Contacts of the strand formed by residues 336 - 344 (chain D) in PDB entry 3V81
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 GLN 336 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331D LYS* 3.9 0.7 - - - -
332D GLN* 2.9 35.7 + - + -
333D GLY 3.2 16.2 + - - +
334D GLN* 3.0 18.0 - - + +
335D GLY* 1.3 77.2 - - - +
337D TRP* 1.3 69.0 + - - +
353D LYS* 3.3 28.2 + - + +
354D TYR 3.5 3.6 - - - -
355D ALA* 3.3 22.4 - - + +
427D TYR* 2.5 37.3 + - + +
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Residues in contact with TRP 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C ALA* 3.8 25.6 - - + -
329D ILE* 3.6 27.6 - - + -
330D GLN 3.5 5.4 - - - +
331D LYS* 3.5 36.8 - - + -
335D GLY 3.5 12.7 + - - -
336D GLN* 1.3 81.8 - - - +
338D THR* 1.3 63.4 + - - +
339D TYR* 4.1 2.9 + - + -
353D LYS* 3.3 2.9 - - - +
354D TYR* 2.8 45.6 + - + +
357D MET* 3.6 16.8 - - + -
364D ASP* 3.8 25.8 - - - -
367D GLN* 3.1 33.7 + - + +
368D LEU* 4.0 25.1 - - + -
371D ALA* 4.9 6.7 - - + -
392D PRO* 4.4 8.1 - - + -
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Residues in contact with THR 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D GLN* 3.6 19.7 - - - +
329D ILE* 3.3 4.4 - - - +
330D GLN* 2.6 61.4 + - - +
332D GLN* 3.4 20.2 + - + +
337D TRP* 1.3 74.2 - - - +
339D TYR* 1.3 60.8 + - - +
340D GLN* 4.2 4.0 - - - -
352D GLY 3.4 6.5 - - - -
353D LYS* 3.8 11.0 - - + -
426D TRP* 3.7 6.4 - - - +
427D TYR* 3.5 31.2 - - + -
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Residues in contact with TYR 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ALA* 6.1 0.4 - - + -
328D GLU 3.0 14.6 - - - +
329D ILE* 4.2 3.8 - - + -
337D TRP* 4.6 2.5 - - + -
338D THR* 1.3 75.6 - - - +
340D GLN* 1.3 77.8 + - - +
341D ILE* 4.3 6.5 - - + -
350D LYS* 3.5 22.8 + - + -
351D THR* 3.3 2.2 - - - -
352D GLY* 2.9 57.5 + - - +
353D LYS 4.2 0.7 - - - -
354D TYR* 3.1 46.0 + + - -
375D ILE* 3.5 46.9 - - + -
378D GLU* 2.8 25.5 + - - -
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Residues in contact with GLN 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D ILE 3.6 1.6 - - - +
327D ALA* 3.4 3.5 - - - +
328D GLU* 2.9 44.5 + - - +
330D GLN* 2.8 42.0 + - - -
338D THR* 3.9 1.8 - - - -
339D TYR* 1.3 95.1 + - - +
341D ILE* 1.3 63.5 + - - +
342D TYR* 4.0 7.1 - - + -
348D ASN* 3.6 16.8 - - - +
350D LYS 3.4 7.6 - - - +
351D THR* 3.5 17.5 - - + -
426D TRP* 3.5 41.3 + - + +
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Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D LEU* 4.3 24.2 - - + -
326D ILE 3.3 9.4 - - - +
327D ALA* 4.5 4.7 - - + -
339D TYR* 4.3 11.2 - - + -
340D GLN* 1.3 75.7 - - - +
342D TYR* 1.3 65.6 + - - +
348D ASN* 3.6 1.4 - - - -
349D LEU* 2.9 25.4 + - + -
350D LYS* 2.9 24.9 + - + +
375D ILE* 3.6 33.9 - - + +
378D GLU* 5.4 2.2 - - + +
379D SER* 3.7 15.9 - - - +
383D TRP* 4.0 32.3 - - + -
387D PRO* 4.7 4.0 - - + -
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Residues in contact with TYR 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D LEU* 4.9 3.1 - - - -
326D ILE* 2.9 64.9 + - + +
328D GLU* 2.8 47.8 + - + -
340D GLN* 4.0 9.9 - - + -
341D ILE* 1.3 76.7 - - - +
343D GLN* 1.3 61.1 + - - +
344D GLU* 3.7 22.2 - - - +
345D PRO* 4.0 18.6 - - + -
346D PHE 5.4 1.1 - - - -
347D LYS 3.4 20.6 - - - +
348D ASN* 3.6 18.4 - - - +
349D LEU* 4.2 4.5 - - - +
390D LYS* 3.9 6.8 + - - -
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Residues in contact with GLN 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D TYR 4.1 3.7 - - - +
319D TYR* 3.0 26.3 - - - -
320D ASP* 2.8 42.5 + - + -
323D LYS* 3.3 28.2 + - + +
324D ASP 3.1 24.0 - - - +
325D LEU* 3.4 12.2 - - + +
326D ILE* 4.8 5.0 - - - +
342D TYR* 1.3 78.5 - - - +
344D GLU* 1.3 72.9 + - + +
345D PRO* 4.8 0.2 - - - +
347D LYS 4.3 3.0 + - - -
349D LEU* 3.3 22.5 - - + +
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Residues in contact with GLU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D LYS* 2.8 46.2 + - - +
342D TYR* 3.7 7.7 - - - -
343D GLN* 1.3 85.3 - - + +
345D PRO* 1.3 80.0 - - + +
346D PHE 3.4 0.3 + - - -
347D LYS* 3.0 30.6 + - + +
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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