Contacts of the helix formed by residues 295 - 306 (chain D) in PDB entry 3VZC
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 SER 295 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293D GLY 4.0 2.0 + - - -
294D VAL* 1.3 75.5 - - - +
296D ARG* 1.3 65.7 + - - +
297D ALA* 4.0 9.3 + - - +
298D MET* 3.1 24.3 + - - +
299D LEU* 3.0 21.5 + - - +
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Residues in contact with ARG 296 (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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200D LEU* 2.9 33.5 + - + +
201D ALA* 2.5 34.0 + - - +
202D ALA 4.3 0.4 - - - -
203D LEU* 3.5 36.9 + - + +
294D VAL 3.8 1.6 + - - -
295D SER* 1.3 72.2 - - - +
297D ALA* 1.3 58.8 + - - +
299D LEU* 3.2 8.7 + - - +
300D LEU* 2.9 30.0 + - - +
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Residues in contact with ALA 297 (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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295D SER* 3.1 9.9 - - - +
296D ARG* 1.3 78.2 - - - +
298D MET* 1.3 56.9 + - - +
300D LEU* 3.3 10.5 + - - +
301D ARG* 2.9 35.4 + - + +
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Residues in contact with MET 298 (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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294D VAL* 4.5 7.6 - - + -
295D SER* 3.1 25.5 + - - +
297D ALA* 1.3 75.5 - - - +
299D LEU* 1.3 60.7 + - - +
301D ARG* 3.5 14.7 + - - -
302D LEU* 2.9 36.8 + - + +
314D TYR* 4.0 41.1 - - + +
316D CYS* 4.2 31.0 - - + -
317D PRO* 6.3 0.2 - - + -
318D TYR* 6.0 0.9 - - + -
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Residues in contact with LEU 299 (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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173D PHE* 4.6 8.3 - - + -
200D LEU* 3.7 17.5 - - + -
203D LEU* 4.1 22.4 - - + -
258D VAL* 3.7 31.9 - - + -
259D LEU* 5.2 0.7 - - + -
290D VAL* 4.9 4.5 - - + -
294D VAL* 3.7 25.7 - - + +
295D SER 3.0 8.3 + - - +
296D ARG 3.2 9.4 + - - +
298D MET* 1.3 77.1 - - - +
300D LEU* 1.3 57.3 + - - +
302D LEU* 3.1 14.5 + - + +
303D PHE* 2.8 28.3 + - - +
1001D UUL 3.8 36.0 - - + +
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Residues in contact with LEU 300 (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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196D THR* 5.7 1.1 - - + -
197D PHE* 6.0 8.5 - - + -
200D LEU* 3.5 29.3 - - + +
296D ARG 2.9 12.5 + - - +
297D ALA* 3.6 8.5 - - - +
299D LEU* 1.3 73.2 - - - +
301D ARG* 1.3 68.1 + - + +
303D PHE* 3.1 14.2 + - + +
304D LEU* 2.9 52.0 + - + +
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Residues in contact with ARG 301 (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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297D ALA* 2.9 21.9 + - + +
298D MET* 3.6 19.1 - - - +
300D LEU* 1.3 77.9 - - + +
302D LEU* 1.3 57.5 + - - +
304D LEU* 3.9 10.7 - - - +
305D ALA* 2.9 31.9 + - - +
314D TYR* 2.7 49.2 + - + +
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Residues in contact with LEU 302 (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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290D VAL* 5.1 10.1 - - + -
294D VAL* 5.4 4.5 - - + -
298D MET* 2.9 22.7 + - + +
299D LEU* 3.1 17.5 + - + +
301D ARG* 1.3 73.9 - - - +
303D PHE* 1.3 67.0 + - - +
305D ALA* 3.4 0.4 + - - -
306D MET* 3.0 23.6 + - - +
311D HIS* 3.4 40.2 - - + +
314D TYR* 4.2 17.5 - - + -
316D CYS* 4.3 24.2 - - + -
319D LEU* 4.4 24.9 - - + -
1001D UUL 4.6 14.6 - - + -
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Residues in contact with PHE 303 (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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192D PHE* 4.6 1.6 - - + -
193D THR* 3.9 42.8 - - + -
196D THR* 3.7 24.2 - - + -
272D MET* 4.1 11.3 - - + +
299D LEU 2.8 15.4 + - - +
300D LEU* 3.1 17.2 + - + +
302D LEU* 1.3 72.7 - - - +
304D LEU* 1.3 75.0 + - + +
306D MET* 3.1 39.2 - - + +
307D GLU* 4.0 2.9 + - - +
1001D UUL 3.4 53.0 - + - +
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Residues in contact with LEU 304 (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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193D THR* 5.5 6.3 - - + -
300D LEU* 2.9 46.3 + - + +
301D ARG* 4.0 11.2 - - - +
303D PHE* 1.3 88.7 - - + +
305D ALA* 1.3 67.3 + - - +
306D MET 3.1 1.9 + - - -
307D GLU* 3.3 20.3 + - - +
308D LYS* 4.5 0.7 + - - +
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Residues in contact with ALA 305 (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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301D ARG 2.9 18.3 + - - +
302D LEU 3.9 0.2 - - - +
304D LEU* 1.3 76.2 - - - +
306D MET* 1.3 63.0 + - - +
308D LYS* 3.0 14.6 + - - +
310D ARG* 3.1 24.9 + - + +
311D HIS* 3.5 28.3 - - - +
314D TYR* 3.6 18.4 - - + +
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Residues in contact with MET 306 (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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268D LEU* 4.3 1.8 - - + -
272D MET* 3.7 29.6 - - + -
273D PHE 3.1 34.3 + - - +
274D ALA* 4.0 17.0 - - - -
302D LEU 3.0 12.0 + - - +
303D PHE* 3.1 46.2 - - + +
305D ALA* 1.3 76.4 - - - +
307D GLU* 1.3 56.2 + - - +
309D GLY 2.9 15.9 + - - -
311D HIS* 3.6 17.2 - - + +
1001D UUL 3.7 45.8 - - + +
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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