Contacts of the helix formed by residues 348 - 357 (chain A) in PDB entry 1ZM9
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 ALA 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ASP* 3.6 40.2 - - + +
343A PRO* 4.4 2.9 - - + -
344A SER 3.5 6.5 + - - +
346A VAL 3.3 0.2 - - - -
347A THR* 1.3 77.0 - - - +
349A GLN* 1.3 50.0 + - - +
350A ALA 3.0 5.4 - - - -
351A TYR* 3.0 30.9 + - + +
352A ARG* 2.8 43.0 + - - +
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Residues in contact with GLN 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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123A ASP* 5.4 0.2 - - - +
345A PRO 3.4 19.8 - - - +
346A VAL 4.0 3.2 + - - +
347A THR 3.6 0.6 - - - -
348A ALA* 1.3 76.8 - - - +
350A ALA* 1.3 56.0 + - - +
352A ARG* 3.7 7.6 - - - +
353A ALA* 3.0 34.7 + - - +
369A ILE* 2.7 34.5 + - + +
370A LYS* 3.4 7.2 - - - +
372A CYS* 3.7 15.0 - - + +
399A ARG* 3.0 39.8 + - - +
401A PHE* 3.1 44.5 + - + -
451A GLY* 4.0 3.6 - - - -
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Residues in contact with ALA 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 VAL 3.9 9.0 + - - +
347A THR* 3.6 14.6 + - - +
348A ALA 3.0 0.6 - - - -
349A GLN* 1.3 80.1 - - - +
351A TYR* 1.3 59.2 + - + +
352A ARG 3.5 0.2 - - - -
353A ALA 4.8 0.3 + - - -
354A GLU* 5.1 0.3 - - - +
370A LYS* 3.0 52.9 + - + +
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Residues in contact with TYR 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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123A ASP 5.0 0.3 + - - -
150A ARG* 3.4 59.0 + - + +
152A LYS* 5.2 4.9 - - - +
196A VAL* 5.5 6.5 - - + -
197A LEU* 3.4 32.2 - - + +
343A PRO* 4.0 16.2 - - + +
347A THR* 3.1 35.0 - - + -
348A ALA* 3.4 23.8 - - - +
350A ALA* 1.3 79.2 - - + +
352A ARG* 1.3 63.0 + - - +
353A ALA 3.7 0.9 - - - -
354A GLU* 5.3 7.7 - - - +
355A GLN* 5.1 2.1 + - - +
370A LYS* 5.2 0.4 - - - +
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Residues in contact with ARG 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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119A LEU 4.5 0.6 + - - -
120A ARG 3.0 29.3 + - - -
122A THR 3.0 22.8 + - - -
123A ASP* 3.5 18.3 + - - +
149A GLU* 3.1 53.0 + - - +
150A ARG* 3.6 24.5 - - + -
151A ILE* 4.6 0.6 - - - +
348A ALA* 2.8 23.2 + - - +
349A GLN* 4.2 3.7 - - + +
351A TYR* 1.3 82.7 - - - +
353A ALA* 1.3 65.0 + - - +
354A GLU 3.5 0.9 - - - -
355A GLN* 3.1 14.0 + - + +
356A LEU* 3.1 45.7 + - + +
399A ARG* 3.6 10.5 - - - +
401A PHE* 4.2 2.0 - - + -
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Residues in contact with ALA 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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349A GLN* 3.0 21.7 + - - +
351A TYR 3.7 0.4 - - - -
352A ARG* 1.3 75.3 - - - +
354A GLU* 1.3 57.1 + - - +
356A LEU* 2.7 27.5 + - - +
357A TYR* 2.9 16.4 + - - +
366A CYS* 3.9 5.2 - - - +
369A ILE* 3.3 36.2 - - + +
370A LYS* 3.6 19.7 - - + +
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Residues in contact with GLU 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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350A ALA 5.1 0.9 - - - +
351A TYR* 5.3 7.2 - - - +
352A ARG 3.5 0.8 - - - -
353A ALA* 1.3 74.8 - - - +
355A GLN* 1.3 57.1 + - - +
357A TYR 3.1 22.8 - - - +
361A ALA* 3.7 24.7 - - + +
366A CYS* 4.2 19.0 - - - -
370A LYS* 3.7 35.9 + - - -
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Residues in contact with GLN 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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148A GLY 2.7 25.7 + - - +
149A GLU* 3.5 23.5 + - - +
150A ARG* 3.2 39.9 + - - +
194A ASP* 4.5 1.2 - - - +
351A TYR 5.2 0.9 + - - +
352A ARG* 3.1 14.4 + - + +
353A ALA 3.0 0.8 - - - -
354A GLU* 1.3 79.7 - - - +
356A LEU* 1.3 62.8 + - + +
357A TYR 3.5 1.8 + - - +
479A LYS* 3.1 35.1 - - + +
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Residues in contact with LEU 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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120A ARG* 3.6 33.9 - - + +
149A GLU* 4.0 10.8 - - - +
352A ARG* 3.1 40.8 + - + +
353A ALA* 2.7 16.1 + - - +
355A GLN* 1.3 80.3 - - + +
357A TYR* 1.3 56.4 + - - +
381A TYR* 6.4 0.2 - - + -
401A PHE* 3.4 41.3 - - + -
478A MET* 3.1 23.5 - - + +
479A LYS* 2.9 31.9 + - + -
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Residues in contact with TYR 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 ALA 2.9 12.6 + - - +
354A GLU 3.1 14.6 - - - +
355A GLN 4.7 1.3 - - - +
356A LEU* 1.3 81.1 - - - +
358A GLU* 1.3 61.0 + - - +
359A GLY* 3.2 42.5 + - - +
363A ASP* 2.7 38.4 + - + -
365A ASN* 4.1 4.6 - - + +
366A CYS* 3.6 32.5 - - + -
369A ILE* 5.1 6.5 - - + -
379A MET* 3.7 24.0 - - + -
475A ALA* 3.6 5.2 - - - -
476A HIS* 2.9 49.9 + - + -
477A ASN 4.2 4.3 - - - -
478A MET* 4.3 4.5 - - + -
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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