Contacts of the helix formed by residues 352 - 359 (chain A) in PDB entry 2Z82
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 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PDJ 3.8 47.1 - - - +
332A TYR* 4.2 10.8 - - + +
350A LEU* 3.4 21.7 - - + +
351A VAL* 1.3 83.4 - - - +
353A CYS* 1.3 58.1 + - - +
354A SER* 3.4 2.9 - - - +
355A PHE* 2.8 51.8 + - + +
356A SER 3.0 4.9 + - - -
379A ASN* 3.7 8.1 - - - +
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Residues in contact with CYS 353 (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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351A VAL 3.4 1.9 + - - -
352A PRO* 1.3 68.9 - - - +
354A SER* 1.3 67.0 + - - +
356A SER* 2.8 18.0 + - - -
357A GLN* 2.9 29.4 + - - +
379A ASN* 2.9 37.9 + - - +
382A CYS* 2.0 47.6 - - + -
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Residues in contact with SER 354 (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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332A TYR* 2.8 35.1 + - - -
352A PRO* 4.6 3.3 + - - +
353A CYS* 1.3 79.6 - - - +
355A PHE* 1.3 60.4 + - - +
357A GLN* 3.4 16.4 + - - +
358A HIS* 3.1 31.8 + - - -
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Residues in contact with PHE 355 (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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1A PDJ 3.6 49.4 - - + -
331A VAL* 4.0 26.5 - - + -
332A TYR* 3.5 33.9 - + - +
335A LEU* 3.4 34.8 - - + -
351A VAL* 3.5 26.7 - - + -
352A PRO* 2.8 26.3 + - + +
354A SER* 1.3 82.8 + - - +
356A SER* 1.3 59.7 + - - +
358A HIS* 3.2 17.9 + - + +
359A LEU* 3.6 15.8 + - + +
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Residues in contact with SER 356 (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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351A VAL* 3.5 17.5 + - - +
352A PRO 3.0 2.5 + - - -
353A CYS 2.8 8.5 + - - -
355A PHE* 1.3 74.7 - - - +
357A GLN* 1.3 65.0 + - - -
359A LEU* 3.0 21.8 + - - +
380A SER 2.9 26.1 + - - -
385A ALA* 3.8 9.2 - - - -
386A TRP* 3.3 43.5 + - - +
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Residues in contact with GLN 357 (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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353A CYS* 2.9 28.7 + - - +
354A SER* 3.7 14.0 - - - +
355A PHE 3.3 0.2 - - - -
356A SER* 1.3 75.1 - - - +
358A HIS* 1.3 59.6 + - - +
359A LEU 3.5 0.7 + - - -
360A LYS* 2.7 35.3 + - - +
382A CYS* 3.6 15.3 - - - +
383A LYS* 4.9 3.0 - - - +
384A GLY* 3.6 42.7 - - - +
387A PRO* 4.7 1.0 - - - +
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Residues in contact with HIS 358 (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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332A TYR* 3.4 59.5 - + + +
333A SER* 5.1 3.7 + - - -
335A LEU* 5.0 1.1 - - + -
336A GLU* 3.7 19.5 - - + +
354A SER* 3.1 22.7 + - - -
355A PHE* 3.2 11.5 + - + +
356A SER 3.1 0.8 - - - -
357A GLN* 1.3 76.0 - - - +
359A LEU* 1.3 53.0 + - + +
360A LYS* 2.8 26.5 + - - +
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Residues in contact with LEU 359 (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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1A PDJ 6.4 0.2 - - + -
335A LEU* 3.3 47.8 - - + +
338A VAL* 5.0 1.6 - - + +
341A ILE* 3.9 16.6 - - + -
351A VAL* 5.3 2.0 - - + -
355A PHE* 3.7 28.9 - - + +
356A SER* 3.0 12.6 + - - +
358A HIS* 1.3 73.3 - - + +
360A LYS* 1.3 61.3 + - - +
361A SER 3.2 4.1 + - - -
362A LEU* 3.5 30.9 + - + +
365A LEU* 6.0 1.1 - - + -
386A TRP* 3.5 29.9 - - + +
387A PRO* 3.6 14.4 - - - +
388A SER 5.2 0.2 + - - -
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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