Contacts of the strand formed by residues 326 - 333 (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 ILE 326 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324D ASP* 4.4 14.1 - - + +
325D LEU* 1.3 79.3 - - - +
327D ALA* 1.3 63.4 + - - +
340D GLN 3.6 1.4 - - - +
341D ILE* 3.3 4.2 - - - +
342D TYR* 2.9 78.6 + - + +
343D GLN 4.8 5.2 - - - +
387D PRO* 4.4 1.3 - - - -
388D LYS* 3.5 28.0 - - + +
390D LYS* 3.9 24.7 - - + -
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Residues in contact with ALA 327 (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* 1.3 74.1 - - - +
328D GLU* 1.3 63.9 + - - +
329D ILE* 5.7 0.7 - - + -
339D TYR* 6.1 0.2 - - + -
340D GLN 3.4 6.7 - - - +
341D ILE* 4.5 9.9 - - + -
375D ILE* 4.5 4.9 - - + -
387D PRO* 3.8 19.5 - - + +
388D LYS 2.9 9.1 + - - +
389D PHE* 3.5 30.3 - - + +
390D LYS* 2.9 31.2 + - - +
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Residues in contact with GLU 328 (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* 1.3 77.8 - - - +
329D ILE* 1.3 64.0 + - - +
330D GLN* 3.9 10.5 + - - +
339D TYR* 3.0 9.4 - - - +
340D GLN* 2.9 49.5 + - - +
342D TYR* 2.8 40.7 + - + +
390D LYS* 3.2 31.6 + - + -
423D VAL* 5.0 6.9 - - - +
426D TRP* 5.6 0.3 + - - -
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Residues in contact with ILE 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D ALA* 5.3 0.7 - - + -
328D GLU* 1.3 80.3 - - - +
330D GLN* 1.3 68.9 + - - +
337D TRP* 3.6 35.2 - - + -
338D THR 3.3 9.6 - - - +
339D TYR* 4.2 1.1 - - + -
368D LEU* 3.6 24.2 - - + -
371D ALA* 4.9 3.4 - - + -
372D VAL* 3.9 20.9 - - + +
375D ILE* 4.0 26.0 - - + -
389D PHE* 4.1 12.6 - - + -
390D LYS 4.0 8.0 + - - +
391D LEU* 4.3 5.2 - - + -
392D PRO* 3.4 26.5 - - + +
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Residues in contact with GLN 330 (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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328D GLU* 3.9 13.7 + - - +
329D ILE* 1.3 85.4 + - - +
331D LYS* 1.3 63.1 + - - +
332D GLN* 3.5 9.5 + - - +
337D TRP* 3.5 3.8 - - - -
338D THR* 2.6 62.6 + - - +
340D GLN* 2.8 36.7 + - - +
392D PRO* 4.9 1.6 - - - -
421D PRO* 4.3 19.7 - - + -
423D VAL* 3.4 34.7 - - + +
424D LYS* 4.9 3.1 - - + -
426D TRP* 3.7 2.1 - - - -
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Residues in contact with LYS 331 (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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402C TRP* 2.6 33.5 + - - -
403C THR* 4.4 9.4 - - - +
405C TYR 2.9 22.4 + - - +
406C TRP* 3.4 19.5 + - - +
407C GLN 3.2 17.3 + - - +
409C THR* 4.8 0.6 - - - +
329D ILE 4.2 0.4 + - - -
330D GLN* 1.3 68.6 - - - +
332D GLN* 1.3 59.2 + - - +
333D GLY* 4.1 12.3 - - - +
336D GLN 4.1 0.4 - - - -
337D TRP* 3.5 37.8 - - + -
364D ASP* 2.8 32.9 + - - +
392D PRO* 4.8 3.3 - - + +
424D LYS* 3.3 25.7 + - - +
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Residues in contact with GLN 332 (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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330D GLN* 3.5 5.5 + - - +
331D LYS* 1.3 74.8 - - - +
333D GLY* 1.3 62.3 + - - +
334D GLN* 5.4 0.7 - - - +
336D GLN* 2.9 24.8 + - + +
338D THR* 3.4 37.2 + - + +
423D VAL 4.4 0.2 + - - -
424D LYS* 3.2 56.8 + - - +
426D TRP 4.1 0.8 - - - +
427D TYR* 3.1 50.4 - - + +
428D GLN 4.5 2.1 - - - +
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Residues in contact with GLY 333 (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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403C THR 4.9 12.6 - - - -
331D LYS* 3.4 16.0 - - - +
332D GLN* 1.3 82.3 - - - +
334D GLN* 1.3 78.2 + - - +
335D GLY 3.3 2.5 - - - -
336D GLN* 3.2 19.6 + - - +
427D TYR* 5.6 0.3 + - - -
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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