Contacts of the helix formed by residues 345 - 354 (chain A) in PDB entry 4X4W
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 GLU 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A LYS* 3.1 50.3 + - - +
320A TYR* 4.4 4.6 + - - +
340A LEU* 3.0 36.2 + - + +
343A GLN* 4.1 24.5 - - + +
344A GLY* 1.3 75.1 - - - +
346A HIS* 1.3 65.7 + - - +
347A CYS* 3.3 4.2 + - - +
348A LEU* 3.2 14.9 + - + +
349A LEU* 3.0 23.6 + - - +
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Residues in contact with HIS 346 (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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257A LYS 4.9 3.3 + - - -
258A ASN* 2.8 32.7 + - - -
260A ASP 5.3 0.2 + - - -
262A PHE* 3.4 45.8 - + + -
340A LEU 5.8 0.4 - - - -
341A LYS* 5.6 3.4 - - - -
344A GLY* 3.0 25.8 + - - -
345A GLU* 1.3 74.0 - - - +
347A CYS* 1.3 63.4 + - - +
348A LEU 3.1 4.9 + - - -
349A LEU* 3.4 17.0 + - + +
350A LYS* 4.2 5.9 + - - +
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Residues in contact with CYS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLU* 3.3 1.9 + - - +
346A HIS* 1.3 82.5 - - - +
348A LEU* 1.4 61.1 + - + +
350A LYS* 5.3 0.7 - - - -
351A GLU* 3.1 22.9 + - - +
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Residues in contact with LEU 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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309A LYS* 3.8 32.1 - - + +
316A PRO* 4.2 20.4 - - + +
317A LEU* 4.0 24.7 - - + +
320A TYR* 4.2 10.3 - - + -
340A LEU* 3.8 3.9 - - + +
345A GLU* 3.2 30.0 + - + +
346A HIS 3.2 0.6 - - - -
347A CYS* 1.4 80.7 - - + +
349A LEU* 1.3 67.9 + - - +
350A LYS 3.5 2.2 - - - -
351A GLU* 3.4 25.3 + - - +
352A MET* 3.1 24.3 + - - +
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Residues in contact with LEU 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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262A PHE* 3.9 29.8 - - + +
337A CYS* 3.5 36.3 - - + +
340A LEU* 4.0 13.0 - - + -
341A LYS* 3.7 27.4 - - + -
345A GLU 3.0 15.8 + - - +
346A HIS* 3.4 10.4 + - + +
348A LEU* 1.3 77.4 - - - +
350A LYS* 1.3 60.4 + - + +
352A MET* 3.2 4.2 + - - +
353A GLN* 2.9 52.5 + - - +
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Residues in contact with LYS 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 HIS 4.2 5.9 + - - +
347A CYS 5.3 0.6 - - - -
348A LEU 3.5 0.2 - - - -
349A LEU* 1.3 79.0 - - + +
351A GLU* 1.3 57.5 + - - +
353A GLN* 3.1 23.1 + - + +
354A GLN* 2.9 58.9 + - + +
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Residues in contact with GLU 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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317A LEU* 4.1 18.2 - - + +
347A CYS 3.1 22.9 + - - +
348A LEU* 3.4 26.3 + - - +
349A LEU 3.2 0.2 - - - -
350A LYS* 1.3 77.8 - - - +
352A MET* 1.3 62.9 + - - +
354A GLN* 3.3 6.2 + - - +
355A TRP* 3.1 23.8 + - - +
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Residues in contact with MET 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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317A LEU* 3.4 34.8 - - + -
320A TYR* 3.7 21.3 - - + -
321A GLN* 4.1 7.6 - - + +
324A ILE* 3.4 28.5 - - + -
333A THR* 4.5 7.4 - - + +
336A VAL* 4.1 7.0 - - + -
337A CYS* 3.6 19.8 - - - -
340A LEU* 3.6 13.9 - - + -
348A LEU 3.1 14.2 + - - +
349A LEU 3.6 3.8 - - - +
351A GLU* 1.3 77.2 - - - +
353A GLN* 1.3 67.2 + - - +
355A TRP* 3.2 31.0 + - - +
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Residues in contact with GLN 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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333A THR* 5.5 3.6 - - - +
337A CYS* 3.6 22.4 - - - +
341A LYS* 4.4 15.0 - - - +
349A LEU* 2.9 38.7 + - + +
350A LYS* 3.1 40.2 + - + +
352A MET* 1.3 77.0 - - - +
354A GLN* 1.3 60.7 + - + +
355A TRP 3.6 2.6 + - - +
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Residues in contact with GLN 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 LYS* 2.9 49.1 + - - +
351A GLU* 3.6 5.7 - - - +
353A GLN* 1.3 78.7 - - + +
355A TRP* 1.3 62.5 + - - +
356A SER* 3.4 6.6 + - - -
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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