Contacts of the helix formed by residues 182 - 195 (chain A) in PDB entry 1A4Y
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ALA* 5.7 2.0 - - - +
180A ASP* 3.6 29.6 + - - +
181A ILE* 1.3 81.9 + - - +
183A GLU* 1.3 62.9 + - - +
184A ALA* 4.5 4.0 - - + +
186A VAL* 2.9 26.9 + - - +
208A CYS 2.8 17.4 + - - -
209A GLY* 3.6 21.6 - - - +
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Residues in contact with GLU 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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182A ASN* 1.3 78.0 - - - +
184A ALA* 1.3 62.3 + - - +
187A ARG* 2.9 53.5 + - - +
209A GLY 3.5 5.5 + - - -
211A THR* 2.8 32.1 + - + +
213A ASP* 3.7 14.1 - - - +
214A ASN* 3.2 27.1 + - - +
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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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155A ALA* 4.3 13.2 - - + -
181A ILE 4.7 0.7 - - - +
182A ASN* 3.3 3.2 - - + +
183A GLU* 1.3 79.8 - - - +
185A GLY* 1.3 64.5 + - - +
187A ARG* 3.6 9.1 - - - +
188A VAL* 3.2 26.0 + - - +
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Residues in contact with GLY 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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155A ALA* 3.7 9.5 - - - +
158A CYS* 3.3 34.4 - - - +
181A ILE* 3.1 19.6 + - - -
184A ALA* 1.3 80.0 - - - +
186A VAL* 1.3 61.2 + - - +
188A VAL* 3.3 3.0 + - - -
189A LEU* 3.0 20.3 + - - +
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Residues in contact with VAL 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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181A ILE* 3.6 25.5 - - + +
182A ASN 2.9 23.0 + - - +
185A GLY* 1.3 76.0 - - - +
187A ARG* 1.3 63.2 + - - +
189A LEU* 3.3 5.8 + - + +
190A CYS* 2.9 36.1 + - - -
205A LEU* 4.7 13.7 - - + -
208A CYS* 4.5 1.6 - - + +
210A VAL* 3.8 28.3 - - + -
214A ASN* 3.4 34.1 - - + +
218A LEU* 5.0 2.0 - - + -
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Residues in contact with ARG 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 GLU* 2.9 60.5 + - - +
184A ALA* 3.6 8.4 - - - +
186A VAL* 1.3 78.5 - - - +
188A VAL* 1.3 58.5 + - + +
190A CYS* 3.3 6.1 + - - +
191A GLN* 3.0 46.7 + - - +
213A ASP* 4.1 15.6 + - - +
214A ASN* 3.9 1.0 - - - +
217A ASP* 3.4 35.8 + - - +
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Residues in contact with VAL 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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155A ALA 5.8 1.3 - - - +
158A CYS* 3.3 35.0 - - + +
159A GLU* 3.8 23.3 - - + +
162A ALA* 4.0 5.9 - - + +
184A ALA 3.2 12.0 + - - +
185A GLY* 3.3 7.6 + - - +
187A ARG* 1.3 76.6 - - + +
189A LEU* 1.3 69.5 + - - +
191A GLN* 2.9 30.9 + - - +
192A GLY* 2.9 11.1 + - - -
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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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158A CYS* 4.1 13.9 - - - +
161A LEU* 3.9 33.9 - - + -
162A ALA* 4.4 5.8 - - - +
165A LEU* 4.6 5.1 - - + +
174A LEU* 4.2 20.2 - - + -
176A VAL* 4.1 14.8 - - + -
181A ILE* 4.1 14.6 - - + -
185A GLY 3.0 9.8 + - - +
186A VAL* 3.4 9.6 - - + +
188A VAL* 1.3 77.9 - - - +
190A CYS* 1.3 63.2 + - - +
192A GLY* 3.1 3.5 + - - -
193A LEU* 3.0 30.2 + - + +
203A LEU* 5.2 2.0 - - + -
205A LEU* 3.9 28.3 - - + -
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Residues in contact with CYS 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 VAL* 2.9 28.4 + - - -
187A ARG 3.3 10.8 - - - +
188A VAL 3.1 0.2 - - - -
189A LEU* 1.3 74.7 - - - +
191A GLN* 1.3 65.6 + - - +
193A LEU* 3.1 9.9 + - - +
194A LYS* 3.0 24.8 + - - +
203A LEU* 5.9 1.3 - - - -
205A LEU* 5.7 2.2 - - - -
217A ASP* 3.8 28.7 - - + +
218A LEU* 4.3 18.4 - - - -
221A ILE* 3.7 24.2 - - + +
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Residues in contact with GLN 191 (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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159A GLU* 5.7 0.9 - - - +
166A ARG* 4.2 5.6 + - - +
187A ARG* 3.0 42.9 + - - +
188A VAL* 2.9 21.3 + - - +
190A CYS* 1.3 75.5 - - - +
192A GLY* 1.3 64.3 + - - +
194A LYS* 3.5 4.3 + - - +
195A ASP* 3.0 37.1 + - - +
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Residues in contact with GLY 192 (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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162A ALA* 3.9 22.4 - - - -
165A LEU* 4.7 3.4 - - - -
166A ARG* 3.5 21.5 - - - +
188A VAL 2.9 10.5 + - - -
189A LEU 3.1 4.9 + - - -
191A GLN* 1.3 78.6 - - - +
193A LEU* 1.3 54.2 + - - +
196A SER* 2.8 33.0 + - - -
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Residues in contact with LEU 193 (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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165A LEU* 3.4 28.7 - - + -
174A LEU* 5.6 0.2 - - + -
189A LEU* 3.0 17.0 + - + +
190A CYS* 3.1 11.4 + - - +
192A GLY* 1.3 76.0 - - - +
194A LYS* 1.3 60.0 + - - +
196A SER* 3.4 19.6 + - - +
198A CYS* 4.2 17.5 - - - -
200A LEU* 3.5 29.2 - - + -
203A LEU* 3.6 34.5 - - + -
221A ILE* 4.0 21.3 - - + -
225A LYS* 3.4 18.2 - - + -
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Residues in contact with LYS 194 (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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190A CYS 3.0 16.0 + - - +
191A GLN* 4.0 5.2 - - - +
193A LEU* 1.3 76.3 - - - +
195A ASP* 1.3 66.8 + - - +
196A SER 3.7 4.7 - - - +
220A GLY 6.1 1.1 - - - -
221A ILE* 4.6 13.6 - - + +
224A SER* 5.5 9.0 - - - +
225A LYS* 5.1 4.5 - - - +
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Residues in contact with ASP 195 (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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166A ARG* 3.5 34.7 + - - +
191A GLN* 3.0 23.9 + - - +
194A LYS* 1.3 79.3 - - - +
196A SER* 1.3 65.3 + - - +
197A PRO* 3.6 3.6 - - - +
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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