEU* 3.3 15.8 + - + +
182A ASP* 3.1 21.3 + - + +
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Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PRO* 3.5 23.8 - - - -
173A ALA* 3.6 26.9 - - - +
174A ASP* 3.8 22.4 - - + +
176A ASP* 2.9 15.6 + - + +
178A ILE* 1.3 74.8 - - - +
180A ALA* 1.3 60.9 + - - +
182A ASP* 3.2 7.2 + - + +
183A VAL* 2.8 39.3 + - + +
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Residues in contact with ALA 180 (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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139A ILE* 4.4 2.4 - - + +
173A ALA* 3.5 14.1 - - + +
176A ASP 2.9 19.3 + - - +
177A ARG 3.7 3.8 - - - +
178A ILE 3.3 0.2 - - - -
179A LYS* 1.3 78.7 - - - +
181A LEU* 1.3 57.1 + - - +
183A VAL* 4.1 1.1 - - - +
184A ALA* 2.9 34.7 + - - +
204A MET* 3.4 40.2 - - + +
207A GLY 4.4 2.2 - - - -
208A VAL* 4.2 6.1 - - + +
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Residues in contact with LEU 181 (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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177A ARG 3.0 13.6 + - - +
178A ILE* 3.5 15.5 - - + +
179A LYS 3.3 0.2 - - - -
180A ALA* 1.3 74.9 - - - +
182A ASP* 1.3 55.5 + - - +
185A THR* 2.7 44.1 + - - +
207A GLY* 3.5 18.0 - - - +
210A GLN* 3.9 20.9 - - + -
211A ALA* 3.5 31.9 - - + +
214A ASN* 4.0 10.1 - - - +
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Residues in contact with ASP 182 (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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178A ILE* 3.1 14.1 + - + +
179A LYS* 3.6 11.0 - - + +
181A LEU* 1.3 76.0 - - - +
183A VAL* 1.3 66.6 + - + +
185A THR* 3.2 6.5 + - - -
186A ASN* 3.0 40.4 + - - +
1289A ZN 2.2 37.0 - - - -
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Residues in contact with VAL 183 (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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139A ILE* 3.9 17.3 - - + -
171A GLN* 3.7 41.3 - - + +
172A PRO 3.8 19.5 - - - +
173A ALA* 4.3 5.2 - - + -
179A LYS* 2.8 41.0 + - + +
180A ALA* 4.1 2.5 - - - +
182A ASP* 1.3 74.3 - - + +
184A ALA* 1.3 59.3 + - - +
186A ASN* 3.1 11.6 + - - +
187A VAL* 2.8 28.9 + - + +
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Residues in contact with ALA 184 (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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139A ILE* 4.5 8.7 - - + +
180A ALA 2.9 19.7 + - - +
183A VAL* 1.3 77.5 - - - +
185A THR* 1.3 57.3 + - - +
187A VAL* 4.3 6.7 - - - -
188A LEU* 2.9 38.0 + - + +
197A ILE* 4.9 3.1 - - + -
208A VAL* 3.9 27.6 - - + -
211A ALA* 3.7 18.6 - - + -
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Residues in contact with THR 185 (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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181A LEU* 2.7 30.7 + - - +
182A ASP* 3.2 8.3 + - - -
184A ALA* 1.3 75.7 - - - +
186A ASN* 1.3 63.8 + - - +
188A LEU* 3.9 3.7 - - - +
189A GLN* 3.0 30.3 + - + +
211A ALA* 3.6 16.1 + - - +
214A ASN* 5.1 4.2 + - + +
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Residues in contact with ASN 186 (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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171A GLN* 5.8 5.2 + - - +
182A ASP* 3.0 33.7 + - - +
183A VAL* 3.5 11.0 - - - +
185A THR* 1.3 84.3 - - - +
187A VAL* 1.3 63.2 + - + +
189A GLN* 3.3 7.0 + - - +
190A ARG* 3.1 23.9 + - - +
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Residues in contact with VAL 187 (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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137A ALA* 4.0 9.2 - - + -
139A ILE* 4.8 6.5 - - + -
169A ALA* 3.7 25.4 - - + -
171A GLN* 3.9 25.8 - - + +
183A VAL* 2.8 28.3 + - + +
184A ALA* 3.8 8.1 - - - +
185A THR 3.3 0.2 - - - -
186A ASN* 1.3 78.6 - - + +
188A LEU* 1.3 57.6 + - + +
190A ARG* 3.4 6.7 + - - +
191A ASN* 3.1 27.6 + - + +
194A ILE* 3.5 23.5 - - + +
197A ILE* 5.5 3.4 - - + -
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Residues in contact with LEU 188 (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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184A ALA 2.9 20.2 + - - +
185A THR* 4.1 3.6 - - - +
187A VAL* 1.3 73.1 - - + +
189A GLN* 1.3 66.8 + - - +
191A ASN 4.1 4.7 - - - +
192A PRO* 3.2 31.1 - - + +
194A ILE* 4.3 26.0 - - + +
197A ILE* 4.3 19.3 - - + -
211A ALA* 4.0 23.6 - - + +
212A VAL* 3.8 26.5 - - + -
215A ALA* 4.7 14.4 - - + -
217A LYS* 5.8 5.2 - - + +
221A VAL* 4.8 14.1 - - + -
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Residues in contact with GLN 189 (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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185A THR* 3.0 21.2 + - + +
186A ASN* 3.6 8.3 - - - +
187A VAL 3.3 0.2 - - - -
188A LEU* 1.3 77.9 - - - +
190A ARG* 1.3 63.1 + - - +
192A PRO* 3.9 9.9 - - - +
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Residues in contact with ARG 190 (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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168A VAL 4.9 10.3 + - - -
171A GLN* 6.0 2.4 - - - +
186A ASN 3.1 15.6 + - - +
187A VAL* 3.4 6.5 + - - +
188A LEU 3.3 0.2 - - - -
189A GLN* 1.3 81.3 - - - +
191A ASN* 1.3 73.3 + - - +
192A PRO* 3.5 6.9 - - - +
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Residues in contact with ASN 191 (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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135A GLU* 2.9 32.7 + - - +
166A LYS* 5.3 1.6 - - - +
168A VAL* 3.8 25.8 - - - +
187A VAL* 3.1 6.7 + - - +
188A LEU* 3.4 7.6 - - - +
190A ARG* 1.3 101.1 + - - +
192A PRO* 1.3 65.4 - - - +
193A ASN 3.1 4.4 + - - -
194A ILE* 3.2 35.3 + - + +
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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