Contacts of the helix formed by residues 176 - 192 (chain A) in PDB entry 1R88
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 ASN 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 TYR* 3.2 57.6 + - + +
174A PRO 3.2 0.8 - - - -
175A SER* 1.3 78.3 + - - +
177A THR* 1.3 73.7 + - - +
178A THR* 2.9 29.1 + - - +
179A THR* 3.1 15.7 + - - +
180A ASN* 2.9 25.1 + - - -
248A GLU* 4.2 0.8 + - - -
255A MET* 4.4 13.4 - - - +
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Residues in contact with THR 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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175A SER 3.4 2.0 + - - -
176A ASN* 1.3 81.3 + - - +
178A THR* 1.3 63.8 + - - +
180A ASN* 3.2 20.8 + - - +
181A GLY* 4.0 3.1 + - - -
177B THR* 3.3 37.7 + - + +
178B THR* 3.3 31.2 - - + +
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Residues in contact with THR 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 ASN* 2.9 19.2 + - - +
177A THR* 1.3 76.2 - - + +
179A THR* 1.3 62.6 + - - +
181A GLY* 3.6 2.6 + - - -
182A ALA* 3.1 21.8 + - - +
248A GLU* 3.2 21.4 + - - +
178B THR* 3.6 26.9 - - + -
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Residues in contact with THR 179 (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 PHE* 4.3 2.2 - - + -
173A TYR 3.5 14.1 - - - +
174A PRO* 3.9 1.8 - - + -
176A ASN* 3.1 15.0 + - - +
178A THR* 1.3 77.0 + - - +
180A ASN* 1.3 59.4 + - - +
182A ALA* 3.1 1.8 + - - +
183A ILE* 2.8 48.8 + - + +
248A GLU* 2.6 33.0 + - + +
252A ASN* 2.9 37.0 + - - +
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Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO 3.3 17.9 + - - +
175A SER* 3.4 12.9 + - - +
176A ASN 2.9 24.7 + - - -
177A THR* 3.2 14.8 + - - +
179A THR* 1.3 76.4 - - - +
181A GLY* 1.3 74.7 + - - +
183A ILE 3.6 0.2 + - - -
184A ALA* 3.2 23.9 + - - +
202A PRO* 3.6 29.5 - - + +
207A TRP* 3.6 30.7 - - + -
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Residues in contact with GLY 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 THR 4.0 3.0 + - - -
178A THR 3.6 4.8 + - - -
179A THR 3.3 0.4 - - - -
180A ASN* 1.3 86.7 + - - +
182A ALA* 1.3 56.2 + - - +
184A ALA* 3.5 6.2 + - - +
185A ALA* 3.1 27.9 + - - +
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Residues in contact with ALA 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 THR 3.1 17.6 + - - +
179A THR 3.1 5.7 + - - +
181A GLY* 1.3 74.4 - - - +
183A ILE* 1.3 61.1 + - + +
185A ALA* 3.4 4.6 + - - +
186A GLY* 3.0 23.0 + - - -
245A GLN* 3.4 41.5 - - + +
248A GLU* 3.7 18.4 - - + +
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Residues in contact with ILE 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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68A PHE* 5.4 0.2 - - + -
104A MET* 4.2 22.4 - - + -
171A PHE* 4.1 26.0 - - + -
174A PRO* 3.7 27.8 - - + +
179A THR* 2.8 35.8 + - + +
180A ASN 4.0 3.8 - - - +
182A ALA* 1.3 72.2 - - - +
184A ALA* 1.3 60.6 + - - +
187A MET* 2.9 50.9 + - + +
195A THR* 4.4 4.9 - - + -
198A MET* 4.9 3.8 - - + -
207A TRP* 4.1 17.3 - - + -
243A ILE* 3.8 12.9 - - + +
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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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180A ASN 3.2 17.5 + - - +
181A GLY* 3.8 7.6 - - - +
182A ALA 3.3 0.2 - - - -
183A ILE* 1.3 78.1 - - - +
185A ALA* 1.3 61.8 + - - +
187A MET* 4.0 1.0 - - - +
188A GLN* 3.2 23.6 + - - +
193A VAL 4.7 1.7 - - - +
195A THR* 3.2 27.9 + - - +
196A ASN* 6.1 0.2 - - - +
202A PRO* 6.3 2.7 - - + -
207A TRP* 5.0 1.3 - - + -
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Residues in contact with ALA 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 GLY 3.1 18.6 + - - +
182A ALA* 3.8 6.3 - - - +
183A ILE 3.3 0.2 - - - -
184A ALA* 1.3 77.2 - - - +
186A GLY* 1.3 56.9 + - - +
188A GLN* 3.4 6.0 + - - +
189A GLN* 3.0 29.9 + - - +
245A GLN* 5.0 7.4 - - - +
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Residues in contact with GLY 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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182A ALA 3.0 15.2 + - - -
183A ILE 3.9 0.4 - - - -
185A ALA* 1.3 75.7 - - - +
187A MET* 1.3 59.1 + - - +
189A GLN* 4.3 7.4 - - - -
190A PHE* 3.0 35.4 + - - +
243A ILE* 3.5 32.6 - - - +
245A GLN* 4.8 2.6 - - - +
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Residues in contact with MET 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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68A PHE* 3.6 30.3 - - - -
102A TYR* 3.4 38.8 - - - +
103A SER 4.2 1.3 - - - +
104A MET* 4.6 4.9 - - + -
108A TRP* 3.7 20.9 - - + -
183A ILE* 2.9 34.3 + - + +
184A ALA 4.0 1.6 - - - +
186A GLY* 1.3 75.6 - - - +
188A GLN* 1.3 57.9 + - - +
191A GLY* 3.0 25.1 + - - +
192A GLY 3.1 6.4 + - - -
193A VAL* 3.3 14.4 + - + +
195A THR* 3.8 25.8 - - + -
198A MET* 4.5 7.4 - - - -
243A ILE* 4.1 6.7 - - + -
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Residues in contact with GLN 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 3.2 17.9 + - - +
185A ALA* 3.7 5.4 - - - +
186A GLY 3.3 0.2 - - - -
187A MET* 1.3 76.5 - - - +
189A GLN* 1.3 65.8 + - - +
192A GLY* 3.1 38.3 + - - +
193A VAL 3.4 21.6 + - - +
194A ASP* 4.3 9.0 + - - +
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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 ALA 3.0 18.5 + - - +
186A GLY* 3.4 7.0 + - - +
188A GLN* 1.3 80.0 - - - +
190A PHE* 1.3 93.4 + - + +
192A GLY 4.8 0.2 + - - -
243A ILE 5.2 0.2 - - - +
244A GLY* 5.9 0.5 - - - -
245A GLN* 5.7 2.6 + - - -
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Residues in contact with PHE 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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102A TYR* 3.4 31.1 + - + +
186A GLY 3.0 18.3 + - - +
189A GLN* 1.3 109.5 - - + +
191A GLY* 1.3 61.3 + - - +
239A PRO* 4.1 21.3 - - + -
240A ALA* 3.7 30.1 - - + -
243A ILE* 3.4 34.8 - - + -
244A GLY* 3.6 5.8 - - - -
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Residues in contact with GLY 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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102A TYR* 3.6 32.2 - - - -
187A MET 3.0 12.7 + - - -
190A PHE* 1.3 78.4 - - - +
192A GLY* 1.3 64.6 + - - +
193A VAL* 3.2 13.9 + - - +
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Residues in contact with GLY 192 (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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187A MET 3.1 0.4 + - - -
188A GLN* 3.1 36.1 + - - -
189A GLN 4.8 0.2 + - - -
190A PHE 3.7 0.8 - - - -
191A GLY* 1.3 78.8 - - - +
193A VAL* 1.3 59.9 + - - +
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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