Contacts of the helix formed by residues 182 - 189 (chain A) in PDB entry 2Q41
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A CYS* 3.7 2.9 - - - -
152A ILE* 3.4 24.9 - - + +
181A GLY* 1.3 75.4 - - - +
183A GLY* 1.3 63.1 + - - +
184A VAL* 3.0 19.4 + - - +
185A ALA* 2.6 41.8 + - + +
186A PHE* 3.3 21.4 + - - +
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Residues in contact with GLY 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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127A ILE* 4.2 23.7 - - - +
150A CYS* 4.2 10.1 - - - -
152A ILE* 4.6 3.8 - - - +
181A GLY 3.6 1.6 + - - -
182A ASP* 1.3 75.8 + - - +
184A VAL* 1.3 66.1 + - - +
185A ALA 3.2 1.6 - - - -
186A PHE* 3.2 7.4 + - - +
187A LEU* 3.1 23.2 + - - +
212A LEU* 5.3 1.8 - - - -
217A PHE* 5.2 1.6 - - - -
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Residues in contact with VAL 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 ASP* 3.0 17.9 - - - +
183A GLY* 1.3 75.5 - - - +
185A ALA* 1.3 67.4 + - + +
187A LEU* 3.5 3.3 + - - +
188A LYS* 3.2 37.6 + - - +
208A PRO 5.3 1.6 - - - +
211A GLU* 3.4 41.5 - - + +
212A LEU* 3.7 26.0 - - + -
217A PHE* 4.6 15.4 - - + -
220A SER* 4.3 1.6 + - - -
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Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ASP* 2.6 29.9 + - + +
184A VAL* 1.3 73.4 - - + +
186A PHE* 1.3 66.2 + - - +
188A LYS* 3.0 19.7 + - - +
189A ASN* 3.0 30.7 + - - +
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Residues in contact with PHE 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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125A LEU* 3.5 19.3 - - + -
127A ILE* 5.5 1.1 - - + -
148A ASP* 4.2 16.8 - - + -
150A CYS* 3.4 26.2 - - + -
177A ASN* 5.6 0.9 - - - -
179A VAL* 4.4 28.9 - - + -
181A GLY* 6.5 0.4 - - - -
182A ASP 3.3 18.4 + - - +
183A GLY 3.2 8.4 + - - +
185A ALA* 1.3 80.1 - - - +
187A LEU* 1.3 62.3 + - + +
189A ASN* 3.7 6.8 - - - +
190A ALA* 3.4 19.0 + - + +
195A TYR* 3.2 29.2 - + - -
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A LEU* 3.8 23.1 - - + -
127A ILE* 4.3 9.9 - - + -
183A GLY 3.1 14.4 + - - +
184A VAL 4.0 3.1 - - - +
185A ALA 3.1 0.4 - - - -
186A PHE* 1.3 74.8 - - + +
188A LYS* 1.3 64.9 + - - +
190A ALA* 3.2 18.3 - - + +
195A TYR* 4.7 0.9 - - + -
198A VAL* 4.9 2.0 - - + -
217A PHE* 3.4 19.1 - - + -
220A SER* 3.2 27.1 + - - +
221A VAL* 3.3 39.5 - - + +
223A ARG* 3.6 9.7 - - - -
224A ALA* 3.4 31.4 - - + -
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Residues in contact with LYS 188 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.2 25.7 + - - +
185A ALA* 3.0 12.9 + - - +
187A LEU* 1.3 73.8 - - - +
189A ASN* 1.3 64.0 + - - +
190A ALA 2.9 14.6 + - - +
211A GLU* 5.9 1.2 + - - -
216A PRO* 6.1 2.7 - - - -
220A SER* 3.9 13.9 - - - +
223A ARG* 4.2 14.7 + - - +
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Residues in contact with ASN 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 ALA* 3.0 33.9 + - - +
186A PHE* 3.7 7.8 - - - +
188A LYS* 1.3 77.9 - - - +
190A ALA* 1.3 57.5 + - - +
191A ALA 4.1 0.9 + - - -
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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