Contacts of the helix formed by residues 182 - 190 (chain A) in PDB entry 2GAU
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 SER 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A TYR 3.9 1.2 + - - -
181A LEU* 1.3 78.9 - - - +
183A ARG* 1.3 63.7 + - - +
184A GLU* 3.5 16.7 + - - +
185A GLU* 2.9 37.8 + - - +
186A LEU* 3.0 21.5 + - - +
215A LYS* 4.3 20.7 - - - +
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Residues in contact with ARG 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 LEU 4.8 2.6 + - - -
182A SER* 1.3 73.2 - - - +
184A GLU* 1.3 59.2 + - - +
186A LEU* 3.4 19.2 + - - +
187A ALA* 2.8 36.4 + - - +
194A VAL* 4.0 20.6 - - + +
197A ALA* 4.6 4.9 - - + +
198A ILE* 3.8 20.3 - - + +
201A LEU* 3.4 28.7 - - - +
212A LEU* 3.6 31.7 - - - +
214A GLY 3.4 26.2 + - - -
215A LYS* 4.4 10.3 - - - +
217A ILE* 4.4 9.1 - - - +
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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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182A SER* 3.1 13.5 - - - +
183A ARG* 1.3 87.5 + - - +
185A GLU* 1.3 61.3 + - + +
187A ALA* 3.5 1.2 + - - +
188A THR* 2.9 35.8 + - - +
194A VAL* 3.7 30.9 - - + +
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Residues in contact with GLU 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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63A LYS* 2.7 42.0 + - - +
75A ILE* 3.6 21.0 - - + +
103A VAL* 4.6 5.8 - - - +
180A TYR 4.8 0.3 - - - +
181A LEU* 3.4 30.2 - - + +
182A SER* 2.9 40.0 + - - +
184A GLU* 1.3 75.3 - - + +
186A LEU* 1.3 59.7 + - - +
188A THR* 4.6 0.2 - - - -
189A LEU* 2.9 33.1 + - - +
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Residues in contact with LEU 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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157A LEU* 4.7 10.7 - - + +
160A THR* 4.4 9.5 - - + +
161A LEU* 4.1 16.2 - - + -
164A LEU* 3.8 29.6 - - + -
181A LEU* 3.9 24.7 - - + +
182A SER 3.0 21.4 + - - +
183A ARG* 3.7 21.5 - - - +
185A GLU* 1.3 76.8 - - - +
187A ALA* 1.3 59.5 + - - +
189A LEU* 3.6 5.2 + - - +
190A SER* 3.0 28.3 + - - -
197A ALA* 5.2 4.3 - - + -
201A LEU* 4.9 5.8 - - + -
217A ILE* 3.7 24.7 - - + -
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Residues in contact with ALA 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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183A ARG 2.8 18.4 + - - +
184A GLU 3.7 4.0 - - - +
185A GLU 3.3 0.2 - - - -
186A LEU* 1.3 74.7 - - - +
188A THR* 1.3 64.9 + - - +
190A SER* 3.1 7.6 + - - -
191A ASN 3.1 5.4 + - - -
192A MET* 3.0 43.7 + - - +
193A THR 3.9 3.8 - - - +
194A VAL* 3.7 28.3 - - + +
197A ALA* 3.9 6.4 - - + +
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Residues in contact with THR 188 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ARG* 5.6 5.3 + - - +
73A PHE* 3.2 33.2 + - + +
74A HIS* 3.8 7.4 + - - -
75A ILE* 3.6 33.6 + - + +
144A ARG* 4.3 3.3 + - - -
148A LEU* 5.5 0.5 - - - +
184A GLU* 2.9 24.6 + - - +
185A GLU 3.9 3.1 - - - -
187A ALA* 1.3 76.0 - - - +
189A LEU* 1.3 64.4 + - - +
190A SER 3.1 0.7 + - - -
191A ASN* 3.2 12.0 + - - +
192A MET 4.7 2.7 - - - +
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Residues in contact with LEU 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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75A ILE* 3.6 30.7 - - + +
77A ARG* 5.0 6.1 - - - +
78A ILE* 3.8 16.2 - - + +
144A ARG* 2.7 46.2 + - - +
148A LEU* 3.8 5.5 - - - +
160A THR* 4.0 25.8 + - + +
164A LEU* 4.3 7.6 - - + -
181A LEU* 3.7 30.7 - - + -
185A GLU 2.9 15.8 + - - +
186A LEU* 3.7 5.8 - - - +
188A THR* 1.3 76.7 - - - +
190A SER* 1.3 58.0 + - - +
191A ASN 3.8 0.5 + - - -
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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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148A LEU* 3.9 7.2 - - - -
156A ARG* 3.2 30.7 + - - +
157A LEU* 4.3 6.7 - - - +
160A THR* 3.2 24.9 - - - -
186A LEU 3.0 16.1 + - - -
187A ALA* 3.1 5.9 + - - -
188A THR 3.1 0.6 - - - -
189A LEU* 1.3 76.8 - - - +
191A ASN* 1.3 68.1 + - - +
192A MET* 3.4 24.8 - - - +
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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