Contacts of the strand formed by residues 325 - 330 (chain D) in PDB entry 5VZU
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 ARG 325 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D PHE* 3.8 1.6 - - - -
322D HIS* 2.9 45.9 + - + +
323D GLY 2.9 4.9 + - - +
324D ARG* 1.3 79.3 + - - +
326D ALA* 1.3 61.6 + - - +
327D ARG* 5.9 0.2 - - - -
345D GLU* 3.1 32.0 + - + +
346D ILE 3.3 12.1 - - - +
347D ASP* 3.3 38.5 + - - +
348D LEU* 3.9 6.7 - - - +
349D ARG* 4.8 10.1 - - - +
377D VAL* 5.2 9.3 - - - +
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Residues in contact with ALA 326 (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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319D LEU* 4.0 17.0 - - + -
320D SER 3.6 4.0 - - - -
321D PHE* 4.2 18.4 - - + -
325D ARG* 1.3 72.6 - - - +
327D ARG* 1.3 60.0 + - - +
345D GLU* 3.3 7.6 - - - +
346D ILE* 2.8 58.9 + - + +
348D LEU* 4.2 8.7 - - + +
488D PHE* 6.4 0.4 - - + -
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Residues in contact with ARG 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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318D MET 3.2 3.5 - - - +
319D LEU* 3.3 5.2 - - - +
320D SER* 2.7 51.5 + - - +
322D HIS* 4.2 11.4 - - + +
325D ARG 4.2 0.6 - - - -
326D ALA* 1.3 71.9 - - - +
328D GLY* 1.3 61.5 + - - +
329D THR* 2.9 37.6 + - - +
340D GLY 4.1 3.8 + - - -
342D GLN* 3.6 41.4 - - + +
344D VAL 3.8 2.2 - - - -
345D GLU* 5.4 0.9 - - + -
531D LEU* 3.6 41.1 + - - +
535D GLN* 3.9 28.7 + - - +
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Residues in contact with GLY 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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317D VAL* 4.0 15.0 - - - -
318D MET 3.4 5.6 - - - -
319D LEU* 4.6 3.8 - - - -
327D ARG* 1.3 73.1 - - - +
329D THR* 1.3 60.3 + - - -
342D GLN* 3.6 5.7 - - - +
343D THR* 3.1 24.2 + - - -
344D VAL* 2.9 34.5 + - - +
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Residues in contact with THR 329 (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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317D VAL* 3.5 3.8 - - - +
318D MET* 2.7 48.2 + - - +
320D SER* 5.1 1.0 + - - -
327D ARG* 2.9 40.0 + - - +
328D GLY* 1.3 73.5 - - - -
330D LYS* 1.3 74.8 + - - +
331D ILE* 3.4 2.9 + - + -
340D GLY 4.1 9.0 - - - +
341D GLN 3.5 10.8 - - - +
531D LEU* 4.2 15.1 - - + +
534D ILE* 4.3 15.5 - - + -
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Residues in contact with LYS 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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150D GLN* 3.7 2.9 + - - -
309D TYR* 3.8 7.2 - - - -
315D GLU* 2.7 28.1 + - - +
316D ILE 3.9 3.6 - - - -
317D VAL* 4.6 6.3 - - + +
328D GLY 4.3 0.2 - - - -
329D THR* 1.3 73.1 - - - +
331D ILE* 1.3 63.3 + - - +
332D THR 3.5 11.9 - - - +
333D GLY* 4.0 1.3 - - - -
334D ASP* 2.9 12.3 + - - -
337D ILE* 2.9 47.2 + - + +
338D PRO 3.8 2.7 - - - +
339D ALA* 3.8 10.5 - - - -
340D GLY* 2.8 29.4 + - - +
341D GLN 2.9 13.8 + - - +
343D THR* 3.6 29.8 - - + -
534D ILE* 5.0 0.2 - - - +
295F ILE* 3.0 14.9 + - - -
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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