Contacts of the helix formed by residues 178 - 194 (chain I) in PDB entry 1DZH
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 178 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174I ASP* 3.1 37.7 + - + +
177I GLU* 1.3 86.1 - - - +
179I ALA* 1.3 64.3 + - - +
180I GLU 3.5 2.2 - - - -
181I GLN* 3.4 19.7 + - + +
182I SER* 3.1 23.5 + - - +
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Residues in contact with ALA 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174I ASP 3.9 1.7 + - - -
175I PHE* 3.9 10.6 + - - +
176I LYS 5.5 0.4 - - - +
177I GLU 3.5 5.8 + - - +
178I ASN* 1.3 74.1 - - - +
180I GLU* 1.3 65.0 + - + +
182I SER* 3.4 2.1 + - - -
183I ARG* 3.1 17.2 + - - +
207I ILE* 3.6 22.5 - - - +
208I ASN* 3.6 35.4 - - - -
209I GLU* 4.1 7.9 - - - +
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Residues in contact with GLU 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178I ASN 3.5 0.6 - - - -
179I ALA* 1.3 75.1 - - + +
181I GLN* 1.3 60.8 + - - +
183I ARG* 2.8 67.1 + - - +
184I ALA* 2.8 16.1 + - + +
204I SER* 4.4 3.5 + - - -
205I GLU* 4.2 14.0 + - - +
207I ILE 4.0 11.6 - - - +
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Residues in contact with GLN 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178I ASN* 3.4 27.0 + - + +
180I GLU* 1.3 73.2 - - - +
182I SER* 1.3 56.3 + - - +
184I ALA* 3.3 10.4 - - - +
185I ALA* 2.9 25.3 + - - +
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Residues in contact with SER 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I LEU* 3.6 29.2 - - - +
174I ASP* 3.6 16.6 + - - +
175I PHE* 3.8 16.2 - - - -
178I ASN* 3.1 13.8 + - - +
179I ALA 3.6 8.3 - - - -
181I GLN* 1.3 70.9 - - - +
183I ARG* 1.3 56.9 + - - +
185I ALA* 3.0 10.1 + - - +
186I ILE* 2.7 38.9 + - - +
207I ILE* 5.2 0.2 - - - -
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Residues in contact with ARG 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179I ALA 3.1 12.2 + - - +
180I GLU* 2.8 51.7 + - - +
182I SER* 1.3 67.9 - - - +
184I ALA* 1.3 70.7 + - - +
186I ILE* 2.8 17.7 + - - +
187I ASN* 2.8 27.2 + - - +
200I ASP* 5.5 4.4 - - - +
202I ILE* 3.1 37.5 + - + -
203I PRO* 3.2 15.8 + - - +
204I SER* 3.0 34.4 + - - +
205I GLU 4.3 2.5 - - - +
206I ALA 5.0 2.9 - - - +
207I ILE* 4.5 19.6 - - + +
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Residues in contact with ALA 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180I GLU* 2.8 15.7 + - + +
181I GLN* 3.3 16.2 - - - +
183I ARG* 1.3 79.8 - - - +
185I ALA* 1.3 56.4 + - - +
187I ASN* 3.7 5.1 - - - +
188I LYS* 2.9 32.9 + - - +
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Residues in contact with ALA 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I PHE* 5.7 0.9 - - + -
173I LEU* 4.4 15.7 - - + -
181I GLN 2.9 17.7 + - - +
182I SER* 3.0 14.1 + - - +
184I ALA* 1.3 72.7 - - - +
186I ILE* 1.3 64.4 + - - +
188I LYS* 3.4 8.8 + - - +
189I TRP* 2.9 24.1 + - - +
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Residues in contact with ILE 186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I PHE* 3.5 64.8 - - + -
173I LEU* 3.7 10.1 - - + -
175I PHE* 4.4 3.4 - - + -
182I SER 2.7 19.2 + - - +
183I ARG 2.8 6.9 + - - +
185I ALA* 1.3 68.9 - - - +
187I ASN* 1.3 55.3 + - - +
189I TRP* 2.7 26.3 + - - +
190I VAL* 3.0 12.2 + - + -
201I VAL* 4.5 4.0 - - + -
202I ILE* 3.4 35.7 - - + -
207I ILE* 3.9 15.3 - - + -
214I VAL* 4.7 1.1 - - + -
216I VAL* 4.1 15.0 - - + -
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Residues in contact with ASN 187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I ARG* 2.8 42.5 + - - +
184I ALA* 3.8 5.2 - - - +
186I ILE* 1.3 71.6 - - - +
188I LYS* 1.3 60.1 + - - +
190I VAL* 3.3 2.8 + - - +
191I SER* 3.0 22.1 + - - -
198I ILE 4.4 0.7 - - - +
199I THR 3.4 23.9 + - - +
200I ASP* 3.8 5.6 - - - +
201I VAL* 2.9 28.6 + - - +
202I ILE* 2.7 37.7 + - - +
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Residues in contact with LYS 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I ALA 2.9 21.1 + - - +
185I ALA* 3.5 8.3 - - - +
187I ASN* 1.3 70.7 - - - +
189I TRP* 1.3 57.8 + - - +
191I SER* 3.3 9.5 + - - +
192I ASN* 3.0 33.9 + - + +
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Residues in contact with TRP 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I ALA* 3.9 22.4 - - + -
144I ASN 4.1 9.0 - - - -
145I ARG* 3.3 71.3 - - + +
147I PHE* 4.2 15.3 - + + -
185I ALA 2.9 11.8 + - - +
186I ILE* 2.7 14.9 + - - +
188I LYS* 1.3 67.2 - - - +
190I VAL* 1.3 94.4 + - + +
192I ASN* 2.9 22.3 + - - +
193I LYS* 3.1 40.3 + - + +
216I VAL* 4.1 9.0 - - + -
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Residues in contact with VAL 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I ALA* 5.0 0.2 - - + -
186I ILE* 3.0 8.8 + - + +
187I ASN 4.0 1.8 - - - +
189I TRP* 1.3 88.6 - - + +
191I SER* 1.3 63.0 + - - +
193I LYS* 3.1 7.0 + - - +
194I THR* 3.0 24.9 + - + +
198I ILE* 3.7 15.9 - - + -
201I VAL* 3.5 39.7 - - + -
216I VAL* 3.5 31.6 - - + -
218I THR* 3.9 23.6 - - + -
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Residues in contact with SER 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ASN 3.0 12.7 + - - -
188I LYS* 3.3 15.3 + - - +
190I VAL* 1.3 72.2 - - - +
192I ASN* 1.3 58.8 + - - +
194I THR* 2.9 21.8 + - - -
196I GLY* 3.0 31.2 + - - +
198I ILE 3.1 20.8 + - - -
199I THR* 4.5 12.4 + - - -
804I NAG 6.0 0.2 - - - +
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Residues in contact with ASN 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I LYS* 3.0 19.8 + - + +
189I TRP* 2.9 14.4 + - - +
191I SER* 1.3 74.8 + - - +
193I LYS* 1.3 68.3 + - - +
194I THR 3.8 0.2 + - - -
195I GLU* 4.1 4.9 - - - +
804I NAG 1.4 85.6 + - + +
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Residues in contact with LYS 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141I VAL* 3.7 32.9 - - + +
142I SER 4.0 18.3 + - - -
143I ALA* 4.3 15.9 - - + -
189I TRP* 3.1 46.3 + - + +
190I VAL 3.9 5.2 - - - +
192I ASN* 1.3 85.7 - - - +
194I THR* 1.3 60.7 + - + +
195I GLU* 3.5 9.9 + - - +
220I TYR* 3.8 9.0 - - - +
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Residues in contact with THR 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I VAL* 3.0 22.7 + - + +
191I SER 2.9 11.8 + - - -
193I LYS* 1.3 77.9 - - + +
195I GLU* 1.3 71.5 + - - +
197I ARG* 3.2 18.1 + - - +
198I ILE* 2.9 51.2 + - + -
218I THR* 4.1 13.9 - - + +
220I TYR* 3.6 25.1 - - + -
372I PHE* 4.4 4.0 - - + -
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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