Contacts of the helix formed by residues 393 - 399 (chain A) in PDB entry 2WSC
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 LEU 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A TYR 3.3 8.5 - - - +
390A ALA* 3.2 34.5 - - - +
392A GLN* 1.3 78.0 - - - +
394A SER* 1.3 68.4 + - - +
395A LEU 2.9 1.1 - - - +
396A PHE* 3.4 10.0 - - - +
397A THR* 2.6 38.0 + - + +
616A PHE* 3.7 23.3 - - + -
617A SER* 4.9 0.4 - - - -
625A TRP* 3.9 8.3 - - + -
750A PHE* 2.6 51.8 - - + -
751A LEU* 6.1 0.2 - - + -
754A ILE* 3.8 20.2 - - + -
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Residues in contact with SER 394 (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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146A THR* 3.2 28.7 + - - -
390A ALA 3.2 13.6 + - - -
391A THR 3.9 0.2 - - - -
392A GLN 3.9 0.2 + - - -
393A LEU* 1.3 87.4 + - - +
395A LEU* 1.4 68.6 + - - +
397A THR* 3.5 0.5 - - - -
398A HIS* 2.6 35.0 + - - +
750A PHE* 6.3 0.2 - - - -
751A LEU* 4.5 7.2 - - - +
1783A CLA 3.2 43.4 - - - +
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Residues in contact with LEU 395 (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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146A THR 4.7 2.7 - - - +
147A SER* 5.5 0.2 - - - -
148A GLY 4.2 10.3 - - - +
376A MET* 4.2 11.9 - - + -
391A THR 2.9 31.9 - - - +
392A GLN* 3.5 16.4 - - + -
393A LEU 2.9 0.6 - - - -
394A SER* 1.4 88.5 + - - +
396A PHE* 1.3 53.4 + - - +
397A THR 2.7 8.1 + - - -
398A HIS* 4.5 4.7 - - - +
399A HIS* 2.7 58.9 + - + +
1783A CLA 4.0 2.6 - - + +
1784A CLA 3.1 55.0 - - + +
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Residues in contact with PHE 396 (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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373A ALA* 2.6 49.1 - - + +
374A GLN* 4.3 7.6 - - + -
376A MET* 5.6 5.6 - - + +
377A TYR* 5.1 7.2 - + + -
392A GLN* 4.5 5.6 - - + +
393A LEU* 3.2 15.1 + - - +
395A LEU* 1.3 73.9 - - + +
397A THR* 1.3 58.0 + - + +
399A HIS* 2.9 13.9 - - - +
400A MET* 3.2 29.5 - - + +
612A VAL* 4.7 4.0 - - + -
613A ILE* 5.3 4.7 - - - -
616A PHE* 2.8 67.3 - + + -
1792A CLA 4.1 13.2 - + + -
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Residues in contact with THR 397 (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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393A LEU* 2.6 39.7 + - + +
394A SER 3.8 1.6 - - - +
395A LEU 2.7 3.8 + - - -
396A PHE* 1.3 76.3 - - + +
398A HIS* 1.3 62.8 + - - +
399A HIS 3.5 1.3 - - - -
400A MET* 3.3 6.3 - - - +
401A TRP* 2.8 33.6 + - - -
613A ILE* 3.0 32.7 - - + +
616A PHE* 5.9 0.9 - - + -
750A PHE* 4.2 16.1 - - + -
1783A CLA 2.9 33.3 - - + +
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Residues in contact with HIS 398 (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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394A SER 2.6 19.4 + - - +
395A LEU* 2.9 3.8 + - - +
397A THR* 1.3 73.1 + - - +
399A HIS* 1.3 81.4 + + - +
400A MET 2.8 9.2 + - - -
401A TRP* 3.0 10.9 + - - +
402A ILE* 3.6 8.9 + - + +
1783A CLA 2.4 100.3 + + + +
1784A CLA 3.3 59.2 - + + +
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Residues in contact with HIS 399 (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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369A THR* 4.9 10.1 - - - +
370A ILE* 4.4 0.4 - - - -
372A VAL* 4.6 15.1 - - + +
373A ALA* 3.6 13.8 - - + +
376A MET* 4.6 7.5 - - + +
395A LEU* 2.7 31.9 + - + +
396A PHE* 2.9 21.7 - - - +
398A HIS* 1.3 81.2 + + - +
400A MET* 1.3 65.0 + - - +
402A ILE* 5.2 3.6 - - + +
1784A CLA 2.1 99.8 + + + -
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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