Contacts of the helix formed by residues 42 - 46 (chain 4) in PDB entry 1ZUD
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 PRO 42 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1723 CYS 4.4 8.7 - - - +
2353 ARG* 3.7 30.7 - - + +
2363 ARG 3.8 14.1 - - - +
2373 ALA* 4.1 19.1 - - + -
404 ILE* 3.7 15.7 - - + +
414 VAL* 1.3 85.5 - - - +
434 ARG* 1.3 55.7 + - - +
444 GLU* 4.2 6.1 - - + -
454 GLN* 2.8 57.6 + - - +
464 TRP* 3.4 3.3 - - - -
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Residues in contact with ARG 43 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1723 CYS 5.2 2.2 + - - -
1733 LEU 5.8 2.1 + - - +
1743 TRP* 4.9 0.8 - - - -
1753 PRO* 3.7 38.5 - - + +
1763 ASP* 3.1 40.4 + - - +
294 GLN* 3.3 20.6 + - - +
304 ALA* 3.8 9.9 - - - +
314 GLY 3.5 2.0 - - - +
324 ALA 3.1 18.7 + - - -
414 VAL 3.3 2.4 + - - -
424 PRO* 1.3 71.6 - - - +
444 GLU* 1.3 64.0 + - - +
454 GLN 2.9 1.4 + - - -
464 TRP* 3.1 68.2 + - + +
474 ALA 4.8 0.5 + - - -
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Residues in contact with GLU 44 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1753 PRO* 6.0 0.6 - - - +
2373 ALA* 3.3 14.7 - - + +
2383 SER* 2.7 34.1 + - - -
2393 GLY* 3.1 25.5 + - - -
424 PRO* 3.0 13.7 + - + -
434 ARG* 1.3 77.3 - - - +
454 GLN* 1.3 70.6 + - + +
464 TRP 3.5 0.2 - - - -
474 ALA* 5.0 3.7 + - - +
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Residues in contact with GLN 45 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2353 ARG* 5.2 7.5 - - - +
2363 ARG 4.8 5.1 + - - -
2383 SER* 5.4 4.2 + - - +
414 VAL* 4.0 13.0 - - + +
424 PRO* 2.8 43.4 + - - +
444 GLU* 1.3 93.0 + - + +
464 TRP* 1.3 59.6 + - - +
474 ALA 3.3 2.7 - - - -
484 GLN* 3.2 7.8 + - + +
494 HIS* 2.9 37.6 + - + +
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Residues in contact with TRP 46 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174 THR* 3.6 0.3 - - - -
184 VAL* 3.4 33.7 + - + +
194 HIS* 2.9 28.1 + - + +
224 LEU* 3.6 23.3 - - + -
294 GLN* 3.6 33.2 - - + +
324 ALA* 3.6 19.5 - - + -
334 ALA* 4.0 3.6 - - - -
344 LEU* 3.5 36.8 - - + +
414 VAL* 2.8 34.1 + - + +
424 PRO 3.4 10.3 - - - -
434 ARG* 3.1 55.1 + - + +
444 GLU 3.5 0.2 - - - -
454 GLN* 1.3 78.3 - - - +
474 ALA* 1.3 62.7 + - - +
484 GLN 3.3 0.7 + - - -
494 HIS* 3.8 1.6 + - - -
594 LEU* 4.7 1.1 - - + -
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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