Contacts of the helix formed by residues 361 - 372 (chain C) in PDB entry 2LXH
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 HIS 361 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335C ALA* 6.1 1.4 - - - +
338C ASN 5.5 2.0 + - - -
340C ASP 4.6 6.3 + - - -
341C CYS* 3.6 22.5 + - + +
344C CYS* 4.1 0.8 - - - -
347C SER* 4.1 5.9 - - - -
348C MET* 3.8 40.7 + - + +
349C GLN 5.3 0.6 + - - -
350C ALA* 2.7 30.3 + - + +
351C ALA* 4.2 8.1 - - + +
352C ARG* 5.1 0.2 - - - -
359C LEU 5.0 2.7 + - - -
360C PHE* 1.3 78.5 - - - +
362C ASN* 1.3 59.9 + - - +
363C SER* 3.3 2.9 - - - +
364C CYS* 3.7 14.0 - - - +
365C LEU* 2.7 34.3 + - - +
900C ZN 2.1 34.6 - - - -
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Residues in contact with ASN 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ALA* 3.0 34.4 - - - +
328C VAL* 4.0 12.3 - - + +
350C ALA* 3.6 23.8 - - + +
351C ALA 4.6 0.4 - - - +
352C ARG* 5.4 4.7 - - - +
360C PHE 3.9 0.2 + - - -
361C HIS* 1.3 73.4 - - - +
363C SER* 1.3 61.5 + - - +
365C LEU* 4.1 2.6 - - - +
366C ARG* 2.7 81.6 + - - +
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Residues in contact with SER 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C MET* 6.1 5.2 - - - -
350C ALA* 5.2 0.6 - - - +
361C HIS* 3.3 3.0 - - - +
362C ASN* 1.3 82.1 + - - +
364C CYS* 1.3 69.3 + - - +
366C ARG* 4.1 6.4 + - - +
367C SER* 3.0 27.5 + - - -
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Residues in contact with CYS 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C CYS* 3.7 6.3 - - - -
343C ILE* 4.2 22.4 - - + +
344C CYS* 3.0 23.3 - - + -
348C MET* 5.5 3.1 - - - -
360C PHE 4.9 0.4 - - - -
361C HIS* 3.4 17.0 + - + +
362C ASN 3.4 0.4 - - - -
363C SER* 1.3 81.4 - - - +
365C LEU* 1.3 62.5 + - - +
367C SER* 3.7 4.3 - - - -
368C TRP* 3.1 21.5 + - - +
900C ZN 2.3 37.5 - - - -
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Residues in contact with LEU 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C ARG* 3.8 41.7 - - + +
354C LEU* 3.7 35.4 - - + -
360C PHE* 3.9 16.7 - - + +
361C HIS 2.7 22.8 + - - +
362C ASN* 4.1 2.5 - - - +
364C CYS* 1.3 71.3 - - - +
366C ARG* 1.3 62.0 + - + +
368C TRP* 2.5 33.0 + - + +
369C LEU* 2.7 53.0 + - + +
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Residues in contact with ARG 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ALA* 6.1 2.0 - - + -
362C ASN* 2.7 70.8 + - - +
363C SER* 4.1 7.2 + - - +
365C LEU* 1.3 74.3 - - + +
367C SER* 1.3 63.2 + - - +
369C LEU* 3.1 12.6 + - + +
370C GLU* 2.4 42.7 + - - +
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Residues in contact with SER 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C SER 3.0 21.7 + - - -
364C CYS* 3.7 5.2 - - - -
366C ARG* 1.3 77.6 - - - +
368C TRP* 1.3 58.7 + - - +
370C GLU* 3.3 7.8 + - - +
371C GLN* 3.0 31.8 + - - +
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Residues in contact with TRP 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C ILE* 3.9 35.4 - - + -
354C LEU* 5.9 2.0 - - + -
360C PHE* 5.7 0.9 - + - -
364C CYS 3.1 12.4 + - - +
365C LEU* 2.5 26.6 + - + +
367C SER* 1.3 69.8 - - - +
369C LEU* 1.3 59.2 + - + +
371C GLN* 3.1 22.2 + - + -
372C ASP* 2.4 70.5 + - + +
374C SER* 2.8 33.9 + - - -
376C PRO* 3.6 34.6 - - + +
382C LEU* 6.0 0.7 - - + -
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Residues in contact with LEU 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C ARG* 6.0 0.4 - - - +
354C LEU* 5.7 0.9 - - + -
365C LEU* 2.7 57.2 + - + +
366C ARG* 3.5 14.1 - - + +
368C TRP* 1.3 76.3 - - + +
370C GLU* 1.3 72.6 + - - +
371C GLN 3.5 0.3 + - - -
372C ASP 3.8 10.1 + - - +
373C THR* 3.8 22.1 - - + +
382C LEU* 4.2 27.1 - - + -
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Residues in contact with GLU 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C ARG* 2.4 46.5 + - - +
367C SER* 3.6 7.6 - - - +
369C LEU* 1.3 89.8 - - - +
371C GLN* 1.3 60.0 + - - +
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Residues in contact with GLN 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C SER* 3.0 20.4 + - - +
368C TRP* 3.7 25.6 - - + +
369C LEU 4.4 0.4 - - - -
370C GLU* 1.3 81.2 - - - +
372C ASP* 1.3 65.9 + - + +
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Residues in contact with ASP 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368C TRP* 2.4 56.3 + - + +
369C LEU* 3.8 1.7 - - - -
370C GLU 3.8 0.2 - - - -
371C GLN* 1.3 84.3 - - + +
373C THR* 1.3 82.1 + - - +
374C SER* 3.3 28.1 + - - +
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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