Contacts of the helix formed by residues 342 - 352 (chain A) in PDB entry 3ZJU
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 ASP 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A VAL 2.9 4.0 + - - +
339A PRO 4.0 0.3 - - - +
341A HIS* 1.3 79.0 - - - +
343A GLN* 1.3 60.4 + - - +
344A ARG* 2.8 43.9 + - - -
345A ASP* 3.0 49.9 + - - +
346A TYR* 2.9 27.9 + - - +
374A ALA* 3.6 3.1 - - - -
376A THR* 5.4 0.4 - - - -
76B DJF 3.5 32.4 - - + +
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Residues in contact with GLN 343 (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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342A ASP* 1.3 74.8 + - - +
344A ARG* 1.3 63.9 + - + +
346A TYR* 3.5 11.1 + - - +
347A GLU* 3.1 64.9 + - - +
372A GLN 5.3 0.4 + - - -
373A GLN* 3.7 15.2 - - - +
374A ALA* 3.2 31.8 + - + +
376A THR* 5.1 6.8 + - - +
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Residues in contact with ARG 344 (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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300A LYS* 3.7 23.1 - - - +
325A PHE* 4.0 26.0 - - + -
342A ASP* 2.8 44.9 + - - +
343A GLN* 1.3 75.1 - - + +
345A ASP* 1.3 65.0 + - - +
347A GLU* 4.1 1.4 - - - +
348A PHE* 3.1 25.6 + - - +
74B C 3.4 35.2 + - - +
75B C 3.4 24.5 + - - -
76B DJF 2.9 66.2 + - - -
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Residues in contact with ASP 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A TYR* 2.9 24.0 + - - +
325A PHE* 3.5 22.2 - - - -
335A VAL* 4.6 4.2 - - - +
336A MET 4.3 2.9 - - - +
337A ALA* 3.6 13.7 - - - +
338A VAL* 3.0 22.7 + - - +
339A PRO* 3.6 19.7 - - + -
342A ASP* 3.0 35.6 + - - +
344A ARG* 1.3 73.5 + - - +
346A TYR* 1.3 59.8 + - - +
348A PHE* 3.5 0.6 + - - -
349A ALA* 2.9 22.5 + - - +
76B DJF 4.8 5.9 - - - +
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Residues in contact with TYR 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PRO* 3.2 30.2 - - - +
342A ASP 2.9 13.4 + - - +
343A GLN* 3.5 15.9 - - - +
344A ARG 3.3 0.2 - - - -
345A ASP* 1.3 77.4 - - - +
347A GLU* 1.3 60.4 + - + +
349A ALA* 3.4 1.8 + - - +
350A SER* 3.1 40.1 + - - -
356A ILE* 3.8 29.1 - - + +
370A LEU* 2.6 31.1 + - + -
371A SER 3.2 8.7 + - - -
372A GLN 3.2 21.0 - - - -
373A GLN* 3.2 24.0 + - - -
374A ALA* 3.5 16.2 - - + -
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Residues in contact with GLU 347 (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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299A GLU* 4.8 3.3 + - - -
300A LYS* 3.0 38.5 + - + +
343A GLN* 3.1 48.7 + - - +
344A ARG 4.1 0.9 - - - +
345A ASP 3.3 0.4 - - - -
346A TYR* 1.3 75.8 - - + +
348A PHE* 1.3 65.2 + - - +
350A SER* 3.9 5.3 + - - -
351A LYS* 3.2 26.9 + - - +
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Residues in contact with PHE 348 (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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258A TYR* 3.4 37.5 - + - +
300A LYS* 4.2 17.8 - - + +
301A LYS 3.7 14.4 - - - -
302A GLY* 3.8 8.7 - - - -
321A TRP* 3.8 42.4 - + + -
323A ALA* 3.5 23.1 - - + -
325A PHE* 3.7 21.3 - + + -
344A ARG 3.1 19.1 + - - +
347A GLU* 1.3 77.6 - - - +
349A ALA* 1.3 60.4 + - - +
351A LYS* 3.6 1.7 + - - -
352A TYR* 3.2 42.7 + + - +
354A LEU* 4.2 4.9 - - + -
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Residues in contact with ALA 349 (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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258A TYR* 3.8 14.4 - - + -
339A PRO* 3.7 20.9 - - + -
345A ASP 2.9 19.4 + - - +
346A TYR 3.8 2.0 - - - +
347A GLU 3.2 0.2 - - - -
348A PHE* 1.3 77.1 - - - +
350A SER* 1.3 59.7 + - - +
352A TYR 3.4 0.3 + - - -
353A GLY* 2.8 8.3 + - - -
354A LEU* 2.6 51.5 + - + +
356A ILE* 4.4 3.6 - - + -
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Residues in contact with SER 350 (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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346A TYR* 3.1 27.2 + - - -
347A GLU* 3.9 6.1 + - - -
349A ALA* 1.3 76.2 - - - +
351A LYS* 1.3 63.5 + - - +
352A TYR 3.7 0.2 + - - -
353A GLY* 3.9 7.7 + - - +
354A LEU 5.1 0.9 - - - -
356A ILE* 4.1 18.6 - - - -
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Residues in contact with LYS 351 (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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299A GLU* 5.3 2.4 + - - -
300A LYS* 2.7 32.5 + - + +
301A LYS* 4.4 6.1 - - - +
347A GLU 3.2 20.0 + - - +
348A PHE 4.0 2.5 - - - +
349A ALA 3.2 0.2 - - - -
350A SER* 1.3 81.0 + - - +
352A TYR* 1.3 93.6 + - + +
353A GLY 3.5 0.4 - - - -
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Residues in contact with TYR 352 (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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300A LYS 4.7 0.2 - - - -
301A LYS* 3.4 15.7 - - - +
302A GLY* 2.9 43.4 + - - -
321A TRP* 3.7 31.9 - + + -
348A PHE* 3.2 49.9 + + - +
351A LYS* 1.3 112.8 + - + +
353A GLY* 1.3 63.6 + - - +
354A LEU* 3.3 13.9 + - + +
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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