Contacts of the helix formed by residues 251 - 269 (chain D) in PDB entry 6V3O
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 251 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D TYR* 2.9 16.4 + - - -
249D HIS 3.5 0.4 - - - -
250D GLU* 1.3 88.1 - - + +
252D VAL* 1.3 63.5 + - - +
253D TRP 3.3 2.0 + - - -
254D LYS* 3.6 6.1 + - - +
255D GLY* 2.9 25.5 + - - -
681D PHE* 2.7 31.1 + - - +
682D GLY 4.0 13.7 - - - +
683D GLU 4.1 1.1 - - - -
684D GLU* 4.0 24.7 - - + +
687D CYS* 4.2 12.9 - - - -
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Residues in contact with VAL 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D PHE* 4.9 4.0 - - + -
247D TYR* 3.3 15.0 + - + +
248D ILE* 3.8 19.1 - - + +
251D THR* 1.3 77.2 - - - +
253D TRP* 1.3 61.2 + - - +
255D GLY* 2.8 14.9 + - - +
256D VAL* 3.1 19.7 + - + +
285D PHE* 3.3 42.8 - - + -
446D PHE* 4.1 9.2 - - + -
681D PHE* 3.8 31.2 - - + -
687D CYS* 4.2 7.6 - - - -
691D LEU* 5.2 1.3 - - + -
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Residues in contact with TRP 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D ILE* 2.9 20.6 + - + +
249D HIS* 4.1 11.2 - - - +
251D THR 3.3 0.4 - - - -
252D VAL* 1.3 78.8 - - - +
254D LYS* 1.3 83.1 + - + +
256D VAL* 3.7 4.2 - - - +
257D PRO* 3.3 16.3 - - - +
315D ALA 4.8 0.2 - - - -
318D LEU* 3.5 56.4 + - + +
319D TYR* 3.5 32.5 - + - -
322D GLN* 3.6 18.6 + - + +
442D GLN* 2.9 32.0 + - + +
446D PHE* 3.7 38.7 - + + -
450D LEU* 3.7 24.7 - - + -
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Residues in contact with LYS 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D HIS 5.3 5.5 + - - +
250D GLU 5.6 4.9 - - - +
251D THR* 3.6 5.8 + - - +
253D TRP* 1.3 92.4 - - + +
255D GLY* 1.3 63.8 + - - +
257D PRO* 3.3 13.2 - - - +
258D LYS* 3.4 34.8 - - - +
322D GLN* 3.5 24.5 - - - +
442D GLN* 5.4 3.4 - - - +
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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
----------------------------------------------------------
251D THR 2.9 16.6 + - - -
252D VAL* 2.8 11.4 + - - -
254D LYS* 1.3 75.9 - - - +
256D VAL* 1.3 63.1 + - - -
258D LYS* 3.2 10.2 + - - +
259D PHE* 3.0 23.0 + - - +
687D CYS* 4.5 11.0 - - - -
688D PHE* 5.1 3.6 - - - -
691D LEU* 4.1 7.0 - - - +
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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
----------------------------------------------------------
252D VAL* 3.1 10.7 + - + +
253D TRP 3.7 0.9 - - - +
255D GLY* 1.3 72.1 - - - +
257D PRO* 1.3 71.8 - - + +
259D PHE* 3.2 2.3 + - - +
260D LEU* 2.8 40.2 + - + +
283D ILE* 4.6 13.2 - - + -
285D PHE* 4.0 27.6 - - + -
441D ARG* 5.6 0.7 - - + +
442D GLN* 4.9 3.6 - - + -
445D THR* 4.2 18.2 - - + +
446D PHE* 3.3 30.3 - - + -
691D LEU* 4.1 18.1 - - + +
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Residues in contact with PRO 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D TRP 3.3 5.8 - - - +
254D LYS* 3.3 17.0 - - - +
256D VAL* 1.3 97.6 - - + +
258D LYS* 1.3 60.4 + - + +
260D LEU* 3.9 9.0 - - + +
261D ARG* 3.0 27.3 + - - +
438D ASP* 3.8 35.5 - - + +
441D ARG* 4.7 6.3 + - + -
442D GLN* 3.5 38.4 - - + +
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Residues in contact with LYS 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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212C GLU* 5.2 2.3 - - - +
254D LYS* 3.4 29.8 - - - +
255D GLY* 3.2 11.3 + - - +
257D PRO* 1.3 79.3 - - + +
259D PHE* 1.3 62.0 + - - +
261D ARG* 3.4 7.7 + - - +
262D ARG* 3.3 15.1 + - - +
684D GLU* 4.7 28.0 - - + +
688D PHE* 3.8 20.7 - - + -
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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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143D ILE* 4.6 11.9 - - + -
255D GLY 3.0 14.5 + - - +
256D VAL* 3.9 2.9 - - - +
258D LYS* 1.3 73.6 - - - +
260D LEU* 1.3 66.5 + - + +
262D ARG* 2.8 20.0 + - + +
263D VAL* 3.0 33.4 + - + -
282D LEU* 4.6 4.0 - - + -
283D ILE* 3.9 19.7 - - + -
688D PHE* 3.6 28.0 - + + -
691D LEU* 4.0 17.9 - - + -
692D GLN* 3.4 45.3 - - + -
695D THR* 3.3 33.4 - - + -
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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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256D VAL* 2.8 31.9 + - + +
257D PRO 4.0 1.3 - - - +
259D PHE* 1.3 79.0 - - + +
261D ARG* 1.3 61.3 + - - +
263D VAL* 3.3 7.9 + - + +
264D ASP* 3.3 24.8 + - - +
276D LEU* 4.2 13.6 - - + +
280D VAL 5.2 8.1 - - - +
282D LEU* 3.8 39.0 - - + +
283D ILE* 5.5 4.3 - - + +
441D ARG* 3.6 49.9 + - + +
445D THR* 4.6 12.8 - - - +
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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
----------------------------------------------------------
212C GLU* 3.6 24.2 - - + +
215C GLU* 5.4 1.5 + - - +
219C ARG* 3.3 28.7 - - - +
257D PRO 3.0 16.6 + - - +
258D LYS* 3.5 7.6 - - - +
259D PHE 3.1 0.2 - - - -
260D LEU* 1.3 76.8 - - - +
262D ARG* 1.3 61.4 + - - +
264D ASP* 3.2 12.0 + - - +
265D THR* 3.2 23.6 + - - +
275D ARG* 3.7 24.0 + - - +
433D ASP 2.7 29.7 + - - -
434D GLY* 3.3 9.5 + - - -
437D LEU* 3.9 11.2 - - - +
438D ASP* 2.8 32.1 + - - -
441D ARG* 3.9 4.2 - - - +
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Residues in contact with ARG 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C THR* 5.1 1.6 + - - -
208C ASP* 3.5 35.4 - - - +
209C ASP* 2.7 36.0 + - - +
212C GLU* 2.8 35.8 + - - +
143D ILE* 3.8 22.2 - - + -
144D GLU* 6.1 1.1 - - - -
258D LYS 3.3 7.0 + - - +
259D PHE* 2.8 14.1 + - + +
261D ARG* 1.3 74.3 - - - +
263D VAL* 1.3 63.3 + - - +
265D THR* 3.3 1.1 + - - -
266D ALA* 3.0 20.7 + - - +
688D PHE* 3.7 41.1 - - + -
692D GLN* 5.0 2.6 + - - +
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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
----------------------------------------------------------
143D ILE* 4.5 13.2 - - + -
147D LEU* 6.0 0.7 - - + -
165D LEU* 4.1 20.2 - - + -
259D PHE* 3.0 45.7 + - + +
260D LEU* 3.5 11.4 - - - +
261D ARG 3.3 0.2 - - - -
262D ARG* 1.3 76.3 - - - +
264D ASP* 1.3 61.8 + - - +
266D ALA* 3.2 8.1 + - + +
267D LEU* 2.9 37.6 + - + +
276D LEU* 4.3 17.9 - - + -
282D LEU* 4.4 10.3 - - + -
695D THR* 4.9 2.0 - - + -
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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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260D LEU 3.4 6.3 - - - +
261D ARG* 3.2 7.5 + - - +
263D VAL* 1.3 76.5 - - - +
265D THR* 1.3 62.3 + - - +
267D LEU* 3.1 10.1 + - - +
268D LYS* 3.0 25.6 + - - +
274D GLU 5.1 1.6 - - - +
275D ARG* 3.1 45.6 + - + +
276D LEU* 2.9 28.1 + - - +
441D ARG* 2.7 37.6 + - - -
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Residues in contact with THR 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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208C ASP* 3.7 21.3 - - + +
211C GLN* 3.2 42.2 - - + +
212C GLU* 2.6 37.1 + - + +
215C GLU* 5.2 3.5 + - - -
144D GLU* 4.2 2.0 - - - +
261D ARG* 3.2 5.4 + - - +
262D ARG 3.3 4.7 + - - -
264D ASP* 1.3 77.2 - - - +
266D ALA* 1.3 62.9 + - - +
268D LYS* 3.3 7.3 + - - +
269D ASN* 3.1 23.1 + - - +
275D ARG* 5.7 0.7 + - - -
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Residues in contact with ALA 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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143D ILE* 4.2 11.9 - - + -
144D GLU* 3.8 34.0 + - + +
147D LEU* 3.6 19.1 - - + -
262D ARG* 3.0 14.9 + - - +
263D VAL* 3.5 9.2 - - - +
264D ASP 3.2 0.4 - - - -
265D THR* 1.3 77.7 - - - +
267D LEU* 1.3 61.7 + - - +
269D ASN* 3.2 11.6 + - - +
270D ILE* 3.3 18.4 + - - +
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Residues in contact with LEU 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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147D LEU* 4.1 10.8 - - + -
161D VAL* 5.0 0.2 - - + -
162D PHE* 3.7 44.0 - - + +
165D LEU* 3.8 24.9 - - + -
263D VAL* 2.9 31.5 + - + +
264D ASP* 3.1 7.2 + - - +
266D ALA* 1.3 75.5 - - - +
268D LYS* 1.3 61.0 + - - +
270D ILE* 3.3 21.2 + - + +
272D ILE* 2.9 40.9 + - + +
274D GLU 4.4 5.6 - - - +
276D LEU* 4.3 16.2 - - + +
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Residues in contact with LYS 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C GLN* 4.7 7.6 - - - +
215C GLU* 5.9 4.3 - - - +
264D ASP 3.0 14.2 + - - +
265D THR* 3.6 11.9 - - - +
266D ALA 3.3 0.2 - - - -
267D LEU* 1.3 76.1 - - - +
269D ASN* 1.3 63.1 + - - +
270D ILE 3.2 0.2 - - - -
271D GLY* 3.3 15.9 + - - -
272D ILE 3.2 9.9 - - - +
273D ASN* 3.1 55.3 + - - +
274D GLU* 4.7 3.8 - - - +
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Residues in contact with ASN 269 (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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208C ASP* 4.4 3.0 + - - -
211C GLN* 3.7 27.9 + - - +
144D GLU* 2.7 37.0 + - + +
148D LYS* 3.3 25.6 + - - +
265D THR* 3.1 15.3 + - - +
266D ALA 3.2 5.8 + - - +
268D LYS* 1.3 78.6 - - - +
270D ILE* 1.3 58.9 + - - +
271D GLY 3.6 0.4 - - - -
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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