Contacts of the helix formed by residues 172 - 188 (chain A) in PDB entry 2OO3
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 GLU 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ARG* 3.0 24.3 + - - +
171A LYS* 1.3 98.4 + - + +
173A GLU* 1.3 56.8 + - - +
175A LYS* 3.0 37.2 + - - +
176A GLU* 2.9 43.6 + - - +
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 4.7 5.4 + - - -
166A PRO* 3.7 14.2 - - - +
167A SER* 3.7 4.7 + - - -
168A TYR* 3.1 35.4 + - + -
169A GLU* 3.1 15.9 + - - +
170A ARG* 3.0 61.5 + - - +
172A GLU* 1.3 76.7 - - - +
174A TYR* 1.3 56.1 + - - +
176A GLU* 3.9 9.6 - - - +
177A ILE* 3.0 42.5 + - + +
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Residues in contact with TYR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.8 42.0 + + + +
170A ARG 4.4 0.4 - - - -
171A LYS* 3.1 27.5 + - - +
173A GLU* 1.3 76.6 - - - +
175A LYS* 1.3 57.1 + - - +
178A PRO* 3.3 16.8 - - - +
197A TYR* 5.5 1.1 - - + -
198A PRO* 3.4 27.3 + - + +
200A VAL* 4.5 12.6 + - - +
201A ASN 5.2 0.9 + - - -
204A TRP* 3.6 47.0 - + + +
205A THR* 4.0 21.9 + - - -
207A GLN* 6.3 0.9 - - + -
208A PHE* 3.4 42.8 + + + +
211A LYS* 5.4 1.0 - - - +
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Residues in contact with LYS 175 (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 LYS 4.4 0.6 + - - +
172A GLU* 3.2 42.2 - - - +
174A TYR* 1.3 78.7 - - - +
176A GLU* 1.3 68.0 + - - +
177A ILE 3.3 1.8 - - - -
178A PRO* 3.5 4.4 - - - +
179A TYR* 3.3 23.3 + - - +
211A LYS* 5.7 7.1 - - + +
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Residues in contact with GLU 176 (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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146A VAL* 4.7 6.4 - - + +
170A ARG* 2.9 44.5 + - - -
172A GLU* 2.9 25.9 + - + +
173A GLU* 3.5 10.8 + - - +
175A LYS* 1.3 81.9 - - + +
177A ILE* 1.3 62.9 + - + +
179A TYR* 3.3 8.1 + - - +
180A ALA* 2.9 30.7 + - - +
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Residues in contact with ILE 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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42A HIS* 4.2 2.9 - - + +
146A VAL* 3.5 36.6 - - + -
164A ILE* 4.4 6.1 - - + -
166A PRO* 3.8 28.3 - - + -
168A TYR* 4.3 2.2 - - + +
173A GLU* 3.0 28.1 + - + +
176A GLU* 1.3 77.3 - - + +
178A PRO* 1.3 67.6 - - + +
180A ALA* 3.2 4.9 + - + +
181A ILE* 3.0 33.2 + - + +
195A VAL* 3.7 29.8 - - + -
208A PHE* 3.9 11.2 - - + -
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Residues in contact with PRO 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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174A TYR 3.3 21.1 - - - +
175A LYS 3.5 7.6 - - - +
177A ILE* 1.3 94.5 - - + +
179A TYR* 1.3 56.4 + - - +
181A ILE* 4.4 0.9 - - + +
182A LYS* 2.8 31.4 + - - +
208A PHE* 3.5 27.8 - - + +
211A LYS* 3.5 33.2 - - + -
212A MET* 3.7 23.6 - - - +
215A ILE* 3.6 3.3 - - - +
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Residues in contact with TYR 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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175A LYS 3.3 18.3 + - - +
176A GLU* 3.4 7.6 - - - +
177A ILE 3.2 0.4 - - - -
178A PRO* 1.3 79.3 - - - +
180A ALA* 1.3 65.8 + - + +
182A LYS* 3.3 10.9 + - + +
183A ASN* 3.1 25.8 + - + +
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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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146A VAL* 3.5 35.9 - - + +
149A LEU* 3.9 17.5 - - + +
176A GLU 2.9 12.8 + - - +
177A ILE* 3.2 4.2 + - + +
179A TYR* 1.3 81.2 - - + +
181A ILE* 1.3 56.5 - - - +
183A ASN* 3.3 7.7 + - - +
184A ALA* 3.0 28.2 + - - +
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Residues in contact with ILE 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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149A LEU* 4.7 4.3 - - + -
164A ILE* 3.6 31.4 - - + -
177A ILE* 3.0 39.5 + - + +
178A PRO 4.0 3.4 - - - +
180A ALA* 1.3 73.0 - - - +
182A LYS* 1.3 60.8 + - - +
184A ALA* 3.2 6.1 + - - +
185A TYR* 2.8 30.3 + - + +
193A TYR* 4.2 20.0 - - + -
195A VAL* 3.9 11.7 - - + -
212A MET* 3.8 20.4 - - + -
215A ILE* 3.9 8.7 - - + -
242A ILE* 3.9 27.8 - - + -
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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
----------------------------------------------------------
178A PRO 2.8 22.9 + - - +
179A TYR* 3.3 11.0 + - + +
181A ILE* 1.3 71.8 - - - +
183A ASN* 1.3 64.6 + - - +
185A TYR* 3.4 3.3 + - + +
186A SER* 3.0 23.0 + - - -
211A LYS 5.9 0.7 - - - +
214A GLU* 5.2 15.1 + - + +
215A ILE* 3.6 30.9 - - + +
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Residues in contact with ASN 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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149A LEU* 5.9 0.2 - - - +
150A ASN* 3.0 41.6 + - - +
179A TYR* 3.1 20.1 + - + +
180A ALA* 3.6 10.2 - - - +
182A LYS* 1.3 76.5 - - - +
184A ALA* 1.3 64.0 + - - +
186A SER* 2.6 29.7 + - - -
187A LYS* 3.5 12.1 + - - +
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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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149A LEU* 4.2 19.3 - - + +
153A LEU* 3.9 16.8 - - + +
180A ALA 3.0 17.1 + - - +
181A ILE* 3.6 6.5 - - - +
183A ASN* 1.3 80.0 + - - +
185A TYR* 1.3 62.6 + - - +
187A LYS* 3.1 11.3 + - - +
188A PHE* 3.0 20.4 + - - +
193A TYR* 3.3 24.3 + - + -
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Residues in contact with TYR 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 ILE* 2.8 22.5 + - + +
182A LYS* 3.7 5.2 - - + +
184A ALA* 1.3 73.0 - - - +
186A SER* 1.3 64.8 + - - +
188A PHE 4.0 0.2 - - - -
189A SER* 3.1 69.8 + - - -
193A TYR* 3.6 21.7 + + + -
215A ILE* 3.6 35.9 - - + -
216A SER* 3.4 18.0 + - - -
218A LYS* 3.8 8.0 + - - -
242A ILE* 3.6 31.0 - - + -
243A ASN* 4.1 0.9 - - - -
302A SO4 3.4 18.3 + - - -
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Residues in contact with SER 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 LYS* 3.0 13.5 + - - -
183A ASN* 2.6 29.6 + - - -
185A TYR* 1.3 79.7 - - - +
187A LYS* 1.3 62.1 + - - +
189A SER* 5.1 3.2 + - - -
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Residues in contact with LYS 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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149A LEU 5.5 0.4 - - - +
150A ASN* 2.7 51.2 + - - +
153A LEU* 3.7 16.3 + - + +
154A PRO* 3.6 29.4 - - + +
183A ASN* 3.8 18.2 - - - +
184A ALA* 3.1 9.6 + - - +
186A SER* 1.3 80.4 + - - +
188A PHE* 1.3 60.2 + - - +
189A SER 4.0 0.7 - - - -
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Residues in contact with PHE 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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153A LEU* 4.0 15.3 - - + -
154A PRO* 3.7 24.9 - - + -
155A PRO* 3.6 27.4 - - + -
158A LYS* 3.7 26.7 - - + -
159A ARG* 4.1 0.4 - - - -
160A GLY* 3.7 24.7 - - - -
162A ILE* 4.3 4.5 - - + -
184A ALA 3.0 6.6 + - - +
185A TYR 3.3 2.8 - - - +
187A LYS* 1.3 81.0 - - - +
189A SER* 1.3 61.0 + - - +
190A THR* 3.2 24.5 + - - -
191A GLY* 3.4 27.0 + - - -
193A TYR* 2.8 32.5 + - - +
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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