Contacts of the helix formed by residues 199 - 214 (chain A) in PDB entry 1D8D
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PRO* 3.1 39.3 + - - +
164A LYS* 4.0 14.4 - - - +
169A TRP* 4.3 0.4 + - - -
192A ILE* 4.5 7.0 - - + +
193A LEU* 4.2 0.6 - - + +
196A ASP* 3.2 33.8 + - + +
197A ALA 3.6 0.6 - - - -
198A LYS* 1.3 72.9 - - - +
200A TYR* 1.3 65.8 + - - +
201A HIS* 3.2 13.1 + - - +
202A ALA* 2.9 39.5 + - + +
203A TRP* 3.0 25.8 + - - -
291B ARG* 5.1 0.4 - - - +
1000B FII 6.0 0.4 - - - -
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Residues in contact with TYR 200 (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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198A LYS 2.9 6.7 + - - -
199A ASN* 1.3 71.1 + - - +
201A HIS* 1.3 66.0 + + - +
203A TRP* 3.3 3.1 + - - -
204A GLN* 3.0 36.9 + - - +
240B GLY* 3.4 1.2 - - - -
241B GLY 2.9 22.4 + - - -
245B MET* 3.5 29.6 - - + +
246B GLU* 2.7 38.7 + - + -
248B HIS* 4.1 12.8 - + + -
251B TYR* 3.4 30.6 - + - -
291B ARG* 3.9 28.3 - - - +
1000B FII 3.8 31.4 + - + -
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Residues in contact with HIS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A PRO 4.0 1.8 - - - -
164A LYS* 3.5 40.3 + - - -
165A ASN 4.1 3.5 + - - -
166A TYR* 3.4 52.4 - + - -
169A TRP* 3.3 33.5 - + + +
199A ASN* 3.2 4.1 + - - +
200A TYR* 1.3 78.2 - + - +
202A ALA* 1.3 58.7 + - - +
204A GLN* 3.3 13.0 + - - +
205A HIS* 2.8 31.0 + - - +
251B TYR* 5.0 2.0 - - - -
1000B FII 4.2 23.2 - - + +
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Residues in contact with ALA 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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169A TRP* 3.7 28.7 - - + -
189A ILE* 3.6 13.2 - - + +
192A ILE* 4.1 6.1 - - + -
193A LEU* 3.9 14.1 - - + -
199A ASN* 2.9 30.1 + - + +
201A HIS* 1.3 76.9 - - - +
203A TRP* 1.3 57.7 + - - +
205A HIS* 3.3 2.1 + - - +
206A ARG* 2.9 29.3 + - - +
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Residues in contact with TRP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.5 23.8 - - + +
197A ALA 2.8 25.8 + - - -
198A LYS 4.0 0.4 - - - -
199A ASN 3.0 29.2 + - - -
200A TYR* 3.3 6.7 + - - +
202A ALA* 1.3 74.3 - - - +
204A GLN* 1.3 57.8 + - - +
206A ARG* 3.3 23.6 + - - +
207A GLN* 2.9 32.6 + - - +
219A GLU* 4.2 2.5 - - - -
222A TYR* 3.9 5.8 - + - -
223A VAL* 5.8 0.7 - - + -
226A LEU* 3.6 30.5 - - + -
235A SER* 3.3 28.2 - - - -
236A VAL* 3.8 16.6 - - + -
239A GLN* 3.6 46.2 - - + +
245B MET* 3.8 17.0 - - + -
246B GLU* 5.6 0.2 - - - -
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Residues in contact with GLN 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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173A ARG* 5.7 4.8 - - - +
200A TYR* 3.0 39.4 + - - +
201A HIS* 3.6 11.4 + - - +
203A TRP* 1.3 75.6 - - - +
205A HIS* 1.3 63.1 + - - +
207A GLN* 3.5 3.6 + - - +
208A TRP* 3.1 21.7 + - - +
198B GLU* 6.3 0.6 - - - +
199B VAL 4.3 7.5 + - - -
200B ASP* 4.8 6.1 + - - +
241B GLY* 4.8 3.3 - - - -
242B VAL* 3.8 36.4 - - + +
245B MET* 3.6 23.2 - - + +
251B TYR* 4.7 5.7 + - - -
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Residues in contact with HIS 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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169A TRP* 3.7 35.0 + + + +
172A ARG* 3.9 8.3 - - + -
173A ARG* 3.9 37.2 + - - +
176A VAL* 4.9 0.2 - - + -
185A GLU* 2.7 25.6 + - - -
189A ILE* 3.5 27.1 - - + -
201A HIS 2.8 16.6 + - - +
202A ALA 3.7 2.9 - - - +
204A GLN* 1.3 75.9 - - - +
206A ARG* 1.3 58.4 + - - +
208A TRP* 3.2 26.3 + + - +
209A VAL* 2.9 36.6 + - + +
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Residues in contact with ARG 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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186A LEU* 3.0 55.0 + - + +
189A ILE* 3.6 23.9 - - + +
190A ALA* 3.5 18.6 - - - +
193A LEU* 4.2 1.3 - - - -
202A ALA 2.9 17.5 + - - +
203A TRP* 3.4 26.2 - - - +
205A HIS* 1.3 72.5 - - - +
207A GLN* 1.3 64.7 + - - +
209A VAL* 3.4 2.3 + - - +
210A ILE* 3.0 34.7 + - + +
219A GLU* 2.8 38.7 + - - -
222A TYR* 3.4 29.2 - - - +
239A GLN* 4.1 2.2 - - - +
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Residues in contact with GLN 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 TRP 2.9 19.1 + - - +
204A GLN* 3.8 5.6 - - - +
205A HIS 3.3 0.2 - - - -
206A ARG* 1.3 74.8 - - - +
208A TRP* 1.3 57.0 + - - +
210A ILE* 3.9 0.4 - - - -
211A GLN* 2.9 35.2 + - - +
238A ASN* 3.4 14.1 - - - +
239A GLN* 3.0 27.1 + - - +
242A PHE* 3.5 38.5 - - + +
242B VAL* 5.4 0.7 - - - +
243B PRO 4.2 3.5 - - - +
244B GLY* 3.0 40.6 + - - +
245B MET* 3.5 18.4 + - - +
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Residues in contact with TRP 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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173A ARG* 3.1 64.7 - - + +
176A VAL* 3.8 29.8 - - + -
177A GLU* 3.5 34.4 + - + -
204A GLN 3.1 14.1 + - - +
205A HIS* 3.2 19.0 + + - +
207A GLN* 1.3 78.1 - - - +
209A VAL* 1.3 84.6 + - + +
211A GLN* 4.8 2.7 - - - -
212A GLU* 2.8 68.1 + - + +
213A PHE* 3.9 11.2 - + - -
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Residues in contact with VAL 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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182A PRO* 4.0 9.0 - - + -
185A GLU* 3.6 35.4 - - + -
186A LEU* 4.5 7.2 - - + -
189A ILE* 4.4 1.6 - - + -
205A HIS* 2.9 39.8 + - + +
206A ARG* 3.8 5.6 - - - +
208A TRP* 1.3 95.8 - - + +
210A ILE* 1.3 63.0 + - - +
213A PHE* 3.0 34.0 + - + +
215A LEU* 3.9 20.6 - - + +
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Residues in contact with ILE 210 (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 LEU* 3.8 17.0 - - + -
206A ARG* 3.0 27.4 + - + +
207A GLN* 3.9 4.3 - - - +
209A VAL* 1.3 75.0 - - - +
211A GLN* 1.3 59.2 + - - +
214A ARG* 2.9 11.4 + - - -
215A LEU* 2.9 46.4 + - + +
216A TRP* 3.4 41.5 + - + -
219A GLU* 3.4 43.7 - - + +
239A GLN* 3.8 9.2 - - - +
242A PHE* 4.3 1.6 - - + -
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Residues in contact with GLN 211 (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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207A GLN 2.9 18.8 + - - +
208A TRP* 4.0 3.8 - - - +
210A ILE* 1.3 81.0 - - - +
212A GLU* 1.3 69.7 + - + +
214A ARG* 3.4 15.8 + - - +
216A TRP* 3.8 17.8 + - + -
242A PHE* 4.1 17.0 - - + -
246A ASN* 3.3 30.1 + - - +
243B PRO 5.5 2.6 - - - +
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Residues in contact with GLU 212 (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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208A TRP* 2.8 54.8 + - + +
211A GLN* 1.3 80.4 - - + +
213A PHE* 1.3 79.3 + - + +
214A ARG* 3.5 6.1 + - - +
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Residues in contact with PHE 213 (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 VAL* 3.7 37.7 - - + -
177A GLU* 5.4 2.5 - - - -
180A LYS* 4.3 16.6 - - + -
182A PRO* 3.5 37.2 - - + -
208A TRP* 3.9 20.0 - + - -
209A VAL* 3.0 23.1 + - - +
212A GLU* 1.3 88.5 - - + +
214A ARG* 1.3 73.2 + - - +
215A LEU* 3.4 20.6 - - + +
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Residues in contact with ARG 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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210A ILE 2.9 11.6 + - - -
211A GLN 3.4 11.3 + - - +
212A GLU 4.9 5.9 + - - +
213A PHE* 1.3 81.8 - - - +
215A LEU* 1.3 57.6 + - - +
216A TRP* 3.4 27.4 + - + +
217A ASP* 5.6 1.6 - - - +
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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