Contacts of the helix formed by residues 341 - 352 (chain A) in PDB entry 2X1L
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 ASN 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A ASN* 4.2 5.4 - - - -
298A ARG* 3.6 40.9 + - + +
309A VAL* 5.0 0.9 - - - -
340A TYR* 1.3 81.1 - - - +
342A GLU* 1.3 66.0 + - - +
343A ASP* 3.4 11.6 + - - +
344A ALA* 2.9 33.3 + - - +
345A ILE* 3.4 17.1 + - - +
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Residues in contact with GLU 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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303A SER* 2.7 29.0 + - - -
305A SER* 2.9 21.3 + - - -
306A ILE* 3.4 32.2 - - + +
309A VAL* 4.7 9.3 - - + +
319A PHE* 4.4 5.4 - - + -
341A ASN* 1.3 76.2 - - - +
343A ASP* 1.3 66.8 + - - +
345A ILE* 3.2 15.8 + - - +
346A ILE* 3.2 42.9 + - + +
512A TYR* 4.8 2.4 + - - -
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Residues in contact with ASP 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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341A ASN* 3.3 12.8 + - - +
342A GLU* 1.3 80.1 - - - +
344A ALA* 1.3 59.3 + - - +
346A ILE* 3.8 19.2 - - - +
347A GLY* 3.0 25.1 + - - -
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Residues in contact with ALA 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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298A ARG* 4.4 9.0 - - - +
327A PHE* 3.5 18.1 - - + -
331A GLU* 4.2 15.2 - - - +
340A TYR* 4.9 1.1 - - - -
341A ASN* 2.9 30.5 + - - +
342A GLU 3.2 0.2 - - - -
343A ASP* 1.3 73.2 - - - +
345A ILE* 1.3 64.1 + - - +
347A GLY* 3.6 1.3 + - - -
348A ARG* 3.2 23.7 + - - +
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Residues in contact with ILE 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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309A VAL* 5.2 0.4 - - + -
315A LEU* 3.9 30.5 - - + -
319A PHE* 3.8 35.7 - - + -
323A GLN 5.5 1.1 - - - +
324A VAL* 5.7 4.5 - - + -
327A PHE* 3.7 37.5 - - + -
340A TYR* 4.1 16.4 - - + -
341A ASN 3.5 15.3 - - - +
342A GLU* 3.2 11.1 + - - +
344A ALA* 1.3 74.3 - - - +
346A ILE* 1.3 54.4 + - - +
348A ARG* 3.1 3.5 + - - +
349A VAL* 2.8 46.7 + - + +
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Residues in contact with ILE 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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319A PHE* 3.7 20.0 - - + -
342A GLU* 3.2 36.7 + - + +
343A ASP* 3.8 22.4 - - - +
344A ALA 3.5 0.2 - - - -
345A ILE* 1.3 74.0 - - - +
347A GLY* 1.3 58.0 + - - +
349A VAL* 3.8 5.3 - - - -
350A ASN* 2.9 52.7 + - - +
512A TYR* 3.9 24.9 - - + +
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Residues in contact with GLY 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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343A ASP 3.0 17.8 + - - -
344A ALA* 4.0 2.5 - - - -
346A ILE* 1.3 77.4 - - - +
348A ARG* 1.3 56.4 + - - +
350A ASN* 4.2 2.7 - - - -
351A ALA* 3.3 30.5 + - - +
352A ASP* 4.6 0.5 - - - +
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Residues in contact with ARG 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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326A TYR* 3.6 23.3 - - + -
327A PHE* 3.7 21.5 - - + -
330A ARG* 3.6 42.7 - - + +
331A GLU* 3.0 31.1 + - - +
344A ALA 3.2 16.0 + - - +
345A ILE 3.1 5.6 + - - +
347A GLY* 1.3 75.4 - - - +
349A VAL* 1.3 65.5 + - + +
352A ASP* 3.1 61.8 + - - +
353A LEU* 3.6 4.8 + - - +
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Residues in contact with VAL 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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319A PHE* 4.5 10.8 - - + +
323A GLN* 3.8 44.6 - - + +
327A PHE* 5.8 0.7 - - + -
345A ILE* 2.8 33.2 + - + +
346A ILE* 3.8 6.1 - - - +
348A ARG* 1.3 78.4 - - + +
350A ASN* 1.3 68.2 + - - +
353A LEU* 3.4 12.0 + - + +
354A ALA* 2.9 27.2 + - - +
510A PRO 4.2 15.5 - - - +
512A TYR* 4.5 9.2 - - + -
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Residues in contact with ASN 350 (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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346A ILE* 2.9 34.1 + - - +
347A GLY* 4.7 2.0 - - - +
349A VAL* 1.3 80.1 - - - +
351A ALA* 1.3 59.1 + - - +
354A ALA* 3.5 8.0 - - - +
355A ASN* 3.3 25.3 + - - +
511A ARG* 3.4 41.4 + - + +
512A TYR* 2.9 46.5 + - - +
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Residues in contact with ALA 351 (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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347A GLY 3.3 18.2 + - - +
350A ASN* 1.3 78.9 - - - +
352A ASP* 1.3 69.0 + - - +
355A ASN* 3.5 8.2 + - - +
356A GLU* 2.9 32.9 + - - +
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Residues in contact with ASP 352 (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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326A TYR* 2.7 33.8 + - + +
330A ARG* 4.2 3.8 + - - -
347A GLY 4.6 0.3 - - - +
348A ARG* 3.1 45.7 + - - +
351A ALA* 1.3 85.6 - - - +
353A LEU* 1.3 59.9 + - - +
356A GLU* 3.2 2.3 - - - +
357A LEU 3.2 17.0 + - - -
417A TRP* 2.8 36.6 + - - +
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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