Contacts of the helix formed by residues 341 - 351 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297B ASN* 4.5 5.2 - - - +
298B ARG* 3.2 41.4 + - + +
309B VAL* 5.0 1.3 - - - -
340B TYR* 1.3 83.7 - - - +
342B GLU* 1.3 64.2 + - - +
343B ASP* 3.3 17.5 + - - +
344B ALA* 2.8 41.0 + - - +
345B ILE* 3.4 17.0 + - - +
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B SER* 2.7 28.6 + - - -
305B SER* 2.7 22.0 + - - -
306B ILE* 3.4 37.3 - - + +
309B VAL* 4.7 8.1 - - + +
319B PHE* 4.3 4.9 - - + -
341B ASN* 1.3 74.8 - - - +
343B ASP* 1.3 66.4 + - - +
345B ILE* 3.4 12.7 + - - +
346B ILE* 3.2 41.0 + - + +
512B TYR* 4.6 2.3 + - - -
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Residues in contact with ASP 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 3.2 15.6 + - - +
342B GLU* 1.3 80.0 - - - +
344B ALA* 1.3 59.7 + - - +
346B ILE* 3.7 13.9 + - - +
347B GLY* 3.1 24.8 + - - -
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Residues in contact with ALA 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG* 5.7 2.0 - - - +
327B PHE* 3.5 22.8 - - + -
331B GLU* 4.3 13.3 - - - +
340B TYR* 4.8 3.1 - - - -
341B ASN* 2.8 30.4 + - - +
343B ASP* 1.3 75.8 - - - +
345B ILE* 1.3 64.2 + - - +
347B GLY* 3.6 2.4 + - - -
348B ARG* 3.5 19.8 + - - +
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Residues in contact with ILE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B ILE* 5.7 0.2 - - + -
309B VAL* 5.1 1.6 - - + -
315B LEU* 3.9 29.6 - - + -
319B PHE* 4.0 35.0 - - + -
323B GLN 5.4 1.1 - - - +
324B VAL* 5.7 4.5 - - + -
327B PHE* 3.7 39.4 - - + -
340B TYR* 4.3 15.7 - - + -
341B ASN 3.4 15.7 + - - +
342B GLU* 3.7 10.8 - - - +
343B ASP 3.4 0.2 - - - -
344B ALA* 1.3 74.1 - - - +
346B ILE* 1.3 65.0 - - - +
348B ARG* 3.1 4.9 + - - +
349B VAL* 3.0 34.5 + - + +
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Residues in contact with ILE 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B PHE* 3.6 19.5 - - + -
342B GLU* 3.2 37.1 + - + +
343B ASP* 4.0 12.8 - - - +
344B ALA 3.5 0.2 - - - -
345B ILE* 1.3 75.3 - - - +
347B GLY* 1.3 57.0 + - - +
349B VAL* 3.3 6.0 + - - -
350B ASN* 3.0 52.2 + - - +
512B TYR* 3.7 29.8 - - + +
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Residues in contact with GLY 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B ASP 3.1 17.4 + - - -
344B ALA* 3.6 3.3 + - - -
345B ILE 3.2 0.6 - - - -
346B ILE* 1.3 78.1 - - - +
348B ARG* 1.3 59.7 + - - +
350B ASN* 4.9 1.5 - - - +
351B ALA* 3.3 28.8 + - - +
352B ASP* 4.4 0.9 - - - +
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Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B TYR* 4.2 10.1 - - + -
327B PHE* 4.3 15.3 - - + +
330B ARG* 3.5 51.2 + - - +
331B GLU* 2.9 35.8 + - - +
344B ALA 3.5 12.6 + - - +
345B ILE 3.1 7.1 + - - +
347B GLY* 1.3 77.5 - - - +
349B VAL* 1.3 65.3 + - - +
350B ASN 3.3 1.8 - - - -
352B ASP* 2.8 63.1 + - - +
353B LEU* 3.3 9.4 + - - +
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Residues in contact with VAL 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B PHE* 4.6 11.0 - - + +
323B GLN* 3.8 44.4 - - + +
326B TYR* 6.5 0.2 - - + -
327B PHE* 5.7 1.1 - - + -
345B ILE* 3.0 34.8 + - + +
346B ILE* 4.0 6.7 - - - +
348B ARG* 1.3 78.7 - - + +
350B ASN* 1.3 65.6 + - - +
353B LEU* 3.7 8.8 - - + +
354B ALA* 3.1 25.8 + - - +
509B PHE* 5.6 0.2 - - - +
510B PRO 4.3 12.5 - - - +
512B TYR* 4.5 12.8 - - + -
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Residues in contact with ASN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ILE* 3.0 35.8 + - - +
347B GLY* 4.9 1.8 - - - +
349B VAL* 1.3 81.2 - - - +
351B ALA* 1.3 59.9 + - + +
354B ALA* 3.4 7.6 - - - +
355B ASN* 3.0 29.6 + - - +
511B ARG* 3.4 46.3 + - + +
512B TYR* 3.1 34.8 + - - +
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B GLY 3.3 19.1 + - - +
350B ASN* 1.3 77.2 - - + +
352B ASP* 1.3 67.9 + - - +
355B ASN* 3.6 9.1 - - - +
356B GLU* 3.1 29.6 + - - +
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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