Contacts of the strand formed by residues 326 - 329 (chain A) in PDB entry 5ZE3
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 VAL 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A PRO* 4.0 11.6 - - + +
325A LEU* 1.3 79.6 - - - +
327A ARG* 1.3 70.8 + - - +
328A LEU* 5.4 0.4 - - + -
339A VAL* 3.9 9.4 - - + -
340A GLU 3.1 15.0 - - - +
341A VAL* 3.9 12.1 - - + -
347A TRP* 3.5 6.3 - - - -
363A VAL* 3.6 26.9 - - + -
366A GLU* 3.4 38.6 - - + +
367A LEU* 3.8 26.3 - - + +
402A ILE* 4.5 2.2 - - + -
403A ILE* 5.7 0.2 - - + -
455B GLN 5.3 0.5 - - - +
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Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PRO* 5.9 2.0 - - + -
326A VAL* 1.3 78.3 - - - +
328A LEU* 1.3 70.7 + - - +
329A ARG* 3.3 44.7 - - - +
338A ARG 3.3 1.2 - - - +
339A VAL* 3.7 0.3 - - - -
340A GLU* 2.9 60.5 + - + +
347A TRP* 3.3 53.8 - - + +
367A LEU* 4.5 8.7 - - - -
750A GLY* 2.7 32.5 + - - -
751A SER* 4.4 2.4 - - - +
455B GLN 5.4 6.5 - - - +
456B GLY* 6.5 0.7 - - - -
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A VAL* 5.4 1.8 - - + -
327A ARG* 1.3 83.4 - - - +
329A ARG* 1.3 80.0 + - - +
335A GLY* 3.6 14.8 - - - +
336A GLU 3.6 41.5 - - - +
337A GLY* 4.1 3.6 - - - +
338A ARG 3.1 11.0 - - - +
339A VAL* 4.1 11.9 - - + -
363A VAL* 5.5 0.9 - - + -
367A LEU* 4.0 25.1 - - + +
369A PHE* 5.2 1.8 - - + -
422A VAL* 3.7 26.5 - - + -
424A CYS* 4.7 1.8 - - - -
456B GLY 5.9 2.0 - - - +
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ARG* 3.3 48.8 - - + +
328A LEU* 1.3 88.3 + - - +
330A GLY* 1.3 72.0 + - - +
337A GLY* 3.4 0.2 - - - -
338A ARG* 2.8 53.3 + - - +
340A GLU* 3.5 27.8 - - - +
381A LEU 4.3 0.7 - - - +
724A ASP* 3.5 25.8 - - - +
726A SER* 3.7 17.4 + - - -
750A GLY* 5.0 1.0 + - - -
455B GLN 6.1 3.0 - - - -
456B GLY* 6.2 1.6 - - - -
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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