Contacts of the helix formed by residues 248 - 267 (chain D) in PDB entry 4WLU
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 248 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C GLN* 4.2 5.7 + - - -
67C ASP* 2.8 11.9 + - - -
35D GLY* 3.4 39.7 - - - -
36D ILE* 3.9 11.2 - - - +
241D LYS* 2.9 18.3 + - - +
245D GLY* 6.1 0.7 - - - -
246D SER 3.3 14.8 - - - +
247D ALA* 1.3 73.1 - - - +
249D LEU* 1.3 68.3 + - - +
250D SER 3.5 0.9 - - - -
251D MET* 3.5 2.9 + - - +
252D ALA* 2.9 29.1 + - - +
402D NAD 3.7 13.5 - - - +
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Residues in contact with LEU 249 (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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38C GLN* 3.7 55.4 - - + +
39C PRO* 4.3 1.1 - - + -
42C LEU* 3.6 22.4 - - + +
64C VAL* 4.0 9.0 - - + +
67C ASP* 3.0 9.2 + - - +
68C LEU* 3.6 39.3 - - + -
71C ILE* 4.4 0.2 - - - -
39D PRO* 4.1 25.4 - - + -
248D THR* 1.3 85.0 + - - +
250D SER* 1.3 60.9 + - - +
252D ALA* 3.3 5.4 + - - +
253D TYR 3.0 22.0 + - - -
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Residues in contact with SER 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASP* 2.7 40.8 + - - -
70C HIS* 4.5 6.5 + - - +
71C ILE* 3.8 23.5 - - - +
172D LEU* 3.6 21.1 - - - +
176D ARG* 5.0 0.5 + - - -
247D ALA* 3.6 14.2 - - - +
249D LEU* 1.3 75.6 - - - +
251D MET* 1.3 60.2 + - - +
253D TYR* 3.4 4.7 + - - +
254D ALA* 2.9 28.1 + - - +
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Residues in contact with MET 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ILE* 3.6 17.4 - - + +
140D ILE* 3.7 29.6 - - + -
169D VAL* 3.8 21.3 - - + +
172D LEU* 3.9 24.2 - - + +
247D ALA 3.7 19.3 - - - +
248D THR 3.5 4.8 + - - +
249D LEU 3.2 0.6 - - - -
250D SER* 1.3 79.8 + - - +
252D ALA* 1.3 55.0 + - - +
254D ALA* 4.2 3.1 - - + -
255D GLY* 2.7 35.9 + - - +
402D NAD 3.0 48.9 - - + +
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Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 4.5 0.7 - - + -
36D ILE* 4.0 5.6 - - - +
39D PRO* 3.8 16.4 - - + +
40D LEU* 3.5 38.5 - - - +
43D LEU* 3.5 5.4 - - + +
248D THR 2.9 18.3 + - - +
249D LEU 3.5 6.1 - - - +
250D SER 3.3 0.2 - - - -
251D MET* 1.3 74.5 - - - +
253D TYR* 1.3 61.0 + - - +
256D ALA* 2.9 32.4 + - - +
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Residues in contact with TYR 253 (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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42C LEU* 4.4 4.0 - - + -
46C ASN* 3.5 29.2 - - + -
71C ILE* 4.0 27.4 - - + -
72C GLU* 2.7 48.3 + - + +
73C THR* 4.9 7.0 - - + +
43D LEU* 3.7 12.0 - - + +
175D VAL* 3.8 17.7 - - + -
249D LEU 3.0 13.4 + - - +
250D SER 3.5 9.6 - - - +
251D MET 3.3 0.2 - - - -
252D ALA* 1.3 76.0 - - - +
254D ALA* 1.3 60.7 + - - +
256D ALA* 3.7 1.4 - - - +
257D ARG* 2.9 37.6 + - + +
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Residues in contact with ALA 254 (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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171D THR* 3.4 22.6 - - + +
172D LEU* 3.6 41.5 - - + +
175D VAL* 4.4 4.0 - - + -
250D SER 2.9 18.1 + - - +
251D MET* 3.8 7.0 - - + +
253D TYR* 1.3 79.1 - - - +
255D GLY* 1.3 65.2 + - - +
257D ARG* 3.6 1.6 + - - +
258D PHE* 3.1 18.2 + - - +
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Residues in contact with GLY 255 (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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40D LEU* 3.8 10.3 - - - -
97D VAL* 5.8 0.2 - - - -
140D ILE* 4.4 9.0 - - - -
169D VAL* 4.4 16.6 - - - +
251D MET* 2.7 25.3 + - - +
252D ALA 3.9 0.7 - - - -
254D ALA* 1.3 70.2 - - - +
256D ALA* 1.3 59.5 + - - +
258D PHE* 3.5 2.8 + - - +
259D VAL* 3.1 33.7 + - - +
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Residues in contact with ALA 256 (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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40D LEU* 3.5 10.8 - - + +
43D LEU* 3.7 31.6 - - + -
44D LEU* 4.7 3.4 - - + -
252D ALA 2.9 19.0 + - - +
253D TYR 3.7 2.0 - - - +
255D GLY* 1.3 74.0 - - - +
257D ARG* 1.3 55.3 + - - +
259D VAL* 3.2 5.1 + - - +
260D PHE* 2.8 56.1 + - + -
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Residues in contact with ARG 257 (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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72C GLU* 2.7 48.7 + - - -
171D THR* 3.9 15.9 - - + +
174D ILE* 3.9 19.0 - - - +
175D VAL* 4.1 7.0 - - - +
178D ASN* 4.1 6.7 - - - +
193D ASN* 4.8 9.1 - - - +
253D TYR* 2.9 25.9 + - + +
254D ALA* 3.7 4.5 - - - +
256D ALA* 1.3 74.9 - - - +
258D PHE* 1.3 57.1 + - - +
260D PHE* 3.2 12.8 + - - +
261D SER* 2.8 34.0 + - - +
273D VAL 5.0 3.6 + - - -
274D GLU* 3.0 36.3 + - - +
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Residues in contact with PHE 258 (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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138D CYS* 3.8 23.6 - - + -
167D PHE* 3.7 46.4 - + + -
168D GLY 5.7 0.2 - - - -
169D VAL* 4.3 19.3 - - + -
171D THR* 3.4 26.7 - - - +
254D ALA 3.1 9.9 + - - +
255D GLY 3.8 4.3 - - - +
256D ALA 3.3 0.2 - - - -
257D ARG* 1.3 79.2 - - - +
259D VAL* 1.3 59.8 + - + +
261D SER* 3.4 2.1 + - - -
262D LEU* 2.9 35.3 + - + +
274D GLU* 3.7 37.5 - - + -
275D CYS 4.0 0.7 - - - -
276D SER* 3.8 18.6 - - - -
294D LEU* 4.8 8.1 - - + -
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Residues in contact with VAL 259 (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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27D VAL* 4.6 8.7 - - + -
40D LEU* 5.4 0.7 - - + -
44D LEU* 3.8 26.7 - - + -
50D VAL* 6.0 0.9 - - + -
95D VAL* 4.3 16.8 - - + -
97D VAL* 3.5 31.9 - - + -
138D CYS* 4.8 7.0 - - + -
255D GLY 3.1 19.9 + - - +
256D ALA 3.2 3.8 + - - +
258D PHE* 1.3 77.0 - - + +
260D PHE* 1.3 60.3 + - + +
262D LEU* 3.3 7.1 + - - +
263D VAL* 2.8 41.2 + - + +
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Residues in contact with PHE 260 (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 LEU* 3.5 28.5 - - + -
44D LEU* 3.8 21.3 - - + -
47D SER* 3.4 30.7 - - - -
49D LEU* 4.0 18.5 - - + +
50D VAL* 4.9 2.9 - - + -
256D ALA* 2.8 38.3 + - + +
257D ARG* 3.5 9.0 - - - +
259D VAL* 1.3 72.8 - - + +
261D SER* 1.3 57.1 + - - +
263D VAL* 3.2 3.1 + - + +
264D ASP* 2.8 43.4 + - - +
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Residues in contact with SER 261 (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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257D ARG* 2.8 15.8 + - - +
258D PHE 3.6 3.1 - - - -
260D PHE* 1.3 75.1 - - - +
262D LEU* 1.3 63.3 + - - +
264D ASP* 3.7 5.4 - - - +
265D ALA* 3.1 20.3 + - - +
272D VAL* 3.4 27.3 - - - +
274D GLU* 2.6 44.7 + - - +
294D LEU* 4.1 1.6 - - - -
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Residues in contact with LEU 262 (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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95D VAL* 4.6 8.5 - - + -
136D MET* 3.6 40.8 - - + -
138D CYS* 3.6 24.2 - - - -
167D PHE* 4.0 28.3 - - + -
258D PHE* 2.9 23.3 + - + +
259D VAL* 3.5 5.6 - - - +
261D SER* 1.3 77.9 - - - +
263D VAL* 1.3 56.5 + - + +
265D ALA* 3.7 3.4 - - - +
266D MET* 3.0 35.6 + - + +
294D LEU* 4.0 23.5 - - + +
295D GLY 5.4 0.7 - - - +
298D GLY* 4.7 7.0 - - - -
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Residues in contact with VAL 263 (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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25D ALA* 3.7 33.4 - - + +
27D VAL* 4.9 2.7 - - + -
49D LEU* 3.9 23.3 - - + +
50D VAL* 5.9 1.6 - - + -
95D VAL* 4.1 16.8 - - + -
259D VAL* 2.8 38.9 + - + +
260D PHE* 3.8 5.8 - - + +
262D LEU* 1.3 70.2 - - - +
264D ASP* 1.3 66.9 + - - +
266D MET* 3.2 10.4 + - + +
267D ASN* 3.0 35.7 + - - +
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Residues in contact with ASP 264 (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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49D LEU* 3.4 28.8 - - - +
260D PHE* 2.8 27.2 + - - +
261D SER* 3.7 6.4 - - - +
263D VAL* 1.3 72.7 - - - +
265D ALA* 1.3 60.0 + - - +
267D ASN* 3.1 15.4 + - - +
268D GLY 3.3 0.3 + - - -
269D LYS* 3.0 58.1 + - + +
272D VAL* 4.5 3.4 - - + -
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Residues in contact with ALA 265 (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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261D SER 3.1 17.2 + - - +
262D LEU* 3.7 3.8 - - + +
264D ASP* 1.3 76.8 - - - +
266D MET* 1.3 57.6 + - - +
268D GLY* 3.0 15.9 + - - -
269D LYS* 3.7 14.3 - - - +
272D VAL* 4.3 5.3 - - + +
294D LEU* 3.4 42.6 - - + +
295D GLY* 3.5 5.7 - - - +
296D LYS* 3.5 16.6 + - - +
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Residues in contact with MET 266 (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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94D ASP* 3.8 33.2 - - + +
95D VAL* 4.1 13.7 - - - -
136D MET* 3.8 43.3 - - + -
262D LEU* 3.0 22.6 + - + +
263D VAL* 3.2 13.2 + - + +
265D ALA* 1.3 75.5 - - - +
267D ASN* 1.3 65.0 + - - +
268D GLY 3.2 1.0 + - - -
295D GLY 4.3 4.3 - - - +
296D LYS* 3.8 27.9 - - - +
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Residues in contact with ASN 267 (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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24D ASN* 4.4 22.2 + - - +
25D ALA* 5.7 1.6 - - - +
49D LEU* 4.1 13.9 - - - +
263D VAL* 3.0 27.6 + - - +
264D ASP* 3.1 10.5 + - - +
266D MET* 1.3 81.7 + - - +
268D GLY* 1.3 59.2 + - - +
269D LYS 3.5 0.8 + - - +
296D LYS* 5.0 0.9 - - - -
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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
------------------------------------------------------------
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