Contacts of the helix formed by residues 213 - 224 (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 ASP 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A GLU* 3.7 24.0 - - - +
187A ARG* 4.1 8.5 + - - +
211A THR* 3.5 5.9 + - - +
212A SER* 1.3 81.6 - - - +
214A ASN* 1.3 63.3 + - - +
215A CYS 2.9 1.0 + - - -
216A ARG* 3.1 20.6 + - - +
217A ASP* 3.8 7.0 + - - +
245A GLU* 4.7 5.6 - - - -
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Residues in contact with ASN 214 (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* 3.2 46.3 + - - +
186A VAL* 3.4 21.8 - - + +
187A ARG* 3.9 2.8 - - - +
210A VAL* 3.6 18.9 - - + -
211A THR* 3.1 32.2 + - - +
212A SER 3.2 0.6 - - - -
213A ASP* 1.3 76.8 - - - +
215A CYS* 1.3 56.0 + - - +
217A ASP* 2.9 24.1 + - - +
218A LEU* 2.8 31.1 + - + +
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Residues in contact with CYS 215 (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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211A THR 3.7 11.4 - - - -
212A SER 2.9 15.0 + - - +
214A ASN* 1.3 75.8 - - - +
216A ARG* 1.3 58.4 + - - +
218A LEU* 4.2 11.9 - - - +
219A CYS* 2.8 30.0 + - - +
238A LEU* 3.7 23.3 - - - -
242A GLY* 3.6 39.0 - - - +
245A GLU* 3.7 9.5 - - + +
246A LEU* 3.7 14.1 - - + +
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Residues in contact with ARG 216 (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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212A SER 4.0 0.8 + - - -
213A ASP* 3.1 12.2 + - - +
215A CYS* 1.3 77.4 - - - +
217A ASP* 1.3 65.0 + - - +
219A CYS* 3.4 8.7 - - - +
220A GLY* 3.4 13.3 + - - -
245A GLU* 4.2 19.4 - - + +
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Residues in contact with ASP 217 (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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187A ARG* 3.4 39.5 + - - +
190A CYS* 3.8 21.0 - - + +
213A ASP 3.9 3.8 - - - +
214A ASN* 2.9 34.1 + - - +
216A ARG* 1.3 78.9 - - - +
218A LEU* 1.3 59.7 + - - +
220A GLY* 3.0 12.3 + - - -
221A ILE* 3.2 19.1 + - - +
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Residues in contact with LEU 218 (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* 5.0 0.9 - - + -
190A CYS* 4.3 12.3 - - - -
203A LEU* 4.4 8.5 - - + -
205A LEU* 4.0 23.6 - - + -
210A VAL* 4.1 17.9 - - + -
214A ASN* 2.8 25.8 + - + +
215A CYS* 3.9 6.5 - - - +
216A ARG 3.4 0.2 - - - -
217A ASP* 1.3 70.2 - - - +
219A CYS* 1.3 66.4 + - - +
221A ILE* 3.0 12.1 + - + +
222A VAL* 2.9 27.8 + - + +
231A LEU* 4.2 21.8 - - + -
233A LEU* 3.8 28.9 - - + -
246A LEU* 3.7 16.2 - - + -
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Residues in contact with CYS 219 (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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215A CYS 2.8 19.6 + - - +
216A ARG* 3.4 9.4 - - - +
217A ASP 3.2 0.2 - - - -
218A LEU* 1.3 75.5 - - - +
220A GLY* 1.3 57.7 + - - +
222A VAL* 4.5 2.9 - - - -
223A ALA* 3.1 28.7 + - - +
245A GLU 3.6 19.7 - - - +
246A LEU* 3.8 10.7 - - - +
248A PRO* 4.2 7.9 - - - -
249A GLY* 3.2 31.8 - - - -
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Residues in contact with GLY 220 (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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194A LYS* 6.1 2.0 - - - -
216A ARG 3.4 5.8 + - - -
217A ASP 3.0 8.7 + - - -
218A LEU 3.0 1.0 - - - -
219A CYS* 1.3 77.6 - - - +
221A ILE* 1.3 59.2 + - - +
223A ALA* 3.4 4.8 + - - +
224A SER* 2.6 35.4 + - - -
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Residues in contact with ILE 221 (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* 3.7 35.9 - - + +
193A LEU* 4.0 34.1 - - + -
194A LYS* 4.6 12.6 - - + +
200A LEU* 5.5 1.1 - - + -
203A LEU* 4.9 9.0 - - + -
217A ASP 3.2 16.8 - - - +
218A LEU* 3.0 13.8 + - + +
220A GLY* 1.3 76.3 - - - +
222A VAL* 1.3 57.8 + - + +
224A SER* 3.9 3.8 - - - -
225A LYS* 2.8 47.4 + - + +
228A LEU* 4.2 18.8 - - + -
231A LEU* 5.7 0.7 - - + -
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Residues in contact with VAL 222 (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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218A LEU* 2.9 19.9 + - + +
219A CYS* 3.9 5.8 - - - +
221A ILE* 1.3 80.0 - - + +
223A ALA* 1.3 62.9 + - - +
224A SER 3.4 0.3 + - - -
225A LYS 3.8 13.3 - - - +
228A LEU* 3.9 19.9 - - + +
231A LEU* 3.9 28.3 - - + -
246A LEU* 4.8 5.6 - - + +
249A GLY 3.5 25.4 - - - +
250A LEU* 3.8 23.3 - - + +
255A SER* 4.0 18.1 - - - +
257A LEU* 5.5 3.1 - - + -
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Residues in contact with ALA 223 (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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219A CYS* 3.1 20.2 + - - +
220A GLY* 3.4 5.4 + - - +
222A VAL* 1.3 77.8 - - - +
224A SER* 1.3 57.6 + - - +
225A LYS 5.4 0.2 - - - -
249A GLY* 3.9 17.0 - - - -
252A HIS* 3.5 31.4 + - + +
254A SER* 3.0 25.1 + - - -
255A SER 5.0 0.2 + - - -
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Residues in contact with SER 224 (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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194A LYS* 5.5 8.3 - - - +
220A GLY 2.6 24.4 + - - -
221A ILE* 3.5 4.2 + - - -
223A ALA* 1.3 77.5 - - - +
225A LYS* 1.3 66.1 + - - +
226A ALA* 3.0 11.4 + - - +
254A SER* 5.2 1.2 + - - -
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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