Contacts of the helix formed by residues 380 - 388 (chain A) in PDB entry 1W6T
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 THR 380 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 3.6 32.8 - - + +
120A ARG* 3.0 18.2 + - - +
130A LEU* 4.0 17.3 - - + -
134A LEU* 5.2 1.6 - - + -
350A LEU* 4.9 4.7 - - + -
378A ASP* 2.7 33.2 + - - -
379A SER* 1.3 76.7 - - - +
381A ILE* 1.3 58.1 + - + +
383A ASP* 3.0 6.8 + - - +
384A ILE* 2.9 42.4 + - + +
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Residues in contact with ILE 381 (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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344A VAL* 4.6 21.1 - - + -
369A VAL* 3.6 20.3 - - + +
370A SER* 3.8 13.5 - - - +
371A HIS* 3.7 27.1 - - + +
375A GLU* 5.1 2.0 - - - +
378A ASP* 4.6 1.3 + - - +
379A SER 3.1 0.2 + - - -
380A THR* 1.3 74.6 - - - +
382A ALA* 1.3 68.3 + - - +
384A ILE* 3.6 13.7 - - + +
385A ALA* 3.0 24.3 + - - +
393A ILE* 4.0 9.0 - - + +
395A THR* 3.7 26.9 - - - +
406A LYS* 3.8 23.1 - - + -
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Residues in contact with ALA 382 (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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379A SER 3.0 12.5 + - - +
381A ILE* 1.3 82.2 - - - +
383A ASP* 1.3 61.7 + - - +
385A ALA* 3.2 11.8 + - - +
386A VAL* 3.2 18.7 + - - +
393A ILE* 4.2 6.7 - - - -
406A LYS* 3.7 23.3 - - + +
409A GLN* 3.8 16.2 - - + -
410A LEU* 3.7 23.0 - - + +
413A ILE* 4.1 2.9 - - + -
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Residues in contact with ASP 383 (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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120A ARG* 5.0 1.6 + - - -
130A LEU* 3.5 32.9 + - + +
131A TYR* 3.1 40.9 + - - +
134A LEU* 4.6 1.6 - - + -
379A SER* 3.7 7.1 + - - +
380A THR 3.0 9.0 + - - +
382A ALA* 1.3 72.5 - - - +
384A ILE* 1.3 61.5 + - - +
386A VAL 3.4 0.3 + - - -
387A ALA* 2.8 32.8 + - - +
409A GLN* 2.9 35.8 + - - +
413A ILE* 3.8 8.5 - - - -
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Residues in contact with ILE 384 (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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134A LEU* 4.2 13.5 - - + -
344A VAL* 3.6 31.4 - - + -
350A LEU* 3.7 17.9 - - + -
353A THR* 4.8 3.4 - - + -
354A PHE* 3.9 13.7 - - + -
357A ILE* 3.8 27.4 - - + -
369A VAL* 4.3 11.4 - - + -
380A THR* 2.9 31.6 + - + +
381A ILE* 3.6 15.7 - - + +
382A ALA 3.2 0.2 - - - -
383A ASP* 1.3 77.9 - - - +
385A ALA* 1.3 62.7 + - - +
387A ALA* 3.6 6.2 - - - +
388A THR* 2.9 25.8 + - - +
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Residues in contact with ALA 385 (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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141A VAL 4.2 3.0 - - - +
143A PRO* 4.0 25.4 - - + -
369A VAL* 4.0 21.3 - - + -
381A ILE 3.0 16.1 + - - +
382A ALA 3.2 5.3 + - - +
384A ILE* 1.3 78.2 - - - +
386A VAL* 1.3 61.2 + - - +
388A THR* 4.1 1.6 - - - -
389A ASN* 3.2 1.6 + - - -
390A ALA* 3.0 29.5 + - + -
391A GLY 4.5 1.0 + - - -
392A GLN 4.2 9.9 - - - +
393A ILE* 4.4 7.4 - - + -
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Residues in contact with VAL 386 (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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131A TYR* 4.3 16.8 - - + -
139A THR* 3.8 10.1 - - - -
140A LYS 4.4 3.8 - - - +
141A VAL 3.6 22.0 - - - +
142A LEU* 3.9 8.1 - - + -
143A PRO* 4.0 3.4 - - + -
382A ALA 3.2 15.4 + - - +
383A ASP 4.1 2.0 - - - +
384A ILE 3.2 0.2 - - - -
385A ALA* 1.3 72.7 - - - +
387A ALA* 1.3 67.3 + - - +
388A THR 3.1 2.0 - - - -
389A ASN* 3.0 19.8 + - - +
410A LEU* 3.8 19.7 - - + -
413A ILE* 3.8 31.6 - - + -
417A LEU* 4.3 12.1 - - + -
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Residues in contact with ALA 387 (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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131A TYR* 3.5 25.9 - - - +
134A LEU* 3.7 21.5 - - + -
135A GLY* 3.4 21.6 - - - +
138A ASN 5.8 0.2 - - - -
139A THR* 3.7 10.2 - - - +
354A PHE* 4.1 6.3 - - + -
383A ASP 2.8 19.8 + - - +
384A ILE* 3.4 8.3 + - - +
386A VAL* 1.3 77.5 - - - +
388A THR* 1.3 58.1 + - - +
389A ASN* 3.8 1.7 + - - -
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Residues in contact with THR 388 (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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354A PHE* 3.3 39.7 - - + +
357A ILE* 3.9 33.4 - - + +
361A LYS* 3.0 22.2 + - - -
384A ILE 2.9 16.4 + - - +
385A ALA 3.5 0.3 + - - -
386A VAL 3.1 0.4 - - - -
387A ALA* 1.3 76.1 - - - +
389A ASN* 1.3 69.3 + - - +
390A ALA* 3.1 19.1 + - - +
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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