Contacts of the helix formed by residues 181 - 190 (chain A) in PDB entry 2ABQ
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 181 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LYS* 3.8 5.4 + - - +
180A PRO* 1.3 77.1 - - - +
182A HIS* 1.3 69.3 + - + +
183A HIS* 2.8 16.7 + - - +
184A GLU* 2.7 63.6 + - - +
185A LEU* 2.9 15.2 + - - +
217A SER* 3.7 20.9 - - - +
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Residues in contact with HIS 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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181A ASN* 1.3 74.5 - - + +
183A HIS* 1.3 99.0 + + - +
185A LEU* 3.4 3.0 + - - +
186A SER* 2.8 31.7 + - - -
193A ILE* 3.4 26.1 - - + +
194A ALA* 4.4 6.7 - - - -
216A VAL* 3.6 10.5 - - + +
217A SER 2.8 24.4 + - - +
218A PHE* 3.6 45.1 - + + -
219A ALA* 4.8 8.3 - - + -
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Residues in contact with HIS 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 ASN* 2.8 15.6 + - - +
182A HIS* 1.3 108.9 + + - +
184A GLU* 1.3 62.0 + - + +
186A SER* 3.3 9.0 + - - -
187A GLU* 3.0 28.1 + - - +
193A ILE 5.4 1.3 + - - -
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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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38A LYS* 6.0 1.7 - - - -
161A ASP* 4.3 7.5 - - - +
162A THR 3.6 19.1 - - - +
163A SER* 3.9 20.9 - - - -
167A LEU* 4.7 5.4 - - + +
179A LYS* 4.1 4.3 + - - +
180A PRO* 3.5 14.7 - - + +
181A ASN* 2.7 59.3 + - - +
183A HIS* 1.3 74.7 - - + +
185A LEU* 1.3 63.1 + - - +
187A GLU* 3.3 12.4 + - - +
188A LEU* 3.0 22.5 + - - +
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Residues in contact with LEU 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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180A PRO* 4.0 16.1 - - + +
181A ASN 2.9 16.1 + - - +
182A HIS 3.7 4.7 - - - +
184A GLU* 1.3 76.4 - - - +
186A SER* 1.3 63.6 + - - +
188A LEU* 3.2 22.5 + - + -
189A VAL* 3.1 24.6 + - + +
193A ILE* 3.6 25.1 - - + -
199A ALA* 4.1 12.1 - - + +
202A HIS* 5.0 9.4 - - + -
203A VAL* 4.5 7.9 - - + -
206A LEU* 4.4 15.5 - - + -
214A ILE* 5.9 0.4 - - + -
216A VAL* 3.7 32.5 - - + -
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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 HIS 2.8 21.7 + - - -
183A HIS* 3.3 10.1 + - - -
185A LEU* 1.3 75.6 - - - +
187A GLU* 1.3 53.8 + - - +
189A VAL* 3.4 2.2 + - - -
190A SER* 2.8 30.7 + - - -
191A LYS 3.0 29.3 + - - -
192A PRO* 4.1 2.9 - - - -
193A ILE* 3.0 31.0 + - - +
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Residues in contact with GLU 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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163A SER* 4.5 7.6 - - - -
164A GLY* 3.5 34.0 + - - -
183A HIS 3.0 16.4 + - - +
184A GLU* 3.5 10.4 - - - +
186A SER* 1.3 79.3 - - - +
188A LEU* 1.3 61.2 + - - +
190A SER* 3.6 13.1 + - - +
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Residues in contact with LEU 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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164A GLY 5.5 0.9 - - - +
167A LEU* 4.0 28.5 - - + -
168A HIS* 3.9 37.8 - - + +
171A LEU* 3.9 33.9 - - + -
178A ILE* 5.4 4.5 - - + -
180A PRO* 5.6 2.5 - - + -
184A GLU 3.0 12.7 + - - +
185A LEU* 3.2 26.7 + - + +
187A GLU* 1.3 79.6 - - - +
189A VAL* 1.3 59.2 + - + +
190A SER* 3.7 2.6 + - - -
206A LEU* 4.4 13.5 - - + -
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Residues in contact with VAL 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 LEU* 3.1 20.8 + - + +
186A SER* 3.5 3.4 - - - +
188A LEU* 1.3 76.8 - - + +
190A SER* 1.3 70.8 - - - +
191A LYS* 3.3 36.5 + - + +
193A ILE* 4.4 4.7 - - + -
202A HIS* 2.9 44.9 - - + +
205A ARG* 3.4 20.0 - - - +
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Residues in contact with SER 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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186A SER 2.8 11.7 + - - -
187A GLU* 3.6 10.4 + - - +
188A LEU 3.4 4.2 + - - -
189A VAL* 1.3 80.9 - - - +
191A LYS* 1.3 61.2 + - - +
192A PRO* 4.8 0.5 - - - +
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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