Contacts of the helix formed by residues 201 - 215 (chain D) in PDB entry 3Q91
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 THR 201 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C TYR* 4.0 2.0 - - - +
143C TRP* 3.5 13.5 - - + +
146C VAL* 4.8 11.2 - - + -
100D THR* 5.6 2.2 - - - +
101D VAL 3.2 9.5 + - - +
102D GLU* 3.9 27.1 - - + +
103D LEU 4.2 2.1 + - - -
200D LYS* 1.3 84.1 - - - +
202D LEU* 1.3 64.0 + - - +
203D GLY* 3.5 5.4 + - - -
204D VAL* 3.1 31.0 + - - +
205D ILE* 3.4 11.3 + - - +
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Residues in contact with LEU 202 (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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142C TYR* 3.5 53.2 - - + +
143C TRP 4.0 6.1 + - - -
144C SER* 6.1 0.9 - - - +
153C GLN* 5.2 2.0 - - - +
155C MET* 5.6 0.4 - - - -
202C LEU* 3.3 34.8 - - + -
203C GLY* 3.6 22.0 - - - +
206C PHE* 3.9 27.6 - - + -
201D THR* 1.3 73.1 - - - +
203D GLY* 1.3 51.7 + - - +
205D ILE* 3.0 10.5 + - + +
206D PHE* 2.6 33.6 + - - +
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Residues in contact with GLY 203 (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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202C LEU* 3.7 15.5 - - - +
103D LEU* 3.8 23.6 - - - +
142D TYR* 5.7 2.7 - - - -
155D MET* 4.3 0.7 - - - +
201D THR* 3.1 7.7 + - - -
202D LEU* 1.3 75.2 - - - +
204D VAL* 1.3 56.5 + - - +
205D ILE 3.1 0.9 - - - -
206D PHE* 4.0 6.2 - - - +
207D GLY* 2.6 31.9 + - - -
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LEU* 5.9 0.2 - - - +
57D LEU* 4.0 14.1 - - + -
101D VAL* 3.1 42.6 - - + +
102D GLU* 3.7 11.9 - - - +
103D LEU* 4.0 9.9 - - - +
192D PHE* 3.7 30.3 - - + -
193D ALA* 5.8 0.7 - - - -
200D LYS* 4.0 11.2 - - + -
201D THR* 3.1 18.9 + - - +
203D GLY* 1.3 74.2 - - - +
205D ILE* 1.3 58.9 + - - +
207D GLY* 3.1 1.6 + - - -
208D VAL* 2.8 35.6 + - + +
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Residues in contact with ILE 205 (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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140C ALA* 3.9 17.3 - - + -
141C THR 3.4 26.0 - - - +
142C TYR* 3.8 16.2 - - + -
206C PHE* 3.6 32.5 - - + -
193D ALA* 4.0 27.8 - - + +
200D LYS* 3.9 21.1 - - + -
201D THR 3.4 3.7 + - - +
202D LEU* 3.0 14.7 + - + +
204D VAL* 1.3 77.3 - - - +
206D PHE* 1.3 67.6 + - - +
207D GLY 3.1 0.3 + - - -
208D VAL* 3.2 3.1 + - - +
209D SER* 3.1 22.7 + - - -
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Residues in contact with PHE 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C LEU* 3.6 31.9 - - + -
205C ILE* 3.7 24.5 - - + -
206C PHE* 3.7 34.3 - + + -
209C SER* 4.1 14.1 - - - -
139D VAL* 4.0 10.1 - - + -
140D ALA* 4.4 8.1 - - + -
142D TYR* 5.3 0.2 - + - -
155D MET* 3.6 31.6 - - + -
202D LEU 2.6 18.7 + - - +
203D GLY* 4.0 2.9 - - - +
205D ILE* 1.3 73.6 - - - +
207D GLY* 1.3 56.3 + - - +
209D SER* 5.3 0.2 - - - -
210D TRP* 3.0 55.2 + + + +
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Residues in contact with GLY 207 (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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46D LEU* 3.7 18.8 - - - +
155D MET* 3.9 19.7 - - - -
203D GLY 2.6 24.4 + - - -
204D VAL* 3.3 2.5 - - - -
205D ILE 3.1 0.2 - - - -
206D PHE* 1.3 74.6 - - - +
208D VAL* 1.3 56.1 + - - +
210D TRP* 3.9 1.7 - - - +
211D PHE* 3.0 29.8 + - - +
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Residues in contact with VAL 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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46D LEU* 6.0 1.3 - - + -
55D LEU* 4.2 22.2 - - + -
57D LEU* 5.4 2.0 - - + -
184D LEU* 4.3 13.9 - - + -
189D ALA* 3.9 26.0 - - + +
190D GLN* 4.4 4.9 - - - +
192D PHE* 5.0 0.4 - - + -
193D ALA* 4.4 14.1 - - + -
204D VAL* 2.8 36.9 + - + +
205D ILE 4.1 2.0 - - - +
207D GLY* 1.3 70.7 - - - +
209D SER* 1.3 67.6 + - - +
211D PHE* 3.5 0.7 + - - +
212D LEU* 3.0 44.6 + - + +
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Residues in contact with SER 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C PHE* 4.0 21.9 - - - -
209C SER* 5.4 3.9 + - - -
210C TRP* 4.6 14.1 + - - -
213C SER* 4.6 10.9 + - - -
214C GLN* 5.2 3.5 + - - +
190D GLN* 5.0 10.2 + - - +
205D ILE 3.1 16.6 + - - -
206D PHE* 3.9 3.6 - - - -
208D VAL* 1.3 77.2 - - - +
210D TRP* 1.3 62.2 + - - +
212D LEU* 3.1 5.9 + - - +
213D SER* 2.9 25.0 + - - -
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Residues in contact with TRP 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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209C SER* 4.4 10.8 - - - -
46D LEU* 4.6 5.8 - - + -
137D ARG* 3.7 27.8 - - - -
139D VAL* 3.5 39.0 + - + +
155D MET* 6.0 1.1 - - + -
157D TYR* 3.9 38.8 - + + -
206D PHE* 3.0 41.2 + + + +
207D GLY* 3.9 4.7 - - - +
209D SER* 1.3 73.9 - - - +
211D PHE* 1.3 76.2 + + + +
213D SER* 4.1 5.2 - - - -
214D GLN* 2.9 47.6 + - + +
215D VAL* 3.3 29.6 - - + -
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Residues in contact with PHE 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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46D LEU* 4.3 6.3 - - + -
48D PHE* 3.6 35.7 - + + -
55D LEU* 4.1 17.9 - - + -
157D TYR* 3.6 21.8 - + - -
186D LEU* 3.4 36.6 - - + -
207D GLY 3.0 18.6 + - - +
208D VAL 3.8 3.8 - - - +
210D TRP* 1.3 86.2 - + + +
212D LEU* 1.3 69.3 + - + +
215D VAL* 2.7 64.4 + - + -
216D ALA* 3.0 16.7 + - + -
219D LEU* 4.1 5.6 - - + -
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Residues in contact with LEU 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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186D LEU* 4.8 19.5 - - + +
189D ALA* 4.8 4.7 - - + -
190D GLN* 3.8 30.7 - - + +
208D VAL* 3.0 36.5 + - + +
209D SER* 3.8 3.4 - - - +
211D PHE* 1.3 90.3 - - + +
213D SER* 1.3 59.0 + - - +
216D ALA* 3.4 31.5 - - + +
217D PRO* 3.4 5.4 - - - +
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Residues in contact with SER 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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209C SER* 4.6 6.1 + - - -
213C SER* 3.8 31.0 - - - -
214C GLN* 5.5 0.9 - - - -
209D SER 2.9 14.3 + - - -
210D TRP* 3.6 6.6 + - - -
212D LEU* 1.3 77.5 - - - +
214D GLN* 1.3 90.3 + - - +
217D PRO* 3.2 23.2 - - - +
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Residues in contact with GLN 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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190C GLN* 5.4 9.7 + - - +
209C SER* 5.4 2.2 - - - +
137D ARG* 5.2 6.4 + - - +
210D TRP* 2.9 52.2 + - + +
213D SER* 1.3 101.6 + - - +
215D VAL* 1.3 58.5 + - + +
217D PRO* 4.1 1.8 - - - +
218D ASN* 3.2 23.0 + - - -
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Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D PHE* 5.1 1.1 - - + -
137D ARG* 4.6 7.6 - - - +
157D TYR* 3.5 22.0 - - + +
210D TRP* 3.3 39.7 - - + -
211D PHE* 2.7 46.3 + - + +
214D GLN* 1.3 74.9 - - - +
216D ALA* 1.3 63.6 + - - +
217D PRO* 3.4 1.9 - - - -
218D ASN* 3.5 6.3 + - - +
219D LEU* 3.2 25.1 + - + +
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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