Contacts of the helix formed by residues 207 - 215 (chain D) in PDB entry 4G1U
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 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264C LEU* 5.0 2.6 - - - +
43D ILE* 5.0 0.2 - - - +
180D LEU* 4.7 9.6 - - - +
183D GLN* 5.2 4.7 - - - +
205D LEU* 3.4 7.2 - - + +
206D HIS* 1.3 78.2 - - - +
208D LEU* 1.3 63.7 + - - +
209D ASN* 2.9 34.5 + - - +
210D LEU* 3.2 37.4 + - + +
211D ALA* 3.4 19.6 + - - +
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Residues in contact with LEU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ILE* 3.6 28.7 - - + -
206D HIS 3.6 7.1 + - - +
207D ASP* 1.3 71.5 + - - +
209D ASN* 1.3 62.0 + - - +
211D ALA* 3.3 5.3 + - - +
212D ALA* 2.9 28.5 + - - +
236D LEU* 3.6 11.4 - - + +
241D LEU* 3.6 33.0 - - + -
245D TYR* 3.5 37.0 - - + +
249D LEU* 4.0 18.2 - - + -
262D ILE* 4.1 20.4 - - + -
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Residues in contact with ASN 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ILE 5.6 1.0 + - - -
263C TYR* 5.2 2.4 - - - +
264C LEU* 4.6 26.5 - - + +
207D ASP* 2.9 10.1 + - - +
208D LEU* 1.3 78.6 - - - +
210D LEU* 1.3 58.1 + - - +
212D ALA* 3.2 7.2 + - - +
213D LEU* 2.9 38.9 + - + +
261D GLN* 4.2 18.2 - - - +
262D ILE* 3.2 44.5 + - - +
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Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C LEU* 3.6 24.7 - - + -
180D LEU* 3.8 22.7 - - + -
183D GLN* 3.7 33.4 - - + +
184D GLN* 4.5 9.4 - - + -
187D LEU* 3.9 6.5 - - + -
205D LEU* 3.8 17.2 - - + +
207D ASP* 3.2 27.1 + - + +
208D LEU 3.3 0.2 - - - -
209D ASN* 1.3 76.0 - - - +
211D ALA* 1.3 57.6 + - - +
213D LEU* 4.7 0.7 - - + -
214D TYR* 2.9 59.0 + - + +
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Residues in contact with ALA 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA* 4.2 0.4 - - + -
43D ILE* 3.9 12.1 - - + -
205D LEU* 3.7 25.9 - - + +
207D ASP 3.4 9.6 + - - +
208D LEU* 3.3 7.7 + - - +
209D ASN 3.2 0.2 - - - -
210D LEU* 1.3 76.9 - - - +
212D ALA* 1.3 63.8 + - - +
215D ALA* 3.0 31.4 + - - +
218D ILE* 3.4 28.3 - - + +
232D PRO* 4.3 0.3 - - - +
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Residues in contact with ALA 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D LEU 2.9 15.6 + - - +
209D ASN* 3.4 11.4 - - - +
211D ALA* 1.3 79.1 - - - +
213D LEU* 1.3 63.1 + - + +
215D ALA 4.0 2.3 - - - +
232D PRO* 3.4 25.0 - - + +
236D LEU* 3.6 21.3 - - + +
259D LEU* 3.3 15.8 - - - +
260D PRO* 3.8 23.3 - - + +
262D ILE* 4.9 0.9 - - + -
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Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C LEU* 3.1 37.2 - - + +
265C ARG 3.2 17.7 - - - +
266C GLN* 2.9 43.8 + - + +
191D ARG* 4.3 3.3 + - - -
209D ASN* 2.9 25.5 + - + +
212D ALA* 1.3 85.7 - - + +
214D TYR* 1.3 82.0 + - + +
215D ALA 3.6 1.8 + - - +
254D HIS* 3.9 22.9 - - + +
259D LEU* 3.7 13.0 - - + +
260D PRO 4.9 3.6 - - - +
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Residues in contact with TYR 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C ARG 3.0 19.8 + - - -
266C GLN* 3.6 24.9 - - + -
39D MET* 3.3 28.2 - - + +
184D GLN* 3.1 28.7 + - + +
187D LEU* 3.9 38.8 - - + +
188D ARG* 3.4 33.8 + - + -
191D ARG* 3.5 23.4 + - + +
210D LEU* 2.9 44.4 + - + +
211D ALA* 4.1 0.9 - - - -
213D LEU* 1.3 87.2 - - + +
215D ALA* 1.3 57.4 + - - +
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Residues in contact with ALA 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D MET* 3.3 9.6 - - + +
40D VAL 4.6 0.2 - - - -
41D ALA* 3.7 19.7 - - + -
191D ARG* 3.6 7.2 + - - +
203D CYS* 5.9 0.9 - - - -
205D LEU* 5.7 0.2 - - + -
211D ALA* 3.0 20.6 + - - +
212D ALA 4.0 1.7 - - - +
213D LEU 3.6 0.9 - - - +
214D TYR* 1.3 79.8 - - - +
216D ASP* 1.3 62.3 + - - +
217D ARG 3.4 20.6 - - - +
218D ILE* 4.5 2.0 - - + -
232D PRO* 3.4 20.1 - - + +
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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