Contacts of the helix formed by residues 327 - 332 (chain L) in PDB entry 4EC4
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 CYS 327 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252L ASN 4.3 0.9 - - - -
302L HIS* 4.3 0.2 - - - -
303L CYS* 3.7 20.4 - - + +
320L HIS* 3.5 6.5 - - - +
324L TYR 3.1 15.9 + - - +
325L PRO 3.2 3.9 - - - +
326L GLY* 1.3 76.5 - - - +
328L LYS* 1.3 66.1 + - - +
329L TYR* 3.5 21.8 - - - -
330L LEU* 3.6 16.1 - - + +
331L LEU* 3.5 21.0 + - - +
339L ILE* 4.9 0.7 - - - +
401L ZN 2.3 38.1 - - - -
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Residues in contact with LYS 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E 2PE 4.8 7.4 + - - -
252L ASN 5.1 1.2 + - - -
253L SER* 3.3 31.6 - - - +
254L THR 3.6 16.7 + - - +
255L ASN* 3.4 25.8 - - - +
302L HIS* 3.8 12.8 + - + -
326L GLY* 3.1 29.1 + - - +
327L CYS* 1.3 72.5 - - - +
329L TYR* 1.3 63.7 + - - +
331L LEU* 3.9 26.1 + - + +
332L GLU* 3.4 23.0 + - - +
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Residues in contact with TYR 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263L ALA 5.9 0.2 - - - -
268L ARG* 3.9 12.1 + - - -
286L ARG 3.2 18.1 + - - -
287L ALA* 3.6 33.4 - - - -
288L GLY* 4.0 2.9 - - - -
300L CYS* 5.2 0.4 - - - -
301L PHE* 3.7 33.4 - + - -
302L HIS* 3.5 30.5 + + + -
317L TRP* 4.7 1.6 - + - -
320L HIS* 5.0 3.4 - + - -
327L CYS* 3.3 5.4 - - - -
328L LYS* 1.3 77.6 - - - +
330L LEU* 1.3 67.3 + - - +
332L GLU* 3.2 19.1 + - - +
333L GLN* 3.1 58.0 + - + +
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Residues in contact with LEU 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317L TRP* 3.9 31.6 - - + +
320L HIS* 4.0 25.1 - - + +
321L ALA* 3.4 35.0 - - + +
324L TYR 4.4 11.0 - - - +
325L PRO* 4.8 0.7 - - + -
327L CYS* 3.6 18.6 - - + +
328L LYS 3.5 0.2 - - - -
329L TYR* 1.3 82.9 - - - +
331L LEU* 1.3 53.0 + - - +
333L GLN* 3.1 4.0 + - - +
334L LYS* 2.8 42.1 + - + +
338L TYR* 4.7 2.2 - - + -
339L ILE* 3.6 26.2 - - + -
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Residues in contact with LEU 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325L PRO 5.3 2.9 - - - +
326L GLY* 6.5 0.2 - - - -
327L CYS 3.5 12.4 + - - +
328L LYS* 4.0 30.3 - - + +
329L TYR 3.4 0.2 - - - -
330L LEU* 1.3 78.4 - - - +
332L GLU* 1.3 57.2 + - - +
335L GLY* 3.1 28.9 + - - +
336L GLN* 3.6 50.3 - - + +
339L ILE* 4.0 10.5 - - + +
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Residues in contact with GLU 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328L LYS 3.4 17.1 + - - +
329L TYR* 3.2 13.8 + - - +
330L LEU 3.2 0.6 - - - -
331L LEU* 1.3 78.4 - - - +
333L GLN* 1.3 85.4 + - - +
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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