Contacts of the helix formed by residues 438 - 445 (chain A) in PDB entry 6RUT
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 GLY 438 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A THR* 1.3 75.2 - - - +
439A TYR* 1.4 65.1 + - - -
440A LYS 3.4 2.2 - - - -
441A ASP* 3.1 6.1 + - - -
442A LEU* 3.1 20.4 + - - +
532A GLU* 2.8 17.3 + - - -
675A ASN* 3.4 30.1 - - - -
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Residues in contact with TYR 439 (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 GLU* 6.1 1.1 - - + -
352A GLN* 4.1 9.5 + - - -
438A GLY* 1.4 68.6 - - - -
440A LYS* 1.3 66.6 + - - +
442A LEU* 3.1 11.9 + - + +
443A VAL* 3.1 55.7 + - + +
532A GLU* 4.6 3.4 + - - -
535A PRO* 5.7 4.3 - - + -
574A GLN* 5.6 0.9 - - - -
575A SER 3.6 15.6 + - - -
576A ARG* 3.6 33.4 + - - -
577A TYR 4.9 1.0 + - - -
674A ASN 3.9 4.5 - - - +
675A ASN 2.8 17.9 + - - +
676A ILE 4.9 0.4 - - - -
677A ALA* 3.4 32.5 - - + +
678A PRO* 3.5 25.8 - - + -
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Residues in contact with LYS 440 (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 GLU* 3.5 37.4 + - - +
438A GLY 3.4 0.6 - - - -
439A TYR* 1.3 79.8 - - - +
441A ASP* 1.3 62.6 + - - +
443A VAL* 3.4 6.9 + - - +
444A THR* 2.8 45.2 + - + +
674A ASN* 3.3 46.3 + - + +
675A ASN* 5.7 0.2 - - - -
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Residues in contact with ASP 441 (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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435A SER* 3.7 4.2 + - - -
436A LYS* 3.6 48.8 + - + +
437A THR 3.9 7.1 - - - +
438A GLY 3.1 6.2 + - - +
440A LYS* 1.3 84.1 - - - +
442A LEU* 1.3 62.7 + - - +
444A THR* 4.1 7.3 + - - -
445A ASN* 3.3 22.7 + - - +
674A ASN* 6.0 0.5 - - - +
675A ASN* 4.4 9.0 - - - +
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Residues in contact with LEU 442 (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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431A THR* 2.7 41.0 + - + +
435A SER* 3.6 11.9 - - - +
436A LYS 3.4 18.2 - - - +
437A THR* 4.5 4.3 - - + -
438A GLY 3.1 15.1 + - - +
439A TYR* 3.1 11.2 + - + +
441A ASP* 1.3 76.7 - - - +
443A VAL* 1.3 62.2 + - + +
445A ASN* 3.4 8.3 - - - +
526A ASN* 5.6 0.9 - - - +
532A GLU* 3.4 43.5 - - + +
533A ARG 4.2 13.7 - - - +
534A LEU* 4.0 15.5 - - + -
535A PRO* 4.1 13.7 - - + -
537A ARG* 3.8 0.9 + - - -
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Residues in contact with VAL 443 (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 GLU* 4.2 9.2 - - + -
351A LYS* 4.7 1.4 - - - +
352A GLN* 3.7 41.8 - - + +
355A PHE* 4.6 4.0 - - - -
431A THR* 4.8 0.2 - - - -
439A TYR* 3.1 48.7 + - + +
440A LYS* 3.4 16.6 - - - +
442A LEU* 1.3 78.5 - - - +
444A THR* 1.4 56.2 + - - +
445A ASN 3.3 0.4 - - - -
535A PRO* 4.1 20.0 - - + -
536A SER 6.0 0.2 - - - +
537A ARG* 2.7 29.5 + - - +
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Residues in contact with THR 444 (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 GLU* 4.1 23.6 - - + +
351A LYS* 3.4 36.5 - - + +
440A LYS* 2.8 48.1 + - + +
441A ASP* 3.7 7.5 + - - -
442A LEU 3.4 0.2 - - - -
443A VAL* 1.4 78.0 - - - +
445A ASN* 1.4 64.4 + - - +
446A ASP* 3.4 4.3 + - - +
537A ARG* 4.1 0.2 - - - -
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Residues in contact with ASN 445 (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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355A PHE* 3.2 5.0 - - - -
431A THR* 3.8 4.9 - - + -
432A SER* 3.3 11.4 + - - -
435A SER* 3.2 30.1 + - - +
436A LYS 5.0 0.4 - - - +
441A ASP 3.3 10.7 + - - +
442A LEU 3.4 16.4 - - - +
443A VAL 3.3 1.6 - - - -
444A THR* 1.4 74.3 - - - +
446A ASP* 1.3 58.2 + - - +
447A THR* 2.6 38.2 + - - -
470A SER* 3.9 11.5 + - - -
537A ARG* 2.7 34.4 + - - +
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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