Contacts of the helix formed by residues 182 - 195 (chain A) in PDB entry 1R1H
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 THR 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ALA 5.7 0.2 - - - +
180A SER 3.2 9.8 + - - +
181A TRP* 1.3 93.1 - - - +
183A ALA* 1.3 57.5 + - - +
184A GLU* 2.5 27.5 + - - +
185A LYS* 2.9 28.8 + - - +
186A ALA* 2.8 28.9 + - - +
318A LYS* 4.4 20.6 + - + +
324A ASN* 5.1 0.5 + - - -
753A NAG 5.0 7.5 - - - +
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Residues in contact with ALA 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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181A TRP* 3.4 28.5 - - + -
182A THR* 1.3 68.9 - - - +
184A GLU* 1.3 71.9 + - - +
186A ALA* 4.5 0.7 - - - +
187A ILE* 3.0 48.2 + - + +
199A LEU* 5.8 0.9 - - + -
315A ILE* 3.8 28.7 - - + -
318A LYS* 5.7 1.2 - - - +
320A PHE* 4.2 7.2 - - + -
366A LEU* 5.5 0.2 - - + -
370A MET* 5.4 2.5 - - + -
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Residues in contact with GLU 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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182A THR* 2.5 23.7 + - - +
183A ALA* 1.3 77.8 + - - +
185A LYS* 1.3 60.6 + - + +
188A ALA* 3.1 24.4 + - - +
315A ILE* 5.9 0.2 - - - +
318A LYS* 2.8 41.5 - - - +
320A PHE* 3.7 34.7 - - + -
321A SER 4.0 16.6 - - - +
324A ASN* 3.4 25.4 - - - +
325A PHE* 3.7 18.2 - - - -
328A GLU* 5.1 2.0 - - + -
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Residues in contact with LYS 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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164A TYR* 3.3 25.7 + - + +
180A SER* 2.2 46.8 + - - +
182A THR* 2.9 27.5 + - - +
184A GLU* 1.3 81.2 - - + +
186A ALA* 1.3 58.2 + - - +
188A ALA* 3.4 2.1 + - - +
189A GLN* 2.9 31.2 + - - +
324A ASN* 5.3 0.2 - - - +
328A GLU* 3.9 33.3 - - + +
753A NAG 5.0 20.1 + - - +
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Residues in contact with ALA 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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163A ILE 5.4 1.1 - - - +
164A TYR* 3.7 20.8 - - + -
181A TRP* 3.7 15.3 - - + +
182A THR 2.8 19.0 + - - +
183A ALA 4.3 0.9 - - - +
185A LYS* 1.3 71.5 - - - +
187A ILE* 1.3 66.7 + - - +
189A GLN* 3.2 12.5 + - - +
190A LEU* 3.3 19.2 + - - +
367A GLN* 3.3 28.7 - - - +
370A MET* 4.6 4.0 - - - -
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Residues in contact with ILE 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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183A ALA* 3.0 31.6 + - + +
186A ALA* 1.3 75.5 - - - +
188A ALA* 1.3 58.0 + - - +
190A LEU* 3.6 3.3 + - - +
191A ASN* 3.0 29.0 + - + +
196A LYS 4.6 0.7 - - - +
197A LYS* 6.1 0.2 - - - -
198A VAL* 3.4 33.8 - - + +
199A LEU* 4.2 21.8 - - + -
200A ILE* 4.2 24.2 - - + +
320A PHE* 4.4 8.3 - - + -
325A PHE* 3.5 23.3 - - + -
370A MET* 4.3 17.5 - - - -
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Residues in contact with ALA 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 GLU 3.1 19.6 + - - +
185A LYS 3.7 2.9 - - - +
186A ALA 3.2 0.4 - - - -
187A ILE* 1.3 77.9 - - - +
189A GLN* 1.3 56.2 + - - +
191A ASN* 3.6 1.9 - - - +
192A SER* 2.7 40.3 + - - -
325A PHE* 4.0 7.6 - - + +
328A GLU* 3.9 22.9 - - + +
329A ILE* 3.5 28.5 - - + +
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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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162A ASP* 3.1 45.2 + - - +
163A ILE* 5.0 4.7 - - + -
164A TYR* 3.8 27.8 - - + +
185A LYS 2.9 10.2 + - - +
186A ALA 3.2 8.9 + - - +
188A ALA* 1.3 75.0 - - - +
190A LEU* 1.3 57.7 + - - +
192A SER* 4.0 8.4 + - - -
193A LYS* 2.9 52.7 + - - +
194A TYR* 4.7 2.6 - - - -
332A THR* 5.6 0.2 + - - -
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Residues in contact with LEU 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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163A ILE* 3.8 22.9 - - + +
186A ALA 3.3 11.9 + - - +
187A ILE* 3.9 6.5 - - - +
189A GLN* 1.3 79.4 - - + +
191A ASN* 1.3 61.7 + - - +
194A TYR* 3.3 11.8 + - + +
195A GLY 3.1 6.6 + - - -
196A LYS* 2.9 35.0 + - + +
198A VAL* 4.0 14.6 - - + -
367A GLN* 4.4 8.5 - - - +
370A MET* 3.7 38.8 - - + +
371A SER* 4.5 0.7 - - - +
374A PHE* 3.7 41.7 - - + -
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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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187A ILE* 3.0 21.5 + - + +
188A ALA* 3.6 7.2 - - - +
190A LEU* 1.3 76.5 - - - +
192A SER* 1.3 61.0 + - - +
195A GLY* 3.1 17.3 + - - -
196A LYS 3.2 12.9 + - - +
197A LYS* 3.1 18.5 - - - +
200A ILE 5.0 3.0 + - - -
202A LEU* 2.9 33.3 + - - +
325A PHE* 5.3 0.8 - - - -
329A ILE* 3.9 26.5 - - + +
518A GLN* 3.0 28.2 + - - +
522A LEU* 4.9 0.5 - - - +
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Residues in contact with SER 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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188A ALA 2.7 21.0 + - - -
189A GLN* 3.7 10.9 + - - -
191A ASN* 1.3 78.0 - - - +
193A LYS* 1.3 64.8 + - - +
328A GLU 4.5 2.8 + - - -
329A ILE* 3.9 24.7 - - - -
332A THR* 3.2 36.7 + - - +
515A LYS 5.0 1.6 - - - +
518A GLN* 3.3 20.5 - - - +
519A SER* 4.6 3.1 + - - -
522A LEU* 4.3 4.0 - - - +
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Residues in contact with LYS 193 (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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162A ASP* 2.7 36.6 + - - +
189A GLN* 2.9 33.7 + - - +
192A SER* 1.3 81.7 + - - +
194A TYR* 1.3 71.0 + - + +
195A GLY 3.7 0.9 - - - -
332A THR* 6.0 0.2 - - - -
514A LEU 4.9 0.4 - - - -
515A LYS* 2.4 81.6 + - + +
518A GLN* 5.0 0.2 - - - -
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Residues in contact with TYR 194 (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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159A LEU* 2.7 35.9 - - + +
162A ASP* 2.6 28.3 + - - -
163A ILE* 3.5 30.5 - - + -
189A GLN* 4.0 7.9 - - - -
190A LEU* 3.3 12.0 + - - +
193A LYS* 1.3 104.0 + - + +
195A GLY* 1.3 62.7 + - - +
196A LYS* 3.1 7.8 + - + +
374A PHE* 3.5 32.3 - + + -
511A ILE* 3.9 25.8 - - + -
514A LEU* 3.8 33.9 - - + +
515A LYS* 4.2 7.6 + - + -
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Residues in contact with GLY 195 (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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191A ASN 3.1 19.5 + - - -
193A LYS 3.7 1.0 - - - -
194A TYR* 1.3 77.7 - - - +
196A LYS* 1.3 60.6 + - - +
197A LYS* 3.7 18.7 + - - +
514A LEU* 5.3 1.3 - - - -
518A GLN* 4.0 23.7 - - - +
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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