Contacts of the strand formed by residues 336 - 342 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C LYS* 3.7 30.9 - - + +
276C VAL 4.3 0.3 + - - -
277C ARG* 2.9 41.9 + - + +
278C GLN* 5.7 0.4 - - - +
302C GLU* 4.1 1.0 + - - +
331C LYS* 4.1 0.5 - - - +
332C GLN* 3.0 36.4 + - + +
333C GLY 3.0 19.6 + - - +
334C GLN* 3.0 34.6 + - - +
335C GLY* 1.3 76.4 - - - +
337C TRP* 1.3 73.3 + - - +
353C LYS* 5.9 1.7 - - - -
354C TYR 3.8 4.0 - - - +
355C ALA* 4.4 9.7 - - + +
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Residues in contact with TRP 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C ILE* 4.1 14.8 - - + -
330C GLN 3.7 3.6 - - - -
331C LYS* 3.4 42.6 - - + -
332C GLN* 4.5 2.5 - - - +
335C GLY* 3.4 19.0 + - - -
336C GLN* 1.3 82.4 - - - +
338C THR* 1.3 66.5 + - - +
339C TYR* 5.4 0.4 - - + -
353C LYS* 3.2 8.0 - - - +
354C TYR* 2.9 60.9 + + + +
364C ASP* 3.9 32.1 - - + -
367C GLN* 3.5 28.8 - - + +
368C LEU* 3.6 29.4 - - + -
371C ALA* 4.5 5.2 - - + -
392C PRO* 5.0 1.8 - - + -
423C VAL* 3.9 23.3 - - + -
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Residues in contact with THR 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C GLY* 4.0 22.0 - - - +
274C ILE 4.2 10.8 - - - +
329C ILE* 3.3 5.8 - - - +
330C GLN* 2.8 53.6 + - - +
332C GLN* 2.9 38.6 + - - +
337C TRP* 1.3 78.4 - - - +
339C TYR* 1.3 64.1 + - - +
340C GLN* 4.6 4.5 - - - -
352C GLY 3.3 10.8 - - - +
353C LYS* 4.4 2.7 - - + +
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Residues in contact with TYR 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C PRO* 5.8 0.3 - - - +
327C ALA* 5.5 0.4 - - + -
328C GLU 3.1 13.7 - - - +
329C ILE* 4.0 7.2 - - + -
337C TRP* 5.4 1.1 - - + -
338C THR* 1.3 78.6 - - - +
340C GLN* 1.3 70.2 + - - +
341C ILE* 3.5 33.9 - - + -
350C LYS* 4.3 1.6 + - - -
351C THR* 3.5 8.4 + - - -
352C GLY* 2.9 67.0 + - - +
353C LYS* 3.5 14.3 + - - -
354C TYR* 4.6 3.1 - - + -
371C ALA* 6.3 0.2 - - + -
374C LYS* 3.3 21.1 + - + -
375C ILE* 3.6 43.0 - - + +
378C GLU* 3.0 20.3 + - - -
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Residues in contact with GLN 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C PRO* 4.3 17.9 - - + +
273C GLY* 5.4 1.0 - - - +
326C ILE 3.7 1.0 - - - +
327C ALA* 3.3 2.8 - - - +
328C GLU* 2.9 38.8 + - - +
330C GLN* 2.7 45.8 + - - -
338C THR* 4.5 4.4 + - - -
339C TYR* 1.3 84.5 + - - +
341C ILE* 1.3 63.3 + - - +
342C TYR* 4.2 9.5 + - + -
348C ASN* 3.6 33.2 - - - +
350C LYS 3.6 5.6 - - - +
351C THR* 4.3 7.4 - - + +
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Residues in contact with ILE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C LEU* 3.8 25.4 - - + -
326C ILE 3.2 13.0 - - - +
327C ALA* 3.6 17.0 - - + -
339C TYR* 3.5 29.2 - - + -
340C GLN* 1.3 75.8 - - - +
342C TYR* 1.3 56.5 + - - +
348C ASN* 3.7 2.2 - - - -
349C LEU* 2.8 30.6 + - + +
350C LYS* 2.9 23.3 + - + +
375C ILE* 4.1 11.4 - - + -
378C GLU* 4.2 10.5 - - - +
379C SER* 4.7 4.0 - - - +
383C TRP* 3.9 32.5 - - + -
387C PRO* 5.1 1.1 - - + -
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Residues in contact with TYR 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C LEU* 4.0 1.0 - - - +
326C ILE* 2.9 64.9 + - + +
328C GLU* 3.3 28.0 + - + +
340C GLN* 4.6 9.2 - - + -
341C ILE* 1.3 74.6 - - - +
343C GLN* 1.3 73.2 + - - +
344C GLU 3.6 11.7 - - - +
345C PRO* 4.8 9.6 - - + -
346C PHE* 4.8 9.0 - - - -
347C LYS 3.4 20.6 - - - +
348C ASN* 3.6 18.6 - - - +
349C LEU* 4.1 6.1 - - - +
390C LYS* 3.2 31.2 + - - +
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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