Contacts of the helix formed by residues 323 - 331 (chain A) in PDB entry 4KZK
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 ASN 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A LEU 3.2 22.0 + - - -
319A ILE* 3.2 6.1 - - - +
320A THR* 2.8 33.7 + - - -
322A ALA* 1.3 81.6 - - + +
324A GLU* 1.3 67.6 + - - +
325A LYS 3.2 2.8 + - - -
326A THR* 3.3 12.3 + - + +
327A ALA* 2.9 27.2 + - + +
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Residues in contact with GLU 324 (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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268A LEU* 3.5 20.3 - - + +
271A PHE* 3.6 35.5 - - + +
319A ILE* 3.9 24.5 - - + -
320A THR 3.0 19.5 + - - +
321A ARG* 4.1 11.3 - - - +
322A ALA 3.8 0.4 - - - -
323A ASN* 1.3 77.4 + - - +
325A LYS* 1.3 104.7 + - + +
327A ALA* 4.0 0.2 - - - +
328A ARG* 3.0 33.1 + - - +
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Residues in contact with LYS 325 (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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272A ALA* 6.3 0.8 - - - +
321A ARG 5.5 3.4 + - - +
323A ASN 3.3 0.8 - - - -
324A GLU* 1.3 110.6 + - + +
326A THR* 1.3 59.1 + - - +
328A ARG* 4.0 3.0 - - - +
329A ALA* 3.0 30.2 + - - +
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Residues in contact with THR 326 (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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323A ASN* 3.3 13.7 + - + +
325A LYS* 1.3 77.4 - - - +
327A ALA* 1.3 62.3 - - - +
329A ALA* 3.3 5.3 + - - +
330A GLN* 2.9 57.7 + - + +
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Residues in contact with ALA 327 (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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284A LEU* 4.0 7.5 - - + +
317A THR* 5.0 5.6 - - - +
318A LEU 5.4 0.2 - - - +
319A ILE* 3.5 27.4 - - + -
323A ASN* 2.9 25.7 + - + +
324A GLU 4.0 0.2 - - - +
326A THR* 1.3 78.1 - - - +
328A ARG* 1.3 64.3 + - - +
330A GLN* 3.4 14.5 + - - +
331A LEU* 3.4 17.7 + - - +
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Residues in contact with ARG 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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49A ASP* 5.0 6.7 + - - -
52A ARG* 4.8 5.1 - - - +
263A GLY 2.9 31.0 + - - -
264A SER* 4.0 8.9 - - - +
265A GLN* 4.1 14.1 + - - -
268A LEU* 3.7 35.4 - - - +
284A LEU* 3.8 28.1 - - + +
319A ILE* 4.6 4.3 - - + -
324A GLU* 3.0 24.2 + - - +
325A LYS* 4.0 3.4 - - - +
327A ALA* 1.3 77.5 - - - +
329A ALA* 1.3 61.1 + - - +
331A LEU* 3.1 11.3 + - - -
333A LEU* 3.1 64.4 + - + +
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Residues in contact with ALA 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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325A LYS 3.0 20.0 + - - +
326A THR* 3.3 5.8 + - - +
328A ARG* 1.3 75.0 - - - +
330A GLN* 1.3 60.0 + - + +
332A GLY* 2.9 20.0 + - - +
333A LEU* 4.6 6.7 - - - +
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Residues in contact with GLN 330 (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 THR* 2.9 42.7 + - + +
327A ALA* 3.9 8.1 - - - +
328A ARG 3.3 0.4 - - - -
329A ALA* 1.3 77.6 - - + +
331A LEU* 1.3 62.8 + - + +
332A GLY 3.4 0.2 - - - -
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Residues in contact with LEU 331 (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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284A LEU* 3.7 31.6 - - + +
285A LEU 4.3 7.4 - - - +
286A ASN* 4.3 27.8 + - + +
288A ARG* 4.0 13.0 + - - -
317A THR* 5.9 0.9 - - - +
327A ALA 3.4 9.1 + - - +
328A ARG 3.1 8.7 + - - +
330A GLN* 1.3 81.2 - - - +
332A GLY* 1.3 59.5 + - - +
333A LEU* 3.8 24.7 - - + +
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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