Contacts of the helix formed by residues 344 - 349 (chain A) in PDB entry 3U7U
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 LEU 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A GLN* 3.6 35.7 - - + +
322A THR* 2.8 26.6 + - + +
342A ILE* 3.8 16.6 - - + -
343A PHE* 1.3 72.0 - - - +
345A VAL* 1.3 66.6 + - - +
346A THR* 3.3 12.8 - - - +
347A GLY 3.0 9.9 + - - -
348A ILE* 3.3 8.8 + - - +
378A ASN* 4.7 0.7 - - - +
380A GLN* 3.5 35.4 - - + +
381A SER* 3.3 9.1 - - - -
404A TYR* 6.5 0.4 - - + -
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 1.3 72.3 - - - +
346A THR* 1.3 60.3 + - + +
347A GLY 3.2 1.4 + - - -
348A ILE 3.4 0.2 + - - -
349A HIS* 2.9 47.8 + - + +
380A GLN* 4.1 22.6 + - + +
381A SER* 3.5 9.3 - - - +
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Residues in contact with THR 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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322A THR* 4.5 5.6 - - - +
324A ASP* 5.0 3.1 - - - +
344A LEU* 3.3 13.0 - - - +
345A VAL* 1.3 74.7 + - + +
347A GLY* 1.3 59.7 + - - +
350A GLY* 3.2 40.7 - - - +
351A ASP* 3.4 30.2 + - + +
352A PRO* 5.3 1.3 - - + -
356A ILE* 5.2 1.2 - - - +
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Residues in contact with GLY 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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322A THR* 3.6 14.5 - - - +
323A VAL 3.3 24.7 - - - -
324A ASP* 4.0 12.4 - - - +
325A SER 4.7 0.2 + - - -
344A LEU 3.0 10.6 + - - -
346A THR* 1.3 79.1 - - - +
348A ILE* 1.3 64.4 + - - +
350A GLY* 3.9 3.5 + - - -
357A GLU 4.8 0.7 - - - +
359A ILE* 3.8 19.1 + - - +
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Residues in contact with ILE 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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323A VAL 5.7 0.2 - - - +
343A PHE* 4.1 24.7 - - + -
344A LEU 3.3 4.7 + - - +
347A GLY* 1.3 76.9 - - - +
349A HIS* 1.3 79.0 + - + +
350A GLY 3.4 0.9 - - - -
358A ALA* 3.3 5.0 - - - +
359A ILE* 3.2 43.5 + - + +
364A LEU* 4.4 5.2 - - + -
381A SER* 3.3 38.4 - - - +
382A TRP* 3.6 5.4 - - + -
383A PRO* 3.5 42.6 - - + -
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Residues in contact with HIS 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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345A VAL* 2.9 28.3 + - + +
348A ILE* 1.3 88.6 + - + +
350A GLY* 1.3 62.9 + - - +
352A PRO* 5.3 1.9 - - - +
358A ALA* 3.5 14.9 - - - +
381A SER* 3.3 22.2 + - - -
382A TRP 4.2 5.9 + - - -
384A PRO* 4.1 28.9 - - + +
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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