Contacts of the helix formed by residues 383 - 395 (chain A) in PDB entry 1XAP
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 LYS 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A LEU* 3.8 28.2 - - + +
301A LEU* 3.4 34.3 - - + -
379A SER* 3.6 26.9 + - - +
380A ILE* 3.0 11.4 + - + +
382A ALA* 1.3 77.1 - - + +
384A GLY* 1.3 62.2 + - - +
385A ALA 3.3 0.6 + - - -
386A GLU* 3.7 7.1 + - - +
387A ARG* 3.4 19.6 + - - +
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Residues in contact with GLY 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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1A TTB 4.0 22.9 - - - -
259A LEU* 4.1 8.7 - - - -
298A LEU* 4.8 0.4 - - - -
380A ILE 3.7 2.0 + - - -
381A SER 2.9 15.1 + - - -
383A LYS* 1.3 77.9 - - - +
385A ALA* 1.3 61.2 + - - +
387A ARG* 3.6 0.6 - - - +
388A VAL* 2.8 32.2 + - - +
407A LEU* 3.5 6.5 - - - -
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Residues in contact with ALA 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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381A SER 4.3 1.4 + - - -
382A ALA 3.6 11.9 + - - +
383A LYS 3.3 0.6 - - - -
384A GLY* 1.3 77.2 - - - +
386A GLU* 1.3 61.4 + - - +
388A VAL* 3.7 2.3 + - - +
389A ILE* 3.2 25.2 + - - +
407A LEU* 3.5 16.7 - - + +
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Residues in contact with GLU 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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382A ALA 4.9 0.2 + - - -
383A LYS* 3.7 8.0 + - - +
384A GLY 3.3 0.2 - - - -
385A ALA* 1.3 77.3 - - - +
387A ARG* 1.3 66.1 + - - +
389A ILE* 3.1 9.8 + - + +
390A THR* 2.9 34.2 + - - +
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Residues in contact with ARG 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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1A TTB 3.7 28.5 - - + -
212A ARG 4.4 10.7 + - - -
213A LEU* 5.2 0.2 - - - +
294A GLY* 2.8 33.0 + - - +
295A PHE 4.0 7.6 + - - -
296A GLY* 3.9 10.1 - - - -
297A PRO* 3.7 27.7 - - - +
298A LEU* 4.0 13.0 - - + -
383A LYS 3.4 13.3 + - - +
384A GLY 3.2 7.7 + - - +
386A GLU* 1.3 79.6 - - - +
388A VAL* 1.3 56.9 + - - +
390A THR* 3.2 30.7 + - - +
391A LEU* 2.9 49.8 + - + +
394A GLU* 4.0 9.5 + - - -
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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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1A TTB 3.3 31.0 - - + -
384A GLY 2.8 20.7 + - - +
385A ALA 4.1 2.9 - - - +
387A ARG* 1.3 72.7 - - - +
389A ILE* 1.3 60.7 + - + +
391A LEU* 3.2 8.7 + - - +
392A LYS* 2.8 42.6 + - - +
399A MET* 3.8 31.6 - - + -
403A ILE* 4.7 5.2 - - + +
404A GLN* 6.0 1.3 - - - -
407A LEU* 3.3 24.0 - - + -
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Residues in contact with ILE 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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385A ALA 3.2 17.5 - - - +
386A GLU* 3.1 11.4 + - + +
388A VAL* 1.3 77.8 - - + +
390A THR* 1.3 64.7 + - - +
392A LYS* 3.3 17.8 + - + +
393A MET* 3.1 22.8 + - + +
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Residues in contact with THR 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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212A ARG* 5.5 0.4 - - - +
386A GLU* 2.9 25.8 + - - +
387A ARG* 3.5 31.5 + - - +
389A ILE* 1.3 78.5 - - - +
391A LEU* 1.3 62.3 + - - +
393A MET* 3.2 18.9 + - + +
394A GLU* 3.1 42.1 + - + +
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Residues in contact with LEU 391 (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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1A TTB 3.8 23.1 - - + -
213A LEU* 4.2 13.7 - - + -
218A TRP* 3.7 29.4 - - + -
294A GLY* 4.0 18.6 - - - +
387A ARG* 2.9 57.0 + - + +
388A VAL* 3.6 4.7 - - - +
390A THR* 1.3 76.6 - - - +
392A LYS* 1.3 63.0 + - - +
394A GLU* 2.8 21.9 + - - +
395A ILE* 2.9 21.5 + - + +
399A MET* 4.0 10.3 - - + -
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Residues in contact with LYS 392 (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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388A VAL* 2.8 29.7 + - + +
389A ILE* 3.6 18.4 - - + +
390A THR 3.3 0.2 - - - -
391A LEU* 1.3 77.2 - - - +
393A MET* 1.3 61.7 + - - +
394A GLU 3.3 0.3 + - - -
395A ILE* 3.8 20.1 + - - +
399A MET* 3.3 47.2 - - + +
404A GLN* 4.4 21.2 + - - +
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Residues in contact with MET 393 (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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212A ARG* 3.7 26.5 - - - +
389A ILE* 3.1 14.1 + - + +
390A THR* 3.5 22.7 - - + +
391A LEU 3.1 0.4 - - - -
392A LYS* 1.3 77.2 - - - +
394A GLU* 1.3 64.8 + - + +
395A ILE 4.7 1.6 - - - +
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Residues in contact with GLU 394 (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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212A ARG* 3.1 47.8 + - - +
213A LEU* 3.9 24.3 - - + +
215A LEU* 5.1 2.6 - - - +
387A ARG* 4.0 10.7 + - - -
390A THR* 3.1 27.7 - - - +
391A LEU* 2.8 27.3 + - - +
393A MET* 1.3 83.1 - - + +
395A ILE* 1.3 63.0 + - - +
396A PRO* 3.8 3.5 - - - +
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Residues in contact with ILE 395 (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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213A LEU* 3.8 17.0 - - + -
215A LEU* 4.4 3.4 - - + -
218A TRP* 3.6 39.0 - - + +
391A LEU* 2.9 19.9 + - + +
392A LYS* 3.8 16.3 - - - +
393A MET 4.7 1.2 - - - +
394A GLU* 1.3 75.0 - - - +
396A PRO* 1.3 69.9 - - + +
397A GLY 3.6 13.4 - - - +
398A SER 3.8 30.7 - - - +
399A MET* 3.9 22.7 - - + +
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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