Contacts of the helix formed by residues 420 - 427 (chain A) in PDB entry 3TVX
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 SER 420 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A HIS* 5.4 0.7 - - - -
419A VAL* 1.3 78.0 - - - +
421A ASN* 1.3 65.2 + - - +
422A GLN* 3.7 9.8 + - - +
423A PHE* 3.2 19.1 + - - +
424A LEU* 3.3 13.2 + - - +
441A LEU* 4.0 4.9 - - - -
555A GLN* 3.1 28.9 + - - -
567A SER* 4.4 2.9 + - - -
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Residues in contact with ASN 421 (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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420A SER* 1.3 73.9 - - - +
422A GLN* 1.3 57.8 + - - +
424A LEU* 2.9 24.0 + - - +
425A ILE* 2.9 27.1 + - + +
437A ASP 5.9 0.7 - - - +
439A SER* 4.1 1.6 - - - +
440A VAL* 3.4 15.4 - - + +
441A LEU* 2.8 40.8 + - - +
442A GLU* 3.1 28.1 + - - -
484A ASP* 4.1 13.5 + - - -
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Residues in contact with GLN 422 (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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420A SER* 3.3 9.4 + - - +
421A ASN* 1.3 78.8 - - - +
423A PHE* 1.3 57.7 + - - +
425A ILE* 3.9 26.5 - - - +
426A ASN* 2.9 65.8 + - - +
567A SER* 5.1 7.9 - - - +
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Residues in contact with PHE 423 (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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419A VAL* 3.7 28.5 - - + -
420A SER* 3.2 13.0 + - - +
422A GLN* 1.3 80.0 - - - +
424A LEU* 1.3 53.8 + - + +
426A ASN* 3.4 1.3 + - - +
427A THR* 2.7 54.6 + - + +
555A GLN* 3.9 16.1 - - + +
558A ARG* 4.2 28.9 - - + -
559A GLU* 3.6 43.0 + - + +
562A ARG* 3.9 27.6 - - - -
564A MET* 3.7 20.9 - - + -
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Residues in contact with LEU 424 (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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417A PRO* 4.6 8.7 - - + -
419A VAL* 4.1 18.8 - - + -
420A SER 3.3 10.5 + - - +
421A ASN* 2.9 9.0 + - - +
423A PHE* 1.3 79.6 - - + +
425A ILE* 1.3 60.3 + - - +
427A THR* 3.2 6.6 + - - +
429A SER* 3.0 50.8 + - - +
431A LEU* 4.4 13.0 - - + -
432A ALA* 3.5 7.9 - - + +
440A VAL* 4.1 18.6 - - + -
441A LEU* 3.7 36.6 - - + -
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Residues in contact with ILE 425 (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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421A ASN* 2.9 31.4 + - + +
422A GLN* 3.7 29.6 - - - +
424A LEU* 1.3 76.3 - - - +
426A ASN* 1.3 67.2 + - - +
428A ASN* 3.1 15.8 + - - +
432A ALA* 3.9 10.5 - - + +
437A ASP* 3.3 59.6 - - + +
440A VAL* 4.4 3.8 - - + -
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Residues in contact with ASN 426 (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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422A GLN* 2.9 48.3 + - - +
423A PHE* 4.0 0.4 - - - +
425A ILE* 1.3 76.9 - - - +
427A THR* 1.3 61.3 + - - +
428A ASN* 3.1 2.1 + - - +
559A GLU* 5.1 3.4 + - - -
564A MET* 3.8 31.5 - - + +
565A GLU 5.4 4.2 + - - -
567A SER* 5.9 0.4 + - - -
456B ASP* 3.8 15.8 - - - +
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Residues in contact with THR 427 (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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423A PHE* 2.7 46.4 + - + +
424A LEU* 3.2 14.0 + - - +
426A ASN* 1.3 73.1 - - - +
428A ASN* 1.3 65.7 + - - +
429A SER* 3.4 6.4 + - - -
562A ARG* 3.7 26.5 - - - +
564A MET* 4.5 11.4 - - - -
455B GLU* 3.3 19.8 + - - +
456B ASP* 3.0 24.8 + - - -
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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