Contacts of the helix formed by residues 361 - 372 (chain A) in PDB entry 2W5X
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 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ALA* 3.3 18.8 - - + +
94A GLY* 3.0 41.7 + - - -
95A ILE* 3.7 18.5 - - - +
96A LYS* 3.6 17.1 - - - +
359A GLU* 3.2 22.7 - - - +
360A ASN* 1.3 78.7 + - - +
362A GLU* 1.3 71.2 + - - +
363A ILE 3.1 6.6 + - - -
364A PHE 3.5 3.1 + - - -
365A HIS* 3.4 18.9 + - - -
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Residues in contact with GLU 362 (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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358A TYR* 3.8 16.8 - - + -
359A GLU* 2.9 35.1 + - + +
361A ASN* 1.3 85.2 + - - +
363A ILE* 1.3 58.7 + - - +
364A PHE 3.2 0.4 - - - -
365A HIS* 3.3 28.5 + - - +
366A LYS* 2.9 43.4 + - - +
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Residues in contact with ILE 363 (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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39A LEU* 4.8 12.6 - - + -
72A ILE* 4.4 4.5 - - + -
91A PHE* 3.8 33.9 - - + +
297A ILE* 4.7 5.2 - - + -
299A THR* 5.1 2.7 - - + -
344A VAL* 4.3 16.4 - - + -
354A PHE* 4.0 16.3 - - + -
358A TYR* 3.8 31.9 - - + +
360A ASN 3.3 16.8 - - - +
361A ASN 3.1 0.4 - - - -
362A GLU* 1.3 78.4 - - - +
364A PHE* 1.3 64.5 + - - +
366A LYS* 3.4 3.1 + - - +
367A ILE* 3.1 45.8 + - + +
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Residues in contact with PHE 364 (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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90A ALA 3.9 0.9 + - - +
91A PHE 3.2 16.5 + - - +
92A SER 3.2 32.8 - - - -
93A CYS* 3.6 15.3 - - - -
94A GLY* 3.3 28.3 - - - -
112A LYS 4.1 4.7 - - - -
114A ILE* 3.7 24.0 - - + +
117A ILE* 3.4 27.4 - - + -
361A ASN 3.5 1.9 + - - +
363A ILE* 1.3 81.2 - - - +
365A HIS* 1.3 83.4 + + - +
367A ILE* 3.2 8.3 + - - +
368A LEU* 3.1 39.8 + - + +
375A GLN* 4.8 4.9 - - - -
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Residues in contact with HIS 365 (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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94A GLY* 3.0 22.7 + - - -
95A ILE* 6.3 0.2 - - + -
361A ASN* 3.4 25.7 + - - -
362A GLU* 3.3 29.0 + - - +
364A PHE* 1.3 95.4 - + - +
366A LYS* 1.3 58.4 + - + +
368A LEU* 3.4 8.5 + - - +
369A LYS* 2.9 29.2 + - - +
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Residues in contact with LYS 366 (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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353A GLU* 2.8 46.1 + - + +
354A PHE* 3.6 25.4 - - + -
355A ILE 4.8 1.8 + - - -
358A TYR* 3.6 50.9 - - + +
362A GLU* 2.9 25.1 + - + +
365A HIS* 1.3 76.5 - - + +
367A ILE* 1.3 65.1 + - - +
369A LYS* 3.2 7.0 + - + +
370A VAL* 3.0 30.0 + - - +
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Residues in contact with ILE 367 (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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37A VAL* 4.4 16.6 - - + -
39A LEU* 4.7 9.0 - - + -
91A PHE 5.5 2.2 - - - +
114A ILE* 4.0 24.2 - - + -
250A PHE* 4.7 11.4 - - + -
295A LEU* 5.1 0.4 - - + -
297A ILE* 3.6 33.4 - - + -
354A PHE* 3.9 2.7 - - + -
363A ILE* 3.1 29.5 + - + +
364A PHE* 3.2 9.2 + - - +
366A LYS* 1.3 75.6 - - - +
368A LEU* 1.3 60.9 + - - +
369A LYS 3.3 0.2 + - - -
370A VAL* 3.4 6.9 + - - +
371A THR* 2.8 46.1 + - + +
373A TRP* 4.4 4.0 - - + -
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Residues in contact with LEU 368 (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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114A ILE* 3.2 33.7 - - + -
117A ILE* 4.2 19.1 - - + -
364A PHE* 3.1 46.8 + - + +
365A HIS* 3.7 11.7 - - - +
367A ILE* 1.3 77.0 - - - +
369A LYS* 1.3 58.8 + - - +
371A THR* 3.4 3.0 + - - -
372A LYS* 3.0 29.6 + - - -
373A TRP* 3.6 29.4 + - + +
375A GLN* 4.2 11.0 - - + +
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Residues in contact with LYS 369 (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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353A GLU* 2.8 44.6 + - + +
365A HIS 2.9 18.4 + - - +
366A LYS* 3.5 6.5 - - + +
367A ILE 3.2 0.4 - - - -
368A LEU* 1.3 79.7 - - - +
370A VAL* 1.3 62.2 + - + +
372A LYS* 3.7 15.2 + - - +
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Residues in contact with VAL 370 (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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32A LYS 4.2 3.4 - - - +
33A THR* 3.4 14.9 + - - +
34A PRO* 3.2 37.0 - - + +
295A LEU* 3.8 20.6 - - + -
350A GLY* 3.8 17.9 - - - +
353A GLU* 3.7 34.5 - - + +
354A PHE* 4.5 0.9 - - + -
366A LYS 3.0 15.6 + - - +
367A ILE* 3.5 10.5 - - - +
369A LYS* 1.3 76.7 - - + +
371A THR* 1.3 67.4 + - + +
372A LYS* 3.5 1.7 + - - +
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Residues in contact with THR 371 (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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33A THR* 3.8 9.7 - - - +
34A PRO* 4.0 21.0 - - + +
37A VAL* 3.5 32.3 - - + -
367A ILE* 2.8 25.2 + - + +
368A LEU* 3.4 4.2 + - - -
370A VAL* 1.3 76.8 - - + +
372A LYS* 1.3 68.9 + - - +
373A TRP* 3.1 56.4 + - + +
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Residues in contact with LYS 372 (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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30A GLN* 2.8 38.5 + - - +
33A THR* 4.2 19.6 + - + +
121A ASN* 4.4 1.4 - - - +
368A LEU 3.0 12.9 + - - -
369A LYS 3.9 11.9 - - - +
370A VAL 3.3 2.9 - - - +
371A THR* 1.3 79.8 - - - +
373A TRP* 1.3 65.2 + - - +
374A ASN* 3.2 25.0 + - - +
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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