Contacts of the helix formed by residues 179 - 196 (chain A) in PDB entry 5Y3R
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A HIS* 2.7 32.7 + - - -
178A ASN* 1.3 86.0 + - - +
180A SER* 1.3 53.4 + - - +
181A ALA* 3.1 21.5 + - - +
182A LYS* 2.5 56.5 + - + +
185A ARG* 4.3 1.6 + - - -
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Residues in contact with SER 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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176A HIS* 3.8 9.4 - - - -
177A GLY 4.3 6.5 + - - -
178A ASN 3.7 4.8 + - - -
179A ASP* 1.3 69.3 - - - +
181A ALA* 1.3 59.0 - - - +
182A LYS 3.1 1.3 - - - -
183A ALA* 2.8 12.2 + - - +
184A SER* 2.8 25.8 + - - -
187A ARG* 4.3 7.6 + - - -
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Residues in contact with ALA 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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179A ASP* 3.1 22.5 + - - +
180A SER* 1.3 76.1 - - - +
182A LYS* 1.3 55.9 + - - +
184A SER* 2.7 23.0 + - - +
185A ARG* 2.9 17.7 + - - +
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Residues in contact with LYS 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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140A ASP* 5.7 2.2 - - - -
141A TYR* 4.3 8.0 + - + +
142A SER* 2.4 40.5 + - - -
143A LEU* 2.9 12.9 - - + +
145A GLU* 4.5 0.4 + - - -
176A HIS* 3.0 37.2 - - + +
178A ASN* 4.8 6.1 - - - +
179A ASP* 2.5 41.5 + - + +
181A ALA* 1.3 76.5 - - - +
183A ALA* 1.3 55.4 + - - +
185A ARG* 3.1 27.0 + - - +
186A ALA 2.8 22.7 + - - -
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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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176A HIS* 3.0 23.6 - - + -
180A SER* 2.8 22.3 + - - +
182A LYS* 1.3 72.5 - - - +
184A SER* 1.3 60.8 + - - +
185A ARG 3.0 0.9 - - - -
186A ALA* 2.8 24.0 + - - +
187A ARG* 2.9 33.9 + - - +
219A ASP* 4.8 0.3 - - - +
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Residues in contact with SER 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 SER 2.8 11.2 + - - -
181A ALA* 2.7 31.7 + - - +
183A ALA* 1.3 71.5 - - - +
185A ARG* 1.3 48.6 + - - +
187A ARG* 2.9 25.9 - - - +
188A THR* 2.0 46.9 + - - -
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Residues in contact with ARG 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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142A SER* 2.2 28.8 + - - -
143A LEU* 2.9 31.9 - - - +
144A SER* 2.6 30.6 + - - +
145A GLU* 2.5 30.8 + - - +
148A TRP* 4.9 6.7 - - + -
179A ASP* 4.3 1.6 + - - -
181A ALA 2.9 17.0 + - - +
182A LYS* 3.1 51.6 - - - +
183A ALA 3.0 0.6 - - - -
184A SER* 1.3 75.0 - - - +
186A ALA* 1.3 54.5 + - - +
188A THR* 3.8 6.3 - - + -
189A LYS* 2.9 24.0 + - + +
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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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143A LEU* 3.1 22.8 - - + +
144A SER* 3.6 2.7 - - - -
147A LEU* 5.4 1.1 - - - -
175A PRO* 6.5 0.4 - - + -
182A LYS 2.8 8.0 + - - +
183A ALA* 2.8 14.3 + - - +
185A ARG* 1.3 70.2 - - - +
187A ARG* 1.3 53.2 + - - +
188A THR 2.8 7.5 + - - -
190A ALA* 2.6 40.3 + - - +
219A ASP* 3.8 15.7 - - + +
220A ILE* 6.2 2.0 - - + -
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Residues in contact with ARG 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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180A SER* 4.2 8.3 + - - -
183A ALA* 2.9 30.1 + - - +
184A SER* 2.9 48.4 - - - +
186A ALA* 1.3 72.4 - - - +
188A THR* 1.3 59.7 + - - +
190A ALA* 4.4 2.2 - - - -
191A GLY* 4.5 5.2 + - - -
219A ASP* 3.2 24.4 + - - +
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Residues in contact with THR 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 SER* 2.0 32.4 + - - -
185A ARG* 3.5 7.9 - - + -
186A ALA 2.8 2.6 + - - -
187A ARG* 1.3 79.4 - - - +
189A LYS* 1.3 69.3 + - + +
190A ALA 3.1 1.2 + - - -
191A GLY* 3.4 8.1 + - - -
192A ASP* 3.1 20.2 - - - +
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Residues in contact with LYS 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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144A SER* 3.4 37.7 - - - +
147A LEU* 3.0 19.5 - - + +
148A TRP* 3.3 43.0 - - + +
151A ALA* 4.9 0.7 - - - -
185A ARG* 2.9 9.2 + - + +
188A THR* 1.3 75.6 - - + +
190A ALA* 1.3 69.3 + - - +
192A ASP* 2.8 29.9 + - + +
193A LEU* 2.9 44.9 + - - +
2383C PHE* 6.2 1.3 - - - -
2384C PHE* 6.5 0.2 - - - -
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Residues in contact with ALA 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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147A LEU* 3.4 17.2 - - + +
186A ALA* 2.6 25.7 + - - +
187A ARG* 4.4 4.9 - - - -
189A LYS* 1.3 75.2 - - - +
191A GLY* 1.3 56.4 + - - +
193A LEU* 2.6 27.5 + - - +
194A ARG* 2.9 21.2 + - - +
219A ASP* 4.4 24.7 - - + +
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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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187A ARG 4.5 5.0 + - - -
188A THR 3.4 7.3 + - - -
189A LYS 3.3 0.6 - - - -
190A ALA* 1.3 79.1 - - - +
192A ASP* 1.3 57.6 + - - +
194A ARG* 4.1 10.4 - - - +
195A ASP* 2.8 41.9 + - - -
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Residues in contact with ASP 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 THR* 3.1 15.9 - - - +
189A LYS* 2.8 36.7 + - + +
191A GLY* 1.3 77.0 - - - +
193A LEU* 1.3 47.9 + - - +
195A ASP* 3.0 10.1 + - - +
196A THR* 2.4 39.9 + - - +
2380C ASN* 3.8 34.4 + - + +
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Residues in contact with LEU 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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147A LEU* 3.7 24.9 - - + +
151A ALA* 3.6 30.7 - - + +
166A ILE* 5.2 4.9 - - + -
189A LYS* 2.9 30.3 + - - +
190A ALA 2.6 14.4 + - - +
192A ASP* 1.3 69.7 - - - +
194A ARG* 1.3 61.6 + - + +
196A THR* 2.9 21.4 - - + +
198A ILE* 2.8 59.0 + - + +
200A LEU* 6.2 3.8 - - + +
2384C PHE* 4.8 2.2 - - + -
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Residues in contact with ARG 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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190A ALA* 2.9 22.4 + - - +
191A GLY* 4.1 6.7 - - - +
193A LEU* 1.3 74.6 - - + +
195A ASP* 1.3 54.5 + - - +
197A GLY* 2.4 31.0 + - - -
198A ILE 3.5 7.4 + - - +
199A PHE* 3.3 17.2 - - + -
218A ARG* 2.4 64.7 + - - +
219A ASP* 3.1 14.5 + - - +
221A ILE 2.2 34.2 + - - -
222A SER* 3.0 25.3 - - - +
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Residues in contact with ASP 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 GLY* 2.8 32.2 + - - +
192A ASP* 3.0 10.0 + - - +
194A ARG* 1.3 74.1 - - - +
196A THR* 1.3 55.9 + - - +
197A GLY 3.1 3.6 + - - -
2354C ASN* 4.8 13.3 + - - +
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Residues in contact with THR 196 (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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154A PHE* 5.1 3.7 - - + -
164A LYS* 3.6 8.5 - - - +
192A ASP* 2.4 37.2 + - - +
193A LEU* 2.9 26.9 - - + +
194A ARG 2.9 0.6 - - - -
195A ASP* 1.3 70.5 - - - +
197A GLY* 1.3 58.9 + - - +
198A ILE* 3.0 27.5 + - + +
2354C ASN* 6.0 1.8 - - - -
2380C ASN* 4.8 12.0 + - - +
2381C ALA* 5.7 5.6 - - - +
2384C PHE* 4.0 21.7 - - + -
2385C LEU* 6.5 0.4 - - + -
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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