Contacts of the helix formed by residues 381 - 391 (chain D) in PDB entry 3DLX
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 381 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228D ARG* 3.7 20.1 - - - +
229D ASN* 3.6 14.4 - - - +
232D LEU* 4.0 20.8 - - - +
346D GLY* 4.8 1.3 - - - -
380D PHE* 1.3 79.2 - - - +
382D SER* 1.3 60.1 + - - +
383D ASP* 2.3 28.3 + - - -
384D GLU* 3.3 9.3 + - - +
385D SER* 2.8 28.3 + - - -
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Residues in contact with SER 382 (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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142D ALA* 3.9 4.5 - - - -
229D ASN* 3.0 39.0 + - - +
230D PHE* 3.3 38.7 - - - -
233D PRO* 5.1 0.7 - - - -
344D GLU 4.5 6.9 + - - -
345D ASN* 4.4 4.4 + - - -
381D SER* 1.3 71.6 - - - +
383D ASP* 1.3 62.9 + - - +
385D SER* 3.3 6.5 - - - -
386D PHE* 3.1 32.6 + - - -
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Residues in contact with ASP 383 (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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146C ARG* 4.3 7.6 + - - +
142D ALA* 3.7 30.3 - - + +
143D GLU* 4.4 10.2 - - - +
146D ARG* 3.8 28.9 - - + +
232D LEU* 4.4 6.4 - - - +
233D PRO* 3.6 21.4 - - + +
236D LYS* 5.1 3.6 + - - -
381D SER* 2.3 34.3 + - - -
382D SER* 1.3 74.7 - - - +
384D GLU* 1.3 54.4 + - - -
386D PHE* 3.5 2.4 + - - +
387D ALA* 3.0 27.5 + - - +
390D ARG* 5.2 1.2 + - - -
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Residues in contact with GLU 384 (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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146C ARG* 5.5 2.5 + - - +
236C LYS* 2.6 28.4 + - - +
262C PRO* 6.0 2.7 - - + -
265C TYR* 2.5 38.7 + - - -
380D PHE* 3.7 28.5 - - + -
381D SER* 3.3 16.5 + - - +
383D ASP* 1.3 77.9 + - - +
385D SER* 1.3 66.3 + - - +
387D ALA* 3.2 9.6 + - - +
388D MET* 3.1 24.6 + - + +
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Residues in contact with SER 385 (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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342D GLN* 3.1 21.7 + - - -
343D SER 3.6 2.1 + - - -
344D GLU* 2.7 36.4 + - - +
346D GLY* 4.3 1.6 - - - -
380D PHE* 3.6 17.9 - - - -
381D SER 2.8 15.3 + - - -
382D SER* 3.3 9.2 - - - -
384D GLU* 1.3 75.0 - - - +
386D PHE* 1.3 59.4 + - - +
388D MET* 3.0 23.4 - - - +
389D ILE* 3.3 6.3 + - - +
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Residues in contact with PHE 386 (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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138D GLN* 3.3 43.3 - - + -
139D GLY* 3.3 25.8 - - - +
142D ALA* 4.9 0.4 - - + -
344D GLU* 3.5 31.0 - - + -
382D SER* 3.1 28.1 + - - +
383D ASP* 4.3 2.5 - - - +
385D SER* 1.3 77.5 - - - +
387D ALA* 1.3 60.1 + - - +
388D MET 3.3 0.2 - - - -
389D ILE* 3.7 22.9 - - + -
390D ARG* 2.9 42.7 + - - +
425D GLY* 3.8 14.1 - - - -
428D ASP* 3.6 32.1 - - + +
429D LEU* 5.2 0.7 - - + -
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Residues in contact with ALA 387 (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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146C ARG* 4.6 8.1 - - - +
149C GLY 3.4 8.4 - - - +
150C ALA* 3.5 29.0 - - + +
236C LYS* 6.1 2.0 - - + -
265C TYR* 4.4 3.6 - - - +
383D ASP 3.0 15.3 + - - +
384D GLU* 3.2 22.6 + - - +
386D PHE* 1.3 72.9 - - - +
388D MET* 1.3 58.1 - - - +
390D ARG* 4.0 4.0 - - - +
391D GLY* 2.7 33.6 + - - -
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Residues in contact with MET 388 (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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262C PRO* 4.0 12.8 - - + -
264C ILE* 4.0 31.4 - - + -
265C TYR* 3.7 27.4 + - + +
342D GLN* 3.8 18.8 - - - +
348D LEU* 4.9 2.9 - - + -
380D PHE* 3.5 45.8 - - + -
384D GLU* 3.1 25.2 + - + +
385D SER 3.0 15.0 - - - +
387D ALA* 1.3 79.6 - - - +
389D ILE* 1.3 56.4 + - + +
392D GLY 3.4 0.3 + - - -
393D HIS* 3.0 38.9 + - + +
394D VAL* 4.1 4.1 + - + -
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Residues in contact with ILE 389 (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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342D GLN* 3.7 26.7 - - - +
344D GLU* 4.3 10.1 - - + -
385D SER 3.3 13.1 + - - +
386D PHE* 3.7 31.0 - - + +
387D ALA 3.3 0.2 - - - -
388D MET* 1.3 77.4 - - - +
390D ARG* 1.3 67.1 + - - +
392D GLY* 3.0 16.1 + - - -
394D VAL* 4.3 16.2 + - + +
428D ASP* 3.5 37.1 - - + +
429D LEU* 3.8 28.0 - - + -
432D SER* 4.0 8.8 - - - -
435D THR* 4.9 1.7 + - - -
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Residues in contact with ARG 390 (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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150C ALA* 3.0 33.4 + - - +
151C GLY* 3.5 26.2 - - - +
152C VAL* 4.0 16.8 - - - +
139D GLY* 3.1 33.7 + - - -
140D THR* 4.8 0.8 - - - +
143D GLU* 3.7 23.6 + - - +
155D PHE* 5.5 0.4 - - - -
157D THR* 3.4 24.4 + - - +
158D PRO* 3.8 19.0 - - + +
159D THR* 4.7 1.6 - - - +
383D ASP 5.2 0.8 + - - -
386D PHE* 2.9 36.1 + - - +
387D ALA* 4.0 4.2 - - - +
389D ILE* 1.3 76.0 - - - +
391D GLY* 1.3 60.5 + - - +
392D GLY* 3.3 1.4 + - - -
428D ASP* 4.3 9.5 + - - +
431D SER* 4.3 12.3 + - - +
432D SER* 4.4 8.7 + - - -
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Residues in contact with GLY 391 (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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148C GLY 5.5 0.4 - - - -
149C GLY 3.5 15.8 - - - -
150C ALA 3.6 0.6 + - - -
151C GLY* 3.5 12.3 - - - -
387D ALA 2.7 25.5 + - - -
390D ARG* 1.3 73.1 - - - +
392D GLY* 1.3 59.7 + - - +
393D HIS* 3.5 11.6 + - - -
432D SER* 4.6 0.4 - - - -
434D LYS* 4.4 13.7 - - - +
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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