Contacts of the helix formed by residues 332 - 340 (chain A) in PDB entry 5E92
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 ASN 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A LYS 4.3 0.2 - - - +
331A GLY* 1.4 75.0 - - - -
333A LEU* 1.4 57.5 + - - +
334A GLN* 3.0 13.4 + - - +
335A GLU* 3.0 48.2 + - - +
336A TYR* 3.1 24.4 + - - +
383A SER* 3.5 28.3 + - - +
385A ILE 3.1 13.0 - - - +
386A LEU* 4.1 4.0 - - + +
387A VAL* 4.5 0.4 - - - -
601A ANP 2.9 36.2 + - - +
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Residues in contact with LEU 333 (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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331A GLY 4.0 0.4 + - - -
332A ASN* 1.4 68.9 - - - +
334A GLN* 1.3 60.0 + - - +
336A TYR* 3.7 2.2 - - + +
337A LEU* 2.9 54.6 + - + +
350A LEU* 4.3 21.5 - - + -
382A SER* 3.3 17.9 + - - +
385A ILE* 2.8 30.5 + - + +
387A VAL* 3.9 23.7 - - + +
393A CYS* 5.2 0.9 - - - -
453A VAL* 3.6 31.0 - - + -
457A MET* 3.6 20.4 - - + -
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Residues in contact with GLN 334 (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 ASN* 3.0 10.5 + - - +
333A LEU* 1.3 77.6 - - - +
335A GLU* 1.3 55.7 + - + +
337A LEU* 3.5 3.6 + - - +
338A THR* 2.7 38.5 + - - +
382A SER* 3.2 26.2 + - - +
383A SER* 4.1 17.9 - - - +
424A TYR* 4.5 4.9 + - - -
456A GLU* 4.3 0.2 + - - -
470A TYR* 2.8 37.8 + - + +
472A PRO* 3.9 17.0 - - - +
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Residues in contact with GLU 335 (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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250A VAL 4.8 9.3 - - - +
330A LYS 5.7 2.0 - - - +
331A GLY* 4.9 3.9 - - - -
332A ASN* 3.0 43.8 + - - +
334A GLN* 1.3 76.5 - - + +
336A TYR* 1.3 61.9 + - - +
338A THR* 3.4 9.2 + - - -
339A ARG* 3.3 26.9 + - - +
601A ANP 4.1 5.0 + - - -
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Residues in contact with TYR 336 (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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330A LYS* 4.1 45.0 + - + +
332A ASN 3.1 16.6 + - - +
333A LEU* 3.7 7.2 - - + +
334A GLN 3.3 0.2 - - - -
335A GLU* 1.3 76.9 - - - +
337A LEU* 1.4 63.8 + - + +
339A ARG* 3.2 2.1 + - - -
340A HIS* 2.9 71.3 + + + +
342A ILE* 3.9 27.2 - - + +
346A ASP* 5.0 2.9 + - - -
350A LEU* 5.2 1.1 - - + -
387A VAL* 3.9 20.2 - - + -
391A LEU* 3.4 35.9 - - + +
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Residues in contact with LEU 337 (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 LEU* 2.9 49.4 + - + +
334A GLN 4.0 1.3 - - - +
336A TYR* 1.4 73.7 - - + +
338A THR* 1.3 56.7 + - - +
340A HIS 3.0 7.4 - - - +
342A ILE* 4.3 25.4 - - + -
350A LEU* 5.1 0.9 - - + -
456A GLU* 3.5 41.3 - - + +
457A MET* 3.7 13.9 - - + +
460A ARG* 2.8 49.0 + - + -
470A TYR* 3.7 20.4 - - + +
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Residues in contact with THR 338 (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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334A GLN* 2.7 24.3 + - - +
335A GLU* 3.6 10.4 - - - -
336A TYR 3.2 0.2 - - - -
337A LEU* 1.3 76.9 - - - +
339A ARG* 1.3 61.4 + - + +
460A ARG* 3.6 9.4 + - - -
470A TYR* 3.1 33.4 + - + +
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Residues in contact with ARG 339 (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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335A GLU 3.3 14.0 + - - +
336A TYR* 3.2 2.0 + - - -
338A THR* 1.3 82.5 - - + +
340A HIS* 1.3 81.7 + - + +
341A VAL* 5.8 0.2 - - - +
460A ARG* 4.0 5.0 + - - -
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Residues in contact with HIS 340 (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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336A TYR* 2.9 70.8 + + + +
337A LEU* 3.0 22.3 - - - +
339A ARG* 1.3 92.7 + - + +
341A VAL* 1.3 66.1 + - - +
342A ILE* 4.1 3.9 + - + +
460A ARG* 3.1 14.4 + - - +
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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