Contacts of the helix formed by residues 306 - 319 (chain D) in PDB entry 3CB4
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 306 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301D PRO* 4.1 10.1 - - + -
302D VAL* 6.0 0.2 - - - +
303D SER* 2.9 28.9 + - - +
305D ASP* 1.3 80.3 - - - +
307D TYR* 1.3 56.5 + - - +
308D GLU 3.4 1.1 - - - -
309D ALA* 3.3 10.6 + - - +
310D PHE* 2.9 29.6 + - - +
360D ASP 5.3 3.9 - - - +
361D LEU* 3.6 23.8 - - + +
362D ASP* 4.7 14.0 + - - +
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Residues in contact with TYR 307 (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 PRO* 4.2 9.5 - - + +
304D SER* 3.3 17.5 + - - +
305D ASP 3.2 1.8 - - - -
306D ASP* 1.3 76.9 - - - +
308D GLU* 1.3 72.7 + - + +
310D PHE* 3.2 5.9 + + - +
311D ARG* 2.8 55.3 + - - +
328D PRO* 4.5 8.5 - - - +
336D PHE* 3.2 56.0 - + + +
337D GLY* 3.9 5.8 + - - -
338D PHE* 3.4 37.9 - + - -
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Residues in contact with GLU 308 (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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305D ASP 4.5 11.2 - - - +
306D ASP 3.4 0.4 - - - -
307D TYR* 1.3 85.5 - - + +
309D ALA* 1.3 58.1 + - - +
311D ARG* 3.3 32.1 + - - +
312D ASP* 2.9 39.0 + - - +
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Residues in contact with ALA 309 (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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305D ASP 5.2 1.0 + - - +
306D ASP* 3.3 13.7 + - - +
308D GLU* 1.3 75.7 - - - +
310D PHE* 1.3 56.0 + - - +
312D ASP* 3.6 7.9 - - - +
313D ALA* 2.7 35.9 + - - +
359D TYR* 5.4 5.3 - - + +
361D LEU* 4.4 13.0 - - + -
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Residues in contact with PHE 310 (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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299D LEU* 3.4 49.6 - - + -
301D PRO* 3.8 24.0 - - + -
306D ASP 2.9 18.5 + - - +
307D TYR* 3.4 7.0 - + - +
309D ALA* 1.3 77.2 - - - +
311D ARG* 1.3 60.8 + - - +
313D ALA* 3.2 1.2 + - - +
314D LEU* 3.0 44.1 + - + +
338D PHE* 3.5 25.6 - + + -
355D LEU* 4.2 13.0 - - + -
361D LEU* 3.6 26.4 - - + +
363D LEU* 3.7 21.8 - - + -
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Residues in contact with ARG 311 (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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307D TYR* 2.8 41.2 + - + +
308D GLU* 3.4 33.1 + - - +
310D PHE* 1.3 73.6 - - - +
312D ASP* 1.3 67.4 + - - +
314D LEU* 3.7 4.0 + - - +
315D GLY* 3.1 22.0 + - - -
326D TYR* 4.7 7.0 + - + -
338D PHE* 3.5 33.4 - - + -
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Residues in contact with ASP 312 (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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308D GLU* 2.9 26.1 + - - +
309D ALA* 3.7 8.3 - - - +
311D ARG* 1.3 86.6 + - - +
313D ALA* 1.3 58.1 + - - +
315D GLY* 3.5 2.3 + - - +
316D LYS* 2.9 46.8 + - - +
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Residues in contact with ALA 313 (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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309D ALA 2.7 21.8 + - - +
310D PHE 3.2 5.4 + - - +
312D ASP* 1.3 71.6 - - - +
314D LEU* 1.3 59.5 + - - +
316D LYS* 3.4 2.9 + - - +
317D LEU* 3.0 35.8 + - - +
355D LEU* 4.2 9.2 - - + -
359D TYR* 3.6 45.8 - - + -
361D LEU* 4.2 4.3 - - + -
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Residues in contact with LEU 314 (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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299D LEU* 5.2 0.7 - - + -
310D PHE* 3.0 37.6 + - + +
311D ARG* 3.9 2.7 - - - +
313D ALA* 1.3 76.0 - - - +
315D GLY* 1.3 56.9 + - - +
317D LEU* 3.4 7.5 + - + +
318D SER* 2.9 30.7 + - - -
324D LEU* 4.0 18.7 - - + +
326D TYR* 3.7 25.9 - - + -
338D PHE* 3.5 48.5 - - + -
340D CYS* 4.2 18.2 - - - -
351D ILE* 5.4 2.0 - - + -
355D LEU* 4.8 13.9 - - + -
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Residues in contact with GLY 315 (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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311D ARG 3.1 15.7 + - - -
312D ASP* 3.5 4.7 + - - -
313D ALA 3.3 0.2 - - - -
314D LEU* 1.3 75.1 - - - +
316D LYS* 1.3 61.0 + - - +
318D SER* 3.2 15.8 + - - -
319D LEU* 3.5 12.1 + - - +
326D TYR* 3.4 16.6 + - - -
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Residues in contact with LYS 316 (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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312D ASP* 2.9 34.7 + - - +
313D ALA* 3.7 2.2 - - - +
315D GLY* 1.3 67.4 - - - +
317D LEU* 1.3 66.2 + - - +
319D LEU* 3.3 31.0 + - + +
320D ASN* 4.2 5.0 + - - +
359D TYR* 3.7 38.2 - - + +
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Residues in contact with LEU 317 (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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313D ALA 3.0 19.5 + - - +
314D LEU* 3.6 8.7 - - + +
316D LYS* 1.3 76.0 - - - +
318D SER* 1.3 57.2 + - - +
320D ASN* 3.0 8.9 + - - +
321D ASP* 2.8 31.8 + - + +
324D LEU* 3.8 14.4 - - + -
351D ILE* 4.5 24.2 - - + +
354D ARG* 3.3 35.7 - - + +
355D LEU* 3.5 29.2 - - + -
359D TYR* 3.3 30.5 - - + +
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Residues in contact with SER 318 (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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265D ILE* 4.3 2.3 - - - +
266D HIS* 4.2 17.5 + - - -
314D LEU 2.9 18.2 + - - -
315D GLY* 3.3 11.7 - - - -
316D LYS 3.2 0.2 - - - -
317D LEU* 1.3 76.1 - - - +
319D LEU* 1.3 59.1 + - - +
320D ASN 3.1 0.9 + - - -
321D ASP 3.5 19.9 + - - +
324D LEU* 4.2 11.5 + - - +
326D TYR* 3.9 20.8 + - - -
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Residues in contact with LEU 319 (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 PHE* 3.6 54.1 - - + +
264D ASP* 5.9 7.6 - - + -
265D ILE* 3.4 19.6 + - - +
315D GLY 3.5 7.8 + - - +
316D LYS* 3.3 24.2 + - + +
317D LEU 3.2 1.2 + - - -
318D SER* 1.3 77.8 - - - +
320D ASN* 1.3 65.9 + - - +
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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