Contacts of the helix formed by residues 424 - 433 (chain A) in PDB entry 6TXC
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 ASP 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A TYR 3.1 15.7 + - - +
147A ILE* 3.6 5.4 - - - -
148A LYS* 2.9 55.0 + - - +
212A PRO* 3.5 1.6 - - - +
213A PHE* 2.7 47.3 + - + -
423A THR* 1.3 70.2 - - - +
425A ASN* 1.3 65.4 + - - +
426A ILE 3.0 3.9 + - - -
427A PHE* 3.1 21.4 + - - +
428A LEU* 4.0 3.1 + - - +
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Residues in contact with ASN 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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146A TYR 4.5 0.6 + - - -
421A LYS 5.4 0.6 + - - +
423A THR* 3.1 18.3 + - - +
424A ASP* 1.3 77.0 - - - +
426A ILE* 1.3 65.1 + - + +
428A LEU* 2.9 8.7 + - - +
429A GLU* 2.9 44.7 + - - +
425B ASN* 2.6 35.0 + - - +
428B LEU* 3.7 23.8 + - + +
429B GLU* 4.7 4.4 + - - +
432B TYR* 3.9 29.2 - - + -
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Residues in contact with ILE 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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212A PRO* 4.5 4.7 - - + -
390A PHE* 3.0 42.8 - - + -
397A ILE* 4.1 23.6 - - + -
399A ILE* 4.6 6.3 - - + -
409A ILE* 3.9 21.8 - - + -
421A LYS 5.9 1.3 - - - +
422A LEU* 3.9 21.3 - - + -
423A THR 3.2 15.1 + - - +
424A ASP 3.0 1.8 - - - +
425A ASN* 1.3 81.0 - - - +
427A PHE* 1.3 62.8 + - - +
429A GLU* 3.3 21.7 + - - +
430A ILE* 3.0 30.1 + - + +
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Residues in contact with PHE 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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155A TYR* 3.8 20.6 - + - -
213A PHE* 3.7 27.1 - + + -
386A ILE* 3.9 23.8 - - + -
390A PHE* 4.4 4.5 - - + -
424A ASP 3.1 13.9 + - - +
426A ILE* 1.3 81.6 - - - +
428A LEU* 1.3 74.7 + - + +
430A ILE* 4.8 0.2 - - - -
431A LEU* 3.0 34.1 + - + +
445A LEU* 3.1 55.9 - - + +
448A ILE* 4.8 8.7 - - + -
449A GLU* 5.8 2.7 - - + -
146B TYR* 3.5 26.2 - + - -
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Residues in contact with LEU 428 (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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424A ASP 5.1 2.7 - - - +
425A ASN* 2.9 6.5 + - - +
427A PHE* 1.3 93.2 - - + +
429A GLU* 1.3 60.6 + - - +
431A LEU* 4.1 9.9 - - + -
432A TYR* 2.9 60.1 + - + +
146B TYR* 3.8 46.4 - - + -
423B THR* 4.2 2.2 - - - +
425B ASN* 3.6 39.3 - - + +
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Residues in contact with GLU 429 (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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397A ILE* 4.1 28.8 - - + +
398A GLU 5.0 4.2 + - - +
399A ILE* 6.1 0.3 - - - +
425A ASN* 2.9 31.2 + - - +
426A ILE* 3.3 22.9 + - + +
428A LEU* 1.3 75.3 - - - +
430A ILE* 1.3 61.7 + - - +
432A TYR* 4.0 2.3 - - - +
433A SER* 3.2 24.8 + - - -
438A LEU* 5.4 0.6 - - - +
425B ASN* 4.7 5.1 - - - +
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Residues in contact with ILE 430 (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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389A ALA 4.4 3.6 - - - +
390A PHE* 3.8 30.7 - - + -
393A ALA* 3.8 20.6 - - + -
397A ILE* 3.6 23.3 - - + -
409A ILE* 4.9 1.3 - - + -
426A ILE* 3.0 22.4 + - + +
427A PHE 3.5 5.8 - - - +
429A GLU* 1.3 75.9 - - - +
431A LEU* 1.3 61.6 + - - +
433A SER* 2.7 25.8 + - - +
438A LEU* 5.0 3.8 - - + +
441A ALA* 3.9 11.0 - - + -
442A ARG* 3.7 29.7 - - - +
445A LEU* 3.6 17.5 - - + -
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Residues in contact with LEU 431 (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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427A PHE* 3.0 26.1 + - + +
428A LEU* 3.3 19.7 + - + +
430A ILE* 1.3 77.4 - - - +
432A TYR* 1.3 79.4 + - + +
442A ARG* 3.3 23.2 - - - +
445A LEU* 4.0 28.9 - - + +
446A LYS* 4.1 28.7 - - + +
449A GLU* 3.7 31.0 - - + +
146B TYR* 5.0 1.6 - - + -
421B LYS* 5.3 2.1 - - - +
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Residues in contact with TYR 432 (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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428A LEU* 2.9 42.9 + - + +
429A GLU* 4.0 2.5 - - - +
431A LEU* 1.3 95.2 - - + +
433A SER* 1.3 65.5 + - - +
434A THR* 3.8 2.3 + - - +
143B ARG* 5.6 0.7 - - - -
146B TYR* 4.2 5.2 - - - -
420B THR 4.4 3.2 + - - -
421B LYS* 3.3 74.1 + - + +
423B THR* 3.1 37.7 + - - +
425B ASN* 3.9 25.1 - - + -
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Residues in contact with SER 433 (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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429A GLU* 3.2 17.5 + - - -
430A ILE 2.7 19.6 + - - -
431A LEU 3.3 1.0 - - - -
432A TYR* 1.3 81.9 - - - +
434A THR* 1.3 60.7 + - - +
435A ASP 4.4 0.9 - - - -
438A LEU* 3.5 28.1 - - - +
442A ARG* 2.7 42.3 + - - -
421B LYS* 5.3 0.3 + - - -
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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