Contacts of the helix formed by residues 200 - 209 (chain A) in PDB entry 1DSG
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A THR* 1.3 74.3 - - - +
201A GLU* 1.3 63.9 + - - +
202A PHE* 3.2 4.5 + - - -
203A TYR* 3.3 20.7 + - + +
204A LEU* 3.6 20.9 + - - +
251A TYR 3.0 26.2 + - - +
252A ALA* 3.6 15.8 + - - +
255A GLN* 4.0 40.0 + - + +
258A PHE* 3.6 25.5 - - + -
259A PHE* 4.6 1.4 - - - -
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Residues in contact with GLU 201 (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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176A ALA* 4.4 6.4 - - + +
192A GLY* 3.4 9.0 - - - -
193A ALA* 3.1 31.2 + - - +
194A ALA* 3.8 23.8 + - - +
199A THR* 2.9 23.4 + - + +
200A ASN* 1.3 79.5 + - - +
202A PHE* 1.3 56.3 + - - +
204A LEU* 3.3 17.2 + - + +
205A ASN* 2.9 43.2 + - - +
229A TYR* 5.2 0.3 + - - -
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Residues in contact with PHE 202 (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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172A MET 4.7 5.2 - - - -
173A GLY* 3.8 29.2 - - - +
175A GLY* 6.1 0.2 - - - -
176A ALA* 4.1 14.4 - - + +
191A TRP* 4.0 17.5 - + + -
199A THR 5.7 0.7 - - - +
200A ASN 3.2 1.2 + - - -
201A GLU* 1.3 77.4 - - - +
203A TYR* 1.3 94.3 + + + +
205A ASN* 4.6 4.3 - - - -
206A LEU* 3.0 47.5 + - + +
231A MET* 3.5 33.1 - - + +
235A ASP* 3.9 27.8 - - + -
238A LEU* 4.0 18.8 - - + -
1500A IMD 4.5 5.8 - + - -
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Residues in contact with TYR 203 (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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169A VAL* 2.8 39.0 + - + -
170A ALA* 3.5 1.0 + - - -
173A GLY* 3.2 16.5 - - - -
199A THR 5.3 0.2 - - - -
200A ASN* 3.3 20.8 + - + +
202A PHE* 1.3 96.1 - + + +
204A LEU* 1.3 65.3 + - - +
206A LEU* 3.1 8.4 - - - +
207A LEU* 3.0 26.2 + - - +
248A VAL* 3.7 34.3 - - + +
251A TYR* 3.7 21.8 - + + -
252A ALA* 3.8 11.9 - - + +
258A PHE* 3.1 47.7 - + - -
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Residues in contact with LEU 204 (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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200A ASN* 3.6 31.4 + - - +
201A GLU* 3.3 19.7 - - + +
203A TYR* 1.3 75.9 - - - +
205A ASN* 1.3 54.4 + - - +
207A LEU* 3.1 3.1 + - - -
208A ASN* 2.7 57.1 + - - +
252A ALA* 3.5 30.5 - - + +
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Residues in contact with ASN 205 (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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191A TRP 2.7 30.8 + - - +
192A GLY* 3.4 15.8 - - - -
201A GLU* 2.9 31.3 + - - +
202A PHE 4.0 2.9 - - - +
204A LEU* 1.3 75.2 - - - +
206A LEU* 1.3 58.5 + - - +
208A ASN* 4.4 2.0 - - - +
209A GLU* 2.7 48.1 + - + +
211A TRP* 3.8 8.3 - - + -
229A TYR* 3.4 24.3 - - - -
231A MET* 4.4 1.6 - - + -
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Residues in contact with LEU 206 (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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202A PHE* 3.0 42.4 + - + +
203A TYR* 3.1 7.0 - - - +
205A ASN* 1.3 78.4 - - - +
207A LEU* 1.3 60.6 + - + +
209A GLU 4.7 0.5 - - - +
211A TRP* 3.1 29.0 + - - +
231A MET* 4.2 19.9 - - + +
235A ASP 3.8 19.3 - - - +
236A TYR* 4.4 11.0 - - + -
238A LEU* 4.5 5.4 - - + -
239A ILE* 3.5 45.6 - - + +
248A VAL* 4.9 5.8 - - + -
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Residues in contact with LEU 207 (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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203A TYR 3.0 12.9 + - - +
204A LEU 3.6 0.7 - - - +
206A LEU* 1.3 78.3 - - - +
208A ASN* 1.3 75.3 + - - +
209A GLU 3.6 3.7 + - - +
239A ILE* 4.2 8.3 - - + -
245A LEU* 3.9 27.6 - - + -
248A VAL* 3.8 18.8 - - + -
249A LYS* 4.0 22.2 - - + -
252A ALA* 3.7 30.3 - - + -
253A ASN* 5.6 1.3 - - - +
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Residues in contact with ASN 208 (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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204A LEU* 2.7 38.6 + - - +
205A ASN* 4.9 1.3 - - - -
207A LEU* 1.3 91.3 + - - +
209A GLU* 1.3 70.5 + - - +
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Residues in contact with GLU 209 (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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205A ASN* 2.7 42.5 + - + +
206A LEU 4.7 0.2 - - - +
207A LEU 3.6 4.9 - - - +
208A ASN* 1.3 83.4 - - + +
210A ASP* 1.3 60.0 + - - +
211A TRP* 3.4 36.5 + - + -
225A SER* 2.8 26.2 + - - -
226A LYS* 4.5 0.9 + - - +
227A SER* 3.0 25.6 + - - -
229A TYR* 4.1 8.9 - - + -
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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