Contacts of the helix formed by residues 245 - 256 (chain D) in PDB entry 3GZN
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 LEU 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336C ILE 5.5 2.5 - - - +
338C ASP* 3.8 28.0 - - + +
346C TYR* 4.2 16.2 - - + +
350C GLN* 5.3 4.5 - - - +
234D PHE* 6.2 1.6 - - + -
244D ARG* 1.3 87.8 - - - +
246D PRO* 1.3 77.9 - - + +
247D GLU* 3.1 20.4 - - + +
248D HIS* 2.9 41.9 + - + +
249D CYS* 3.4 7.4 + - - -
294D ILE* 3.9 4.7 - - - -
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Residues in contact with PRO 246 (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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245D LEU* 1.3 90.3 - - + +
247D GLU* 1.3 75.6 + - - +
249D CYS* 3.3 8.2 + - - +
250D ILE* 3.2 28.5 + - + +
294D ILE* 3.6 16.8 - - + -
295D ARG 3.6 9.4 - - - +
296D GLY* 3.1 30.3 - - - +
297D VAL* 3.6 20.2 - - + +
301D LEU* 4.3 7.2 - - + -
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Residues in contact with GLU 247 (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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234D PHE* 4.3 19.9 - - + -
245D LEU* 3.4 23.8 - - + +
246D PRO* 1.3 83.0 - - - +
248D HIS* 1.3 58.9 + - + +
250D ILE* 3.2 11.3 + - - +
251D GLU* 2.9 30.3 + - - +
301D LEU* 3.7 28.1 - - + +
305D VAL* 3.8 26.1 - - + +
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Residues in contact with HIS 248 (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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338C ASP* 3.6 25.9 + - - -
234D PHE* 3.4 42.8 - + + +
235D PRO* 5.9 1.0 - - - +
238D THR* 4.1 14.7 - - + +
239D ILE* 3.8 21.7 - - + +
243D PRO* 4.0 17.9 - - + -
244D ARG* 3.5 15.3 + - - -
245D LEU* 2.9 44.8 + - + +
247D GLU* 1.3 74.1 - - + +
249D CYS* 1.3 60.4 + - - +
251D GLU* 3.4 0.4 + - - -
252D TYR* 2.9 28.8 + - - +
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Residues in contact with CYS 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 PRO* 4.4 7.2 - - - -
245D LEU 3.8 7.0 - - - -
246D PRO* 3.4 11.7 - - - +
247D GLU 3.3 0.4 - - - -
248D HIS* 1.3 80.0 - - - +
250D ILE* 1.3 61.3 + - - +
252D TYR* 3.4 4.5 - - - +
253D VAL* 3.1 26.0 + - - +
285D SER* 4.1 15.2 - - - +
288D ARG* 4.1 24.2 - - + +
289D ALA* 3.8 24.0 - - + -
294D ILE* 3.7 29.8 - - - -
297D VAL* 4.5 2.5 - - + -
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Residues in contact with ILE 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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246D PRO* 3.2 22.6 + - + +
247D GLU* 3.2 10.5 + - - +
249D CYS* 1.3 75.9 - - - +
251D GLU* 1.3 57.7 + - - +
253D VAL* 3.3 5.2 + - - +
254D ARG* 2.9 25.0 + - + +
281D ILE* 3.7 22.7 - - + +
285D SER* 3.5 17.0 - - - +
297D VAL* 4.3 8.1 - - + -
301D LEU* 3.8 18.6 - - + +
302D THR* 3.8 48.0 - - + +
305D VAL* 4.2 13.7 - - + -
306D VAL* 4.4 5.2 - - + -
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Residues in contact with GLU 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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234D PHE* 3.7 26.7 - - + -
239D ILE* 3.8 21.1 - - + -
247D GLU 2.9 17.9 + - - +
250D ILE* 1.3 75.1 - - - +
252D TYR* 1.3 66.1 + - - +
254D ARG* 3.1 53.4 + - - +
255D MET* 3.2 33.7 + - + +
305D VAL* 3.6 15.1 - - - +
308D ARG* 3.1 22.8 + - - -
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Residues in contact with TYR 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 ILE* 3.4 34.2 - - - +
240D ALA* 4.0 15.7 - - + -
248D HIS 2.9 15.1 + - - +
249D CYS 3.4 8.7 - - - +
251D GLU* 1.3 74.6 - - - +
253D VAL* 1.3 66.4 + - + +
256D LEU* 3.1 39.5 + - + +
257D GLN* 3.1 48.7 + - + +
288D ARG* 3.3 47.0 + - - -
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Residues in contact with VAL 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 CYS 3.1 16.8 - - - +
250D ILE 3.3 6.0 + - - +
251D GLU 3.3 0.2 - - - -
252D TYR* 1.3 76.5 - - + +
254D ARG* 1.3 64.0 + - - +
257D GLN* 3.7 17.3 - - + +
258D TRP* 2.9 27.2 + - - +
280D TRP* 3.5 32.3 - - + -
281D ILE* 3.9 15.9 - - + +
284D LYS* 3.5 30.7 - - + +
285D SER* 3.3 17.9 - - - +
288D ARG* 5.1 0.7 - - - -
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Residues in contact with ARG 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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250D ILE* 2.9 15.9 + - + +
251D GLU* 3.1 40.4 + - - +
253D VAL* 1.3 79.6 - - - +
255D MET* 1.3 93.1 + - - +
258D TRP* 3.5 17.4 - - - +
259D PRO* 4.2 1.0 - - - +
270D LEU* 4.2 29.4 - - + +
281D ILE* 5.1 4.5 - - - -
305D VAL* 4.8 1.3 - - - -
306D VAL* 4.4 37.6 + - + +
308D ARG* 4.6 8.5 - - - +
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Residues in contact with MET 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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236D MET* 5.6 8.1 - - - +
239D ILE* 5.2 11.7 - - + -
251D GLU* 3.2 29.8 + - - +
252D TYR 4.9 0.2 - - - +
254D ARG* 1.3 107.3 - - - +
256D LEU* 1.3 71.4 + - + +
259D PRO* 3.2 22.3 - - - +
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Residues in contact with LEU 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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236D MET* 3.8 26.2 - - + -
239D ILE* 3.7 22.4 - - + -
240D ALA* 3.6 31.2 - - + -
252D TYR* 3.1 22.1 + - + +
255D MET* 1.3 87.6 - - + +
257D GLN* 1.3 65.4 + - - +
258D TRP 3.3 1.1 - - - -
259D PRO* 3.2 10.3 - - - +
260D LYS* 3.2 17.4 + - - +
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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
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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