Contacts of the strand formed by residues 424 - 430 (chain B) in PDB entry 3ZVU
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 ASP 424 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B ILE* 4.7 0.9 - - - +
351B LEU* 3.7 15.0 - - + +
352B PHE 3.8 4.0 - - - -
353B ARG* 2.6 38.2 + - - +
420B ARG* 3.4 20.4 + - - +
421B SER 2.8 42.1 + - - +
422B ARG 3.1 1.9 - - - +
423B GLU* 1.3 69.9 - - - +
425B GLU* 1.3 61.5 + - - +
501B LEU* 3.9 30.4 - - + +
502B LYS* 3.7 19.6 - - - +
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Residues in contact with GLU 425 (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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352B PHE* 2.7 30.1 + - + +
354B GLY* 3.8 23.6 - - - +
423B GLU 3.9 7.8 - - - +
424B ASP* 1.3 74.3 - - - +
426B CYS* 1.3 64.3 + - - +
448B ARG* 3.2 33.4 + - + -
500B ASP* 3.4 0.2 - - - +
501B LEU* 3.1 14.8 + - - -
502B LYS* 3.5 20.2 + - - -
505B ARG* 2.9 54.1 + - - +
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Residues in contact with CYS 426 (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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350B VAL 4.1 0.4 - - - +
351B LEU* 3.3 5.0 - - - +
352B PHE* 2.7 49.0 + - - -
424B ASP 3.9 0.2 - - - -
425B GLU* 1.3 86.2 - - - +
427B LEU* 1.3 61.7 + - - +
428B ILE* 4.1 19.7 - - + +
444B CYS* 4.1 15.3 - - - -
447B ALA* 4.2 7.4 - - - -
448B ARG* 4.4 7.6 - - - -
451B ILE* 4.4 10.5 - - + -
498B VAL* 5.1 0.4 - - + -
499B ILE 3.1 15.0 - - - +
500B ASP* 4.4 2.7 - - - -
501B LEU* 3.9 9.0 - - - +
505B ARG* 5.0 0.2 - - - +
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Residues in contact with LEU 427 (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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332B ALA* 4.2 10.3 - - + -
334B VAL* 3.8 20.6 - - + -
339B ILE* 3.8 29.2 - - + -
341B VAL* 5.1 0.4 - - + -
349B ALA* 4.6 2.9 - - + -
350B VAL 3.4 26.5 - - - +
351B LEU* 4.2 3.8 - - + -
360B LEU* 4.1 19.5 - - + -
426B CYS* 1.3 77.2 - - - +
428B ILE* 1.3 62.1 + - - +
429B LEU* 3.9 15.9 - - + -
497B ILE 3.8 1.4 - - - +
498B VAL* 3.7 1.2 - - - -
499B ILE* 2.8 56.8 + - + +
501B LEU* 4.0 13.0 - - + +
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Residues in contact with ILE 428 (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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348B ARG 3.8 1.6 - - - +
349B ALA* 3.3 3.3 - - - -
350B VAL 2.9 38.3 + - - +
426B CYS* 4.1 12.1 - - - -
427B LEU* 1.3 82.4 - - - +
429B LEU* 1.3 65.3 + - - +
434B LEU* 4.5 2.5 - - + -
435B TRP* 4.0 23.6 - - + -
443B VAL* 4.0 22.4 - - + +
444B CYS* 4.4 12.6 - - - -
447B ALA* 3.7 30.7 - - + -
481B LEU* 5.2 0.2 - - + -
496B ILE* 4.2 19.1 - - + -
497B ILE 3.4 7.9 - - - +
498B VAL* 4.3 12.6 - - + -
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Residues in contact with LEU 429 (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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239B PHE* 3.7 27.8 - - + +
240B GLY* 4.4 2.7 - - - +
241B VAL* 3.9 14.3 - - + +
330B VAL* 3.7 28.9 - - + +
331B VAL 4.1 1.6 - - - -
332B ALA* 3.7 21.5 - - + +
348B ARG 3.5 3.6 - - - +
349B ALA* 3.8 21.8 - - + -
427B LEU* 3.9 20.6 - - + -
428B ILE* 1.3 79.5 - - - +
430B ALA* 1.3 61.1 + - - +
496B ILE* 3.4 2.3 - - - +
497B ILE* 2.7 43.9 + - + +
499B ILE* 4.5 7.9 - - + -
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Residues in contact with ALA 430 (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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241B VAL* 4.1 9.3 - - - +
330B VAL* 4.9 0.2 - - - +
347B SER* 3.6 1.6 - - - -
348B ARG 3.0 23.7 + - - -
428B ILE* 4.6 1.1 - - + -
429B LEU* 1.3 75.8 - - - +
431B SER* 1.3 61.9 + - - +
434B LEU* 3.6 27.1 - - + -
435B TRP* 2.8 32.0 + - + +
495B SER 3.1 15.0 - - - +
496B ILE* 3.7 5.8 - - + -
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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