Contacts of the helix formed by residues 338 - 349 (chain A) in PDB entry 1XAI
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 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A VAL* 5.6 2.2 - - - -
336A HIS* 2.9 30.1 + - + -
337A VAL* 1.3 81.3 - - - +
339A GLN* 1.3 60.7 + - + +
340A LEU* 2.6 49.1 + - - +
341A THR* 3.3 10.9 + - - -
342A LEU 3.7 1.2 + - - -
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Residues in contact with GLN 339 (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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303A PHE* 3.6 3.9 - - + -
307A TYR* 3.2 49.7 + - + -
321A VAL* 5.7 0.6 - - - +
338A ASP* 1.3 73.8 - - + +
340A LEU* 1.3 53.1 + - - +
342A LEU* 3.3 13.7 - - - +
343A GLN* 2.6 40.2 + - + +
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Residues in contact with LEU 340 (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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273A ALA* 5.8 4.5 - - + +
274A LEU* 5.6 2.5 - - + -
338A ASP* 2.6 24.8 + - - +
339A GLN* 1.3 73.8 - - - +
341A THR* 1.3 82.7 + - + +
343A GLN* 2.6 29.3 + - - +
344A HIS* 3.0 45.2 + - + +
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Residues in contact with THR 341 (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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270A VAL* 3.3 40.6 - - + -
273A ALA* 3.4 24.2 - - + -
274A LEU* 3.2 22.9 - - + +
337A VAL* 3.4 16.9 - - - +
338A ASP* 3.3 4.8 + - - -
340A LEU* 1.3 87.9 - - - +
342A LEU* 1.3 55.2 + - - +
343A GLN 3.0 1.0 + - - -
344A HIS* 3.1 3.2 + - - +
345A ALA* 2.6 38.9 + - + +
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Residues in contact with LEU 342 (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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266A TYR* 2.9 29.0 + - + +
270A VAL* 5.0 0.4 - - + -
303A PHE* 3.1 46.5 - - + -
307A TYR* 4.7 4.3 - - + -
310A MET* 4.3 13.5 - - + -
321A VAL* 3.9 30.3 - - + -
323A MET* 3.9 15.0 - - - -
337A VAL* 3.3 40.8 - - + +
338A ASP 3.8 1.6 - - - +
339A GLN* 3.6 7.6 - - - +
340A LEU 3.1 0.6 - - - -
341A THR* 1.3 76.0 - - - +
343A GLN* 1.3 57.3 + - - +
345A ALA 4.2 0.9 - - - -
346A CYS* 3.6 12.3 - - - +
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Residues in contact with GLN 343 (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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303A PHE* 2.9 33.5 - - + +
339A GLN* 2.6 18.1 + - + +
340A LEU* 2.6 17.0 + - - +
342A LEU* 1.3 73.7 - - - +
344A HIS* 1.3 77.1 + - + +
345A ALA 3.5 0.4 - - - -
346A CYS* 4.4 1.3 - - - +
347A GLU* 3.1 46.8 + - - +
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Residues in contact with HIS 344 (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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340A LEU* 3.0 51.3 + - + +
341A THR* 3.5 3.1 - - - +
343A GLN* 1.3 95.2 + - + +
345A ALA* 1.3 59.4 + - - +
346A CYS 3.5 0.7 - - - -
347A GLU* 3.9 16.9 + - - +
348A GLN* 3.2 26.4 + - - +
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Residues in contact with ALA 345 (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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266A TYR* 3.7 21.0 - - + -
269A ILE* 3.5 26.9 - - + +
270A VAL* 3.8 17.0 - - + -
273A ALA* 5.5 1.3 - - + -
341A THR* 2.6 26.8 + - + +
344A HIS* 1.3 72.3 - - - +
346A CYS* 1.3 57.1 + - - +
347A GLU 3.2 4.9 - - - -
348A GLN 3.9 0.4 - - - -
349A LEU* 3.1 27.9 + - - +
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Residues in contact with CYS 346 (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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244A PHE* 4.0 20.9 - - + -
266A TYR* 3.7 13.8 - - + -
301A LEU* 4.4 15.6 - - - +
302A ASP 4.6 0.4 - - - -
303A PHE* 3.9 35.9 - - + -
342A LEU 3.6 19.1 + - - +
343A GLN 4.3 2.4 + - - +
345A ALA* 1.3 78.7 - - - +
347A GLU* 1.3 60.5 + - + +
349A LEU* 4.1 5.5 - - - +
350A LYS* 3.1 29.1 + - - +
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Residues in contact with GLU 347 (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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303A PHE* 6.3 1.3 - - + -
343A GLN* 3.1 43.9 + - - +
344A HIS* 3.9 15.1 + - - +
345A ALA 3.2 0.2 - - - -
346A CYS* 1.3 80.8 - - + +
348A GLN* 1.3 58.8 + - - +
349A LEU 3.1 1.8 - - - -
350A LYS* 3.1 22.3 + - - +
351A THR* 3.1 13.2 + - - -
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Residues in contact with GLN 348 (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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269A ILE* 3.4 36.2 - - + +
272A ASN* 5.2 6.6 - - - +
273A ALA* 5.7 1.6 - - - +
281A ILE* 4.4 10.1 - - - +
344A HIS 3.2 21.0 + - - +
345A ALA 3.8 0.2 + - - -
347A GLU* 1.3 75.0 - - - +
349A LEU* 1.3 57.0 + - - +
350A LYS 3.1 2.0 - - - -
351A THR* 3.0 24.8 - - + +
352A TYR* 3.0 40.6 + - - +
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Residues in contact with LEU 349 (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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244A PHE* 3.7 20.4 - - + -
262A VAL* 4.1 15.3 - - + +
265A ILE* 3.6 27.8 - - + -
266A TYR* 3.6 31.4 - - + +
269A ILE* 3.3 19.7 - - + +
285A ILE* 5.0 2.5 - - + -
298A ILE* 3.8 23.2 - - + +
301A LEU* 4.4 9.4 - - + -
345A ALA 3.1 19.3 + - - +
346A CYS* 4.3 4.9 - - - +
348A GLN* 1.3 76.0 - - - +
350A LYS* 1.3 62.0 + - - +
351A THR 3.3 0.4 - - - -
352A TYR* 3.5 19.1 + - + +
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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