Contacts of the helix formed by residues 248 - 266 (chain D) in PDB entry 5U07
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 248 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243D VAL* 5.8 0.4 - - - -
246D THR* 3.3 10.9 + - - +
247D GLY* 1.3 73.2 - - - +
249D ALA* 1.3 62.4 + - - +
250D GLN* 3.9 12.7 - - + +
251D THR* 2.4 48.5 + - + +
252D ALA* 3.4 3.3 + - - +
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Residues in contact with ALA 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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243D VAL* 5.5 8.1 - - + -
247D GLY 3.4 5.2 + - - +
248D ASP* 1.3 69.8 - - - +
250D GLN* 1.3 72.9 + - - +
252D ALA* 3.2 12.2 - - - +
253D ARG* 3.0 21.7 + - - +
368D PHE* 4.5 24.4 - - + -
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Residues in contact with GLN 250 (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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248D ASP* 3.9 12.1 - - + +
249D ALA* 1.3 87.0 + - - +
251D THR* 1.3 63.5 + - + +
252D ALA 3.1 1.6 - - - -
253D ARG* 2.8 32.4 + - + +
254D THR* 3.0 18.7 + - + +
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Residues in contact with THR 251 (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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165D VAL* 4.4 19.6 - - + +
246D THR* 3.7 19.6 + - - +
248D ASP* 2.4 49.7 + - + +
250D GLN* 1.3 78.4 - - + +
252D ALA* 1.3 55.1 + - - +
254D THR* 3.0 10.2 + - - -
255D ALA* 2.9 32.0 + - - +
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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
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239D LEU* 6.4 0.7 - - + -
242D LEU* 4.9 12.8 - - + -
243D VAL* 4.4 12.3 - - + -
246D THR* 4.5 9.8 + - - +
248D ASP 3.4 2.2 + - - +
249D ALA* 3.2 20.8 + - - +
250D GLN 3.1 0.6 - - - -
251D THR* 1.3 82.5 + - - +
253D ARG* 1.3 60.6 + - - +
255D ALA* 4.3 5.2 - - - -
256D VAL* 2.9 30.0 + - + +
368D PHE* 3.9 21.3 - - + -
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Residues in contact with ARG 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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249D ALA 3.0 7.7 + - - +
250D GLN* 2.8 28.0 + - + +
252D ALA* 1.3 77.3 - - - +
254D THR* 1.3 61.4 + - + +
257D ALA* 2.9 36.5 + - + +
364D VAL* 3.8 32.4 + - + +
365D ALA* 6.0 3.9 - - - +
368D PHE* 4.9 15.2 - - + +
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Residues in contact with THR 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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55D LEU* 5.6 2.4 - - - +
165D VAL* 5.9 1.4 - - - +
250D GLN* 3.0 10.4 + - + +
251D THR* 3.0 18.2 + - - -
253D ARG* 1.3 82.8 - - + +
255D ALA* 1.3 56.5 + - - +
257D ALA* 4.7 2.7 - - - -
258D GLU* 2.8 48.6 + - - +
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Residues in contact with ALA 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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51D VAL* 5.6 2.5 - - - +
55D LEU* 5.5 7.4 - - - -
165D VAL* 3.5 27.4 - - + -
169D LEU* 4.9 10.5 - - + +
242D LEU* 4.5 11.7 - - + -
251D THR 2.9 19.7 + - - +
252D ALA* 3.8 7.0 - - - +
254D THR* 1.3 78.1 + - - +
256D VAL* 1.3 59.0 + - - +
258D GLU* 5.0 0.4 - - - -
259D PHE* 2.7 32.2 + - - +
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Residues in contact with VAL 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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4D VAL* 4.4 15.5 - - + -
169D LEU* 5.3 1.3 - - + -
237D VAL* 4.7 10.8 - - + -
239D LEU* 4.4 24.2 - - + -
242D LEU* 3.7 24.9 - - + -
252D ALA* 2.9 20.6 + - + +
253D ARG 4.2 0.9 - - - +
255D ALA* 1.3 74.2 - - - +
257D ALA* 1.3 62.3 + - - +
259D PHE* 3.7 4.1 - - - +
260D LEU* 2.8 47.1 + - + +
364D VAL* 4.8 16.2 - - + -
368D PHE* 5.9 1.3 - - + -
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Residues in contact with ALA 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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253D ARG* 2.9 21.9 + - + +
254D THR* 4.4 2.5 - - - +
256D VAL* 1.3 78.4 - - - +
258D GLU* 1.3 61.1 + - - +
260D LEU* 3.1 3.5 + - - +
261D ARG* 3.0 25.6 + - - +
360D ILE* 3.8 17.9 - - + +
361D ASP* 5.3 4.9 - - - +
364D VAL* 4.3 23.0 - - + +
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Residues in contact with GLU 258 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D VAL* 3.6 6.0 - - + +
54D ARG* 2.9 50.7 - - + +
55D LEU* 3.0 45.2 + - + +
254D THR* 2.8 33.2 + - - +
255D ALA 4.6 0.4 - - - +
257D ALA* 1.3 74.2 - - - +
259D PHE* 1.3 56.2 + - - +
261D ARG* 3.3 11.2 - - - +
262D ALA* 3.0 29.9 + - + +
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Residues in contact with PHE 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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6D ILE* 5.1 3.1 - - + -
47D VAL* 3.9 9.4 - - + -
51D VAL* 4.0 14.5 - - + +
169D LEU* 3.8 26.5 - - + -
170D PHE* 3.7 27.6 - + - -
186D VAL* 4.3 7.9 - - + -
188D PHE* 3.4 35.4 - + - -
235D ALA* 5.1 2.9 - - + -
236D ASN 5.9 1.1 - - - -
237D VAL* 4.7 20.4 - - + -
255D ALA 2.7 24.4 + - - +
256D VAL* 3.7 4.5 - - - +
258D GLU* 1.3 80.0 - - - +
260D LEU* 1.3 79.2 + - + +
262D ALA* 3.4 1.0 + - - +
263D PHE* 2.8 31.4 + + + +
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Residues in contact with LEU 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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4D VAL* 4.7 5.2 - - + -
6D ILE* 3.3 37.5 - - + -
237D VAL* 5.6 0.7 - - + -
256D VAL* 2.8 36.3 + - + +
257D ALA 3.5 3.8 - - - +
259D PHE* 1.3 90.0 - - + +
261D ARG* 1.3 66.6 + - - +
263D PHE* 2.9 18.5 + - + +
264D LEU* 3.0 15.9 + - - +
286D ILE* 3.6 29.2 - - + -
360D ILE* 3.7 24.7 - - + +
363D MET* 5.6 2.9 - - + -
364D VAL* 6.0 1.3 - - + +
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Residues in contact with ARG 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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54D ARG* 3.0 55.1 - - - +
257D ALA 3.0 13.7 + - - +
258D GLU* 3.3 18.6 - - + +
260D LEU* 1.3 75.6 - - - +
262D ALA* 1.3 67.6 + - - +
264D LEU* 3.1 5.9 + - - +
265D SER* 2.9 32.0 + - - -
357D PRO* 6.0 5.9 - - + +
360D ILE* 3.4 18.7 - - + +
291H ASP* 4.7 12.9 + - - +
329H TRP* 3.7 35.7 - - + -
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Residues in contact with ALA 262 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D VAL* 4.4 6.7 - - + -
50D GLU* 4.5 9.6 - - + -
51D VAL* 3.5 33.2 - - + +
54D ARG* 6.3 1.8 - - - -
258D GLU* 3.0 20.5 + - + +
259D PHE 3.6 2.0 - - - +
261D ARG* 1.3 81.5 - - + +
263D PHE* 1.3 62.3 + - - +
265D SER* 3.4 7.6 + - - -
266D THR* 3.0 30.7 + - - +
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Residues in contact with PHE 263 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.8 26.5 - - + -
8D ALA* 4.4 10.5 - - + -
43D TRP* 2.9 64.9 - + - -
47D VAL* 4.6 3.1 - - - +
188D PHE* 3.9 11.0 - + - -
233D ARG* 3.3 18.6 + - + -
234D TYR* 4.5 12.8 - - - -
235D ALA* 3.5 36.1 - - + -
259D PHE* 2.8 20.2 + + + +
260D LEU* 2.9 19.7 + - + +
262D ALA* 1.3 75.8 - - - +
264D LEU* 1.3 78.1 + - + +
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Residues in contact with LEU 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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6D ILE* 4.6 2.2 - - + -
8D ALA* 5.0 0.9 - - + -
10D GLN* 4.5 2.8 - - - +
260D LEU* 3.0 11.3 + - + +
261D ARG* 3.1 6.7 + - - +
263D PHE* 1.3 101.0 - - + +
265D SER* 1.3 62.9 + - - +
266D THR 3.5 4.5 + - - +
279D THR 5.0 0.5 - - - +
280D LEU* 5.1 0.2 - - - -
281D PRO* 3.6 34.3 - - + +
284D VAL* 3.6 39.5 - - + -
286D ILE* 6.0 0.9 - - + -
356D TYR* 3.7 37.0 - - + -
360D ILE* 3.8 18.6 - - + -
292H ARG* 4.1 1.2 + - - -
329H TRP* 4.8 9.4 - - + -
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Residues in contact with SER 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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50D GLU* 5.2 5.5 - - - +
261D ARG* 2.9 22.8 + - - -
262D ALA* 3.4 9.5 + - - -
264D LEU* 1.3 78.6 - - - +
266D THR* 1.3 66.1 + - - +
280D LEU* 4.8 1.6 - - - -
292H ARG* 2.2 46.9 + - - +
329H TRP* 3.9 24.7 - - - -
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Residues in contact with THR 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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10D GLN* 4.6 0.3 - - - +
43D TRP* 3.3 38.1 + - + +
46D ALA* 4.0 6.7 - - + +
47D VAL* 3.6 22.9 - - + +
50D GLU* 2.9 42.3 + - - +
233D ARG* 4.5 1.6 + - - -
262D ALA 3.0 13.3 + - - +
264D LEU 3.4 4.7 - - - +
265D SER* 1.3 82.6 + - - +
267D VAL* 1.3 76.9 + - - +
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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
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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