Contacts of the helix formed by residues 202 - 222 (chain D) in PDB entry 4NEF
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 TRP 202 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D ALA* 3.7 27.6 - - + +
128D GLY* 5.0 2.5 - - - -
131D VAL* 3.8 26.0 - - + -
200D ASP* 4.3 15.2 + - - +
201D HIS* 1.3 76.2 - - - +
203D VAL* 1.4 77.3 + - + +
205D TRP* 3.1 7.7 + - - -
206D ILE* 2.7 59.7 + - + +
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Residues in contact with VAL 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 5.5 1.3 - - + -
127D ALA* 3.7 22.2 - - + +
130D ALA* 3.9 16.2 - - + +
131D VAL* 3.6 29.3 - - - +
134D GLU* 4.3 4.0 - - + +
179D THR* 4.4 1.8 - - + -
200D ASP* 3.4 19.5 - - + +
201D HIS 3.2 0.2 - - - -
202D TRP* 1.4 108.8 - - + +
204D PHE* 1.3 70.8 + - + +
205D TRP 3.2 0.2 - - - -
207D GLY* 3.0 30.0 + - - -
208D PRO* 3.5 1.0 - - - +
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Residues in contact with PHE 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ASN* 3.2 47.3 - - + -
120D ALA* 3.9 9.2 - - - -
121D LEU* 4.5 3.6 - - + -
134D GLU* 4.7 2.5 - - + -
179D THR* 3.6 34.1 - - + -
182D SER* 3.8 13.8 + - - +
185D PRO* 3.6 17.5 - - - +
188D SER* 3.2 20.6 - - - +
199D ASP 3.7 10.8 - - - -
200D ASP* 3.2 28.7 - - + -
201D HIS* 3.2 24.8 + + - +
203D VAL* 1.3 82.1 - - + +
205D TRP* 1.3 59.3 + - + +
208D PRO* 3.3 22.6 - - - +
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Residues in contact with TRP 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PRO* 5.4 4.9 - - + -
90D VAL* 6.1 2.2 - - + -
94D LEU* 3.8 26.7 - - + -
185D PRO* 3.6 40.7 + - + -
188D SER* 4.9 0.2 - - - -
189D LEU* 4.0 22.2 - - + +
201D HIS* 3.1 49.9 + + - +
202D TRP* 3.1 9.7 + - - +
203D VAL 3.2 0.2 - - - -
204D PHE* 1.3 83.4 - - + +
206D ILE* 1.3 68.9 + - + +
207D GLY 3.5 0.7 - - - -
208D PRO* 3.7 1.1 - - - +
209D LEU* 3.2 51.0 + - + +
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Residues in contact with ILE 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D VAL* 3.9 13.2 - - + -
202D TRP* 2.7 47.2 + - + +
205D TRP* 1.3 73.0 - - + +
207D GLY* 1.3 59.0 + - - +
209D LEU* 4.9 6.3 - - + -
210D VAL* 2.9 52.4 + - + +
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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
----------------------------------------------------------
131D VAL* 3.5 26.9 - - - +
134D GLU* 3.7 10.8 - - - -
135D LEU* 3.5 10.6 - - - +
203D VAL 3.0 15.6 + - - -
206D ILE* 1.3 76.2 - - - +
208D PRO* 1.4 66.5 - - - +
210D VAL* 4.2 1.1 - - - +
211D GLY 3.0 19.2 + - - -
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Residues in contact with PRO 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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70D ALA* 3.9 5.8 - - + -
134D GLU* 3.6 21.7 - - - +
138D THR* 3.3 21.8 - - - +
182D SER* 4.0 7.6 - - - +
183D MET 3.9 11.9 - - - -
184D ASN 4.0 3.8 - - - +
185D PRO* 4.0 14.8 - - + -
203D VAL 3.5 7.2 - - - +
204D PHE* 3.3 28.5 - - - +
205D TRP 3.7 2.7 - - - +
207D GLY* 1.4 86.4 - - - +
209D LEU* 1.4 55.3 + - - +
211D GLY 3.4 0.2 + - - -
212D ALA* 2.9 31.9 + - - +
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Residues in contact with LEU 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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69D PRO* 4.3 3.6 - - + +
70D ALA* 3.8 20.4 - - - +
73D VAL* 3.8 35.7 - - + -
185D PRO* 4.4 7.9 - - + -
205D TRP* 3.2 45.5 + - + +
206D ILE* 4.2 7.2 - - + +
208D PRO* 1.4 77.4 - - - +
210D VAL* 1.3 57.4 + - + +
212D ALA* 3.5 1.6 + - - +
213D ILE* 3.1 35.3 + - + +
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Residues in contact with VAL 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D LEU* 3.7 24.5 - - + -
206D ILE* 2.9 42.5 + - + +
207D GLY* 4.2 2.0 - - - +
209D LEU* 1.3 70.7 - - + +
211D GLY* 1.3 59.2 - - - +
213D ILE* 3.3 17.7 - - + +
214D LEU* 2.9 39.1 + - + +
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Residues in contact with GLY 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D LEU* 3.3 33.1 - - - +
138D THR* 4.5 0.4 - - - -
139D LEU* 3.4 20.7 - - - -
207D GLY 3.0 12.1 + - - -
208D PRO 3.7 2.9 - - - -
210D VAL* 1.3 78.6 - - - +
212D ALA* 1.3 54.6 + - - +
214D LEU* 3.6 4.2 - - - +
215D GLY 3.0 22.5 + - - -
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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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70D ALA* 3.1 36.6 - - + +
74D ALA* 3.7 5.7 - - + +
138D THR* 4.2 3.3 - - + +
142D VAL* 3.6 24.5 - - + +
208D PRO 2.9 17.9 + - - +
209D LEU* 3.8 4.7 - - - +
211D GLY* 1.3 73.5 - - - +
213D ILE* 1.4 59.6 + - + +
215D GLY 3.3 1.0 + - - -
216D SER* 2.9 29.8 + - - -
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Residues in contact with ILE 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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73D VAL* 3.8 27.4 - - + -
74D ALA* 5.3 0.2 - - - +
77D VAL* 3.9 18.8 - - + +
209D LEU* 3.1 21.9 + - + +
210D VAL* 3.3 29.2 - - + +
212D ALA* 1.4 72.7 - - - +
214D LEU* 1.4 56.5 + - + +
216D SER* 3.4 6.5 + - - -
217D LEU* 2.9 47.3 + - + +
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Residues in contact with LEU 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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135D LEU* 4.2 18.8 - - + -
139D LEU* 3.7 20.6 - - + -
210D VAL* 2.9 35.6 + - + +
211D GLY* 3.6 5.8 - - - +
212D ALA 3.3 0.2 - - - -
213D ILE* 1.4 77.7 - - + +
215D GLY* 1.3 56.5 + - - +
217D LEU* 3.4 8.0 + - + +
218D LEU* 2.9 45.3 + - + +
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Residues in contact with GLY 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LEU* 3.6 8.4 - - - +
142D VAL* 3.6 22.2 - - - -
143D LEU* 3.3 25.4 - - - +
146D PHE* 5.8 0.2 - - - -
211D GLY 3.0 12.7 + - - -
212D ALA 3.8 0.2 - - - -
214D LEU* 1.3 74.9 - - - +
216D SER* 1.3 56.5 + - - +
218D LEU* 4.3 0.9 - - - -
219D TYR* 3.0 26.5 + - - +
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Residues in contact with SER 216 (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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74D ALA* 2.8 35.8 + - - -
77D VAL* 3.3 9.1 - - - +
78D GLY* 2.9 20.8 + - - -
142D VAL* 4.1 0.6 - - - +
146D PHE* 3.8 9.8 - - - -
212D ALA 2.9 17.3 + - - -
213D ILE* 3.6 4.9 - - - -
215D GLY* 1.3 73.3 - - - +
217D LEU* 1.3 59.6 + - - +
219D TYR* 4.8 0.9 - - - -
220D ASN* 2.8 38.2 + - - +
221D TYR* 4.9 0.2 - - - -
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Residues in contact with LEU 217 (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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77D VAL* 3.8 16.4 - - + -
213D ILE* 2.9 35.3 + - + +
214D LEU* 3.9 6.5 - - + +
216D SER* 1.3 72.6 - - - +
218D LEU* 1.3 60.5 + - - +
221D TYR* 2.9 64.0 + - + +
222D VAL* 3.6 3.1 + - - +
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Residues in contact with LEU 218 (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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14B PHE* 4.2 24.5 - - + -
18B LEU* 3.8 35.7 - - + -
139D LEU* 4.3 20.2 - - + -
143D LEU* 4.7 2.9 - - + -
214D LEU* 2.9 28.8 + - + +
215D GLY* 3.8 5.6 - - - +
217D LEU* 1.3 77.4 - - + +
219D TYR* 1.4 51.8 + - - +
222D VAL* 3.2 23.3 + - + +
223D LEU* 2.7 41.2 + - + +
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Residues in contact with TYR 219 (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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58B ALA 4.3 3.1 - - - -
59B LEU* 5.8 0.2 - - + -
61B HIS* 3.0 32.2 + + - -
62B ILE* 4.2 13.9 - - + -
143D LEU* 4.3 13.5 - - + -
146D PHE* 3.7 43.3 - + + -
147D ALA* 3.6 19.6 - - + -
150D ASP* 2.6 32.6 + - - -
152D ARG* 4.4 4.3 - - - -
215D GLY 3.0 19.0 + - - +
216D SER 4.1 2.9 - - - +
218D LEU* 1.4 76.1 - - - +
220D ASN* 1.3 67.6 + - - +
221D TYR 3.6 0.2 + - - -
223D LEU* 4.2 11.4 - - + +
224D PHE* 2.8 46.2 + + + +
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Residues in contact with ASN 220 (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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77D VAL 5.3 0.2 - - - +
78D GLY* 3.2 34.3 + - - +
79D CYS* 4.6 1.8 - - - +
146D PHE* 3.2 17.8 - - - -
152D ARG* 5.4 3.4 - - - +
216D SER 2.8 23.2 + - - +
219D TYR* 1.3 85.1 - - - +
221D TYR* 1.3 78.1 + - + +
224D PHE 4.2 6.2 + - - -
225D PRO* 3.3 21.5 - - - +
226D PRO* 3.7 14.7 - - + +
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Residues in contact with TYR 221 (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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11B ARG* 5.2 1.7 + - - -
77D VAL* 4.1 17.5 + - + -
80D HIS* 4.6 10.4 - - - -
216D SER 4.9 0.2 - - - -
217D LEU* 2.9 53.6 + - + +
220D ASN* 1.3 90.8 - - + +
222D VAL* 1.3 65.5 + - + +
225D PRO* 3.6 16.3 - - - +
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Residues in contact with VAL 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 3.2 33.1 + - + +
14B PHE* 3.8 33.7 - - + -
217D LEU 3.6 3.1 + - - +
218D LEU* 3.2 30.6 + - + +
221D TYR* 1.3 82.9 - - + +
223D LEU* 1.3 60.0 + - - +
224D PHE 3.9 0.2 - - - -
225D PRO* 4.5 0.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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