Contacts of the helix formed by residues 381 - 390 (chain A) in PDB entry 2XGZ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ARG* 5.9 0.9 + - - -
379A GLU 3.6 15.7 - - - +
380A ASP* 1.3 73.1 + - - +
382A PHE* 1.3 66.3 + - - +
383A ILE 3.3 2.9 - - - -
384A ALA* 3.1 19.2 + - - +
385A ASP* 3.8 6.3 + - - +
407A ALA* 3.3 35.0 - - + +
408A LYS* 4.4 7.4 - - - -
411A GLN* 4.1 27.6 + - + +
414A ARG* 5.4 2.5 - - - +
379B GLU* 6.2 0.4 - - + -
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 5.2 0.9 - - - -
115A LEU* 3.7 47.8 - - + -
118A SER* 3.2 26.9 - - - -
119A ARG* 4.6 9.2 - - + -
129A LEU* 3.7 28.3 - - + -
133A LEU* 3.8 14.6 - - + -
346A VAL* 4.9 3.8 - - + -
352A LEU* 3.8 20.0 - - + -
380A ASP* 2.8 21.8 + - - +
381A THR* 1.3 77.0 - - - +
383A ILE* 1.3 65.2 + - + +
385A ASP* 3.0 8.7 + - - +
386A LEU* 3.0 44.8 + - + -
408A LYS* 5.5 0.2 - - - +
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Residues in contact with ILE 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A LEU 5.8 0.4 - - - +
346A VAL* 5.1 13.0 - - + +
371A VAL* 3.8 17.2 - - + +
372A SER 3.8 11.2 - - - +
373A HIS* 3.5 32.8 - - + +
377A GLU* 4.7 3.1 - - - +
382A PHE* 1.3 81.1 - - + +
384A ALA* 1.3 57.8 + - - +
386A LEU* 3.6 15.2 - - + +
387A VAL* 2.9 31.0 + - - +
395A ILE* 3.8 14.6 - - + +
397A THR* 3.6 21.3 - - - +
408A LYS* 3.6 21.5 - - + +
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A THR 3.1 12.3 + - - +
383A ILE* 1.3 78.6 - - - +
385A ASP* 1.3 63.9 + - - +
387A VAL* 3.3 18.5 - - - +
388A VAL* 3.5 7.3 + - - +
395A ILE* 4.5 3.1 - - - -
408A LYS* 3.5 30.3 - - + +
411A GLN* 3.7 18.2 - - + -
412A LEU* 3.4 24.2 - - + +
415A ILE* 4.1 1.8 - - - -
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Residues in contact with ASP 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO* 5.2 0.3 - - - +
129A LEU* 3.4 37.7 + - + +
130A TYR* 3.1 47.9 + - - +
133A LEU* 3.7 2.5 - - - +
381A THR* 3.8 8.0 + - - +
382A PHE 3.0 8.2 + - - +
384A ALA* 1.3 75.8 - - - +
386A LEU* 1.3 60.0 + - - +
388A VAL 3.5 0.3 + - - -
389A GLY* 2.8 26.3 + - - -
411A GLN* 3.0 31.7 + - - +
415A ILE* 3.8 4.8 - - - +
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 3.6 18.3 - - + +
344A LEU* 3.8 18.8 - - + -
346A VAL* 3.8 28.5 - - + -
352A LEU* 3.9 23.3 - - + -
355A SER* 5.6 1.1 - - - -
356A ILE* 4.9 4.7 - - + -
371A VAL* 4.1 12.3 - - + -
382A PHE* 3.0 23.5 + - + +
383A ILE* 3.7 11.9 - - + +
384A ALA 3.3 0.4 - - - -
385A ASP* 1.3 77.2 - - - +
387A VAL* 1.3 58.2 + - - +
389A GLY* 3.3 0.7 + - - -
390A LEU* 2.8 53.7 + - + +
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A VAL 4.6 1.6 - - - +
147A PRO* 3.7 34.3 - - + -
371A VAL* 3.9 21.7 - - + +
383A ILE 2.9 16.6 + - - +
384A ALA 3.3 13.5 - - - +
386A LEU* 1.3 77.4 - - - +
388A VAL* 1.3 60.5 + - - +
390A LEU 3.6 0.5 + - - -
391A ARG* 3.0 21.3 + - - -
392A THR* 3.3 38.1 + - - +
393A GLY 4.7 1.0 + - - +
394A GLN 3.3 16.2 - - - +
395A ILE* 3.9 11.2 - - + -
412A LEU* 3.9 6.3 - - + -
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TYR* 4.0 20.2 - - + -
139A SER* 4.9 0.5 + - - -
144A TYR* 4.0 21.0 - - + -
145A VAL 4.0 19.2 + - - +
146A LEU* 4.0 11.9 - - + -
147A PRO* 4.3 2.2 - - + -
384A ALA 3.5 13.4 + - - +
385A ASP 3.9 5.4 - - - +
386A LEU 3.3 0.2 - - - -
387A VAL* 1.3 73.2 - - - +
389A GLY* 1.3 66.3 + - - +
391A ARG* 2.9 16.3 + - - +
412A LEU* 3.8 18.6 - - + -
415A ILE* 3.9 28.9 - - + -
419A LEU* 4.1 6.7 - - + -
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Residues in contact with GLY 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TYR 3.5 22.1 + - - -
133A LEU* 4.0 6.7 - - - -
134A ALA* 3.2 17.4 - - - -
137A SER* 3.2 4.8 + - - -
139A SER* 2.7 28.8 + - - -
385A ASP 2.8 19.6 + - - -
386A LEU 3.3 1.3 + - - -
388A VAL* 1.3 75.1 - - - +
390A LEU* 1.3 53.5 + - - +
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU 5.3 1.1 - - - +
137A SER* 3.6 28.5 - - - -
139A SER* 4.4 4.6 - - - -
344A LEU* 3.7 28.5 - - + -
355A SER 5.5 0.9 - - - +
356A ILE* 4.3 17.3 - - + +
359A ALA* 4.2 17.5 - - + -
360A GLN* 6.2 0.2 - - + -
363A PHE* 3.6 20.8 - - + -
371A VAL* 4.1 9.2 - - + -
386A LEU* 2.8 46.0 + - + +
389A GLY* 1.3 70.1 - - - +
391A ARG* 1.3 70.5 + - - +
392A THR* 3.2 15.2 + - + -
434A ASP* 4.6 1.4 - - - +
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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