Contacts of the helix formed by residues 381 - 390 (chain D) in PDB entry 2XH2
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 381 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379C GLU* 6.3 0.4 - - + -
119D ARG* 3.9 9.8 + - - +
379D GLU 3.6 11.2 + - - +
380D ASP* 1.3 79.4 + - - +
382D PHE* 1.3 65.7 + - - +
383D ILE 3.2 2.5 - - - -
384D ALA* 3.0 20.0 + - - +
385D ASP* 3.6 6.5 + - - +
407D ALA* 3.4 36.3 - - + +
408D LYS* 4.4 5.4 - - - -
411D GLN* 4.1 28.7 + - + +
414D ARG* 5.6 2.5 - - - +
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Residues in contact with PHE 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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115D LEU* 3.5 45.8 - - + -
118D SER* 3.4 24.5 - - - -
119D ARG* 3.5 16.1 - - - +
129D LEU* 3.7 27.1 - - + -
133D LEU* 3.8 15.3 - - + -
346D VAL* 5.1 4.3 - - + -
352D LEU* 3.9 18.6 - - + -
380D ASP* 2.7 26.1 + - - +
381D THR* 1.3 71.4 - - - +
383D ILE* 1.3 66.7 + - + +
385D ASP* 3.1 7.2 + - - +
386D LEU* 2.9 48.0 + - + -
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Residues in contact with ILE 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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346D VAL* 4.5 22.2 - - + -
371D VAL* 3.8 15.8 - - + +
372D SER 3.8 11.2 - - - +
373D HIS* 3.8 28.9 - - - +
377D GLU* 4.6 3.6 - - - +
382D PHE* 1.3 81.4 - - + +
384D ALA* 1.3 58.5 + - - +
386D LEU* 3.7 10.4 - - + +
387D VAL* 2.9 30.3 + - - +
395D ILE* 3.7 10.6 - - + +
397D THR* 3.7 24.0 - - - +
408D LYS* 3.7 24.7 - - + -
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Residues in contact with ALA 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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381D THR 3.0 12.1 + - - +
383D ILE* 1.3 79.5 - - - +
385D ASP* 1.3 65.5 + - - +
387D VAL* 3.3 23.5 - - - +
388D VAL* 3.4 12.6 + - - +
395D ILE* 4.5 3.6 - - - -
408D LYS* 3.5 33.0 - - + +
411D GLN* 3.7 17.5 - - + -
412D LEU* 3.6 11.3 - - + +
415D ILE* 4.3 1.3 - - - -
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Residues in contact with ASP 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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119D ARG* 5.7 0.3 + - - -
128D PRO* 5.2 0.2 - - - +
129D LEU* 3.5 29.5 + - + +
130D TYR* 3.1 53.4 + - - +
133D LEU* 3.8 2.4 - - + +
381D THR* 3.9 7.6 + - - +
382D PHE 3.1 7.6 + - - +
384D ALA* 1.3 78.2 - - - +
386D LEU* 1.3 57.1 - - - +
388D VAL 3.4 1.0 + - - -
389D GLY* 2.9 26.2 + - - -
411D GLN* 3.0 31.6 + - - +
415D ILE* 3.7 6.4 - - - +
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Residues in contact with LEU 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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133D LEU* 3.6 17.6 - - + +
344D LEU* 4.8 3.6 - - + -
346D VAL* 3.4 32.8 - - + -
352D LEU* 4.0 23.8 - - + -
355D SER* 5.4 2.0 - - - -
356D ILE* 4.9 4.5 - - + -
371D VAL* 4.4 17.3 - - + -
382D PHE* 2.9 28.2 + - + +
383D ILE* 3.8 6.7 - - + +
385D ASP* 1.3 73.1 - - - +
387D VAL* 1.3 61.2 + - - +
389D GLY 3.3 0.5 + - - -
390D LEU* 2.8 64.1 + - + +
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Residues in contact with VAL 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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145D VAL 4.8 1.3 - - - +
147D PRO* 3.8 29.6 - - + +
371D VAL* 3.9 20.2 - - + +
383D ILE 2.9 17.1 + - - +
384D ALA 3.3 13.0 - - - +
386D LEU* 1.3 76.0 - - - +
388D VAL* 1.3 62.1 + - - +
390D LEU 3.7 0.3 + - - -
391D ARG* 3.2 15.4 + - - -
392D THR* 3.3 32.7 + - - +
393D GLY 4.8 0.3 + - - -
394D GLN 3.4 20.2 - - - +
395D ILE* 3.8 14.1 - - + -
412D LEU* 4.0 6.3 - - + -
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Residues in contact with VAL 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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130D TYR* 4.0 15.5 - - + -
139D SER* 4.9 0.3 + - - -
144D TYR* 4.0 29.7 - - + -
145D VAL 4.2 15.8 + - - +
146D LEU* 4.2 10.3 - - + -
147D PRO* 4.4 4.0 - - + -
384D ALA 3.6 4.0 - - - +
385D ASP 3.4 6.9 + - - +
386D LEU 3.2 0.4 - - - -
387D VAL* 1.3 76.7 - - + +
389D GLY* 1.3 65.6 + - - +
390D LEU 3.2 0.2 - - - -
391D ARG* 3.0 16.8 + - - +
412D LEU* 3.6 30.1 - - + -
415D ILE* 4.1 23.3 - - + -
419D LEU* 4.4 4.0 - - + -
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Residues in contact with GLY 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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130D TYR 3.5 22.6 + - - -
133D LEU* 4.2 5.6 - - - -
134D ALA* 3.4 10.6 - - - -
137D SER* 3.1 12.4 + - - -
139D SER* 2.7 27.2 + - - -
144D TYR* 5.5 0.4 - - - -
385D ASP 2.9 18.7 + - - -
386D LEU 3.7 1.6 - - - -
388D VAL* 1.3 74.7 - - - +
390D LEU* 1.3 55.8 + - - +
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Residues in contact with LEU 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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133D LEU* 5.5 0.7 - - + +
137D SER* 3.6 28.0 - - - -
139D SER* 4.4 4.4 - - - -
344D LEU* 4.4 10.1 - - + -
355D SER 5.2 2.0 - - - +
356D ILE* 4.3 17.9 - - + +
359D ALA* 4.0 29.6 - - + -
360D GLN* 5.8 1.8 - - + -
363D PHE* 3.5 21.7 - - + -
371D VAL* 4.5 4.0 - - + -
386D LEU* 2.8 47.3 + - + +
389D GLY* 1.3 74.8 - - - +
391D ARG* 1.3 71.1 + - - +
392D THR* 3.2 20.2 + - + -
434D ASP* 4.6 1.2 - - - +
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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