Contacts of the strand formed by residues 338 - 343 (chain B) in PDB entry 4WMJ
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 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A GLU* 4.2 10.3 + - - +
338A THR* 3.6 29.4 - - + -
381A VAL* 4.3 7.8 - - + +
336B ALA* 4.4 4.9 - - - +
337B GLU* 1.3 87.1 - - + +
339B HIS* 1.3 60.8 + - - +
380B PRO* 4.0 4.8 - - - +
381B VAL* 3.1 17.3 - - + +
383B TRP* 3.1 24.9 + - + +
404B LEU 5.3 0.2 + - - -
405B ILE* 3.7 21.0 - - - +
406B PRO* 3.4 22.6 - - - +
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Residues in contact with HIS 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLY* 5.9 5.1 - - - -
338B THR* 1.3 76.0 - - - +
340B ALA* 1.3 63.2 + - - +
341B LEU* 3.7 18.9 - - + +
359B ASP* 5.7 0.2 - - - -
380B PRO* 4.2 18.6 - - + -
381B VAL 2.9 6.0 + - - +
382B VAL* 3.4 13.7 - - + +
383B TRP* 3.2 25.2 + - - -
406B PRO* 3.6 29.2 + - + +
408B ASP* 3.1 42.7 + - - -
478B ASN* 5.1 2.2 - - - -
500B LYS* 3.7 24.7 + - - -
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Residues in contact with ALA 340 (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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339B HIS* 1.3 77.7 + - - +
341B LEU* 1.3 61.0 + - - +
342B LEU* 4.1 14.1 - - + -
383B TRP* 3.2 31.6 - - + +
398B VAL* 6.3 0.2 - - + -
405B ILE* 4.1 4.6 - - + +
406B PRO 3.0 8.0 + - - +
407B CYS* 3.3 25.3 - - - -
408B ASP 2.9 26.0 + - - -
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B HIS* 3.7 14.4 - - + +
340B ALA* 1.3 72.0 - - - +
342B LEU* 1.3 60.1 + - - +
343B PRO* 3.5 9.1 - - + +
351B PHE* 4.5 14.4 - - + -
352B ALA* 3.8 22.9 - - + +
355B PHE* 3.6 37.5 - - + -
382B VAL* 3.8 19.7 - - + -
383B TRP 2.9 6.5 + - - -
384B GLY* 3.4 21.8 - - - -
408B ASP* 3.6 27.8 - - + +
410B LEU* 5.0 1.6 - - + -
497B TYR* 3.6 21.5 - - + +
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Residues in contact with LEU 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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340B ALA* 4.2 9.6 - - + -
341B LEU* 1.3 80.8 - - - +
343B PRO* 1.3 64.7 - - - +
344B TYR* 3.4 13.0 - - + -
384B GLY* 4.1 4.3 - - - -
385B GLU 3.4 20.9 - - - +
394B PHE* 3.8 27.4 - - + -
395B TYR* 3.6 31.4 - - + +
398B VAL* 6.1 0.4 - - + -
407B CYS* 3.7 30.5 - - + -
408B ASP 2.8 16.2 + - - +
409B PHE* 3.4 20.1 - - + -
410B LEU* 3.2 18.5 + - - +
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Residues in contact with PRO 343 (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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341B LEU* 3.5 11.7 - - + +
342B LEU* 1.3 86.7 - - - +
344B TYR* 1.4 57.4 + - - +
345B ASP* 3.0 8.2 + - + +
348B LEU* 3.7 49.8 - - + +
351B PHE* 4.3 10.8 - - + -
352B ALA* 5.3 3.6 - - + +
385B GLU 4.2 0.7 - - - +
386B PRO* 2.9 23.4 - - + +
387B GLY 2.8 20.4 + - - -
410B LEU* 3.7 22.4 - - + +
485B PHE* 5.6 0.4 - - + -
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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