Contacts of the helix formed by residues 432 - 444 (chain A) in PDB entry 2XT6
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 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A VAL* 4.0 29.4 - - + -
373A LEU* 5.2 1.1 - - + -
405A VAL* 4.8 2.2 - - + -
410A LEU* 4.2 26.9 - - + -
411A THR 4.8 1.8 - - - +
414A ASP* 3.4 42.0 - - + +
415A LEU* 3.4 6.8 + - + +
417A ARG 3.1 9.3 + - - -
419A PHE* 3.8 10.7 - - + -
430A LYS 3.5 2.2 + - - -
431A LYS* 1.4 68.9 - - - +
433A ARG* 1.3 53.0 + - - +
435A ILE* 3.1 13.1 + - + +
436A LEU* 2.8 69.3 + - + +
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Residues in contact with ARG 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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134A LYS* 3.9 1.6 - - - +
137A ILE* 5.8 1.2 - - - +
138A ASP* 2.9 30.7 + - - +
141A VAL* 4.8 25.2 - - + +
415A LEU* 2.9 51.2 + - + +
416A ASP* 2.6 45.5 + - - +
431A LYS* 4.8 6.6 - - + +
432A LEU* 1.3 77.0 - - - +
434A ASP* 1.4 66.2 + - - +
436A LEU* 3.5 3.5 + - - +
437A SER* 3.0 30.0 + - - +
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Residues in contact with ASP 434 (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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430A LYS* 5.3 8.8 - - + +
431A LYS* 2.8 42.3 + - - +
433A ARG* 1.4 79.2 - - - +
435A ILE* 1.4 65.8 + - - +
437A SER* 3.1 8.3 + - - -
438A VAL* 3.0 34.1 + - + +
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Residues in contact with ILE 435 (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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370A VAL* 4.1 17.7 - - + -
374A ILE* 3.9 28.5 - - + -
419A PHE* 4.2 5.6 - - + -
421A VAL* 3.7 27.4 - - + -
430A LYS* 3.7 37.0 - - + +
431A LYS 3.0 11.6 + - - +
432A LEU* 3.4 18.8 - - + +
434A ASP* 1.4 76.0 - - - +
436A LEU* 1.3 58.3 + - + +
438A VAL* 3.8 5.2 - - - +
439A LEU* 3.0 39.5 + - + +
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Residues in contact with LEU 436 (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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373A LEU* 3.8 27.4 - - + -
377A TYR* 4.8 10.4 - - + +
405A VAL* 4.1 27.6 - - + -
415A LEU* 3.9 18.2 - - + -
432A LEU* 2.8 43.7 + - + +
433A ARG* 3.8 4.0 - - - +
435A ILE* 1.3 71.5 - - + +
437A SER* 1.3 59.2 + - - +
439A LEU* 3.4 16.9 + - + +
440A ARG* 3.0 28.9 + - - +
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Residues in contact with SER 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASN* 4.6 17.5 - - - -
433A ARG* 3.0 17.1 + - - +
434A ASP* 3.1 18.4 + - - -
436A LEU* 1.3 72.8 - - - +
438A VAL* 1.3 60.6 + - - +
440A ARG* 3.3 5.4 + - - +
441A ASP* 2.9 42.7 + - - +
445A ARG* 5.9 2.7 - - - +
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Residues in contact with VAL 438 (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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434A ASP* 3.0 25.3 + - + +
435A ILE* 3.8 4.7 - - - +
437A SER* 1.3 76.9 - - - +
439A LEU* 1.4 57.5 + - + +
441A ASP* 3.4 8.9 + - - +
442A ALA* 3.0 29.7 + - + +
468A GLU* 3.3 44.2 - - + +
470A LYS* 6.6 0.4 - - + -
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Residues in contact with LEU 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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373A LEU* 4.8 1.3 - - + -
374A ILE* 4.0 31.9 - - + +
377A TYR* 3.8 50.6 - - + -
378A ARG* 5.9 0.2 - - - +
435A ILE* 3.0 38.7 + - + +
436A LEU* 3.7 13.2 - - + +
437A SER 3.3 0.2 - - - -
438A VAL* 1.4 76.4 - - + +
440A ARG* 1.4 55.9 + - - +
442A ALA* 4.6 0.2 - - - -
443A TYR* 2.9 54.0 + - + +
444A CYS 3.9 0.2 + - - -
468A GLU* 4.8 9.4 - - + +
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Residues in contact with ARG 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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142A VAL* 3.6 35.2 + - - +
146A HIS* 6.3 0.6 - - - +
350A TYR* 3.3 57.9 - - + +
351A GLU 4.4 8.9 + - - +
377A TYR* 4.6 9.7 + - + -
436A LEU 3.0 17.4 + - - +
437A SER* 3.7 7.2 - - - +
438A VAL 3.3 0.2 - - - -
439A LEU* 1.4 74.3 - - - +
441A ASP* 1.3 61.6 + - - +
444A CYS* 2.9 32.7 + - + +
445A ARG* 3.2 42.6 + - + +
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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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149A ARG* 3.8 38.1 + - - +
437A SER* 2.9 25.7 + - - +
438A VAL* 3.7 7.6 - - - +
440A ARG* 1.3 75.0 - - - +
442A ALA* 1.3 58.8 + - - +
445A ARG* 2.9 51.1 + - - +
447A VAL* 5.5 3.1 + - - +
471A HIS* 5.5 4.0 + - - +
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Residues in contact with ALA 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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438A VAL 3.0 16.9 + - - +
441A ASP* 1.3 77.5 - - - +
443A TYR* 1.3 80.4 + - + +
447A VAL* 3.6 14.7 - - - +
449A VAL* 3.7 11.1 - - - +
467A VAL* 3.3 40.4 - - + +
468A GLU* 4.2 6.5 - - + -
471A HIS* 6.0 1.1 - - - -
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Residues in contact with TYR 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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377A TYR* 3.8 24.7 - - + +
378A ARG* 3.8 17.7 - - + -
381A GLY* 3.3 24.7 - - - +
382A HIS* 3.8 4.0 + - - +
385A ALA* 3.4 10.9 - - - +
439A LEU* 2.9 37.9 + - + +
442A ALA* 1.3 87.3 - - + +
444A CYS* 1.3 61.9 + - - +
447A VAL 3.6 10.1 - - - +
448A GLY* 4.3 0.3 - - - -
449A VAL* 4.1 19.7 - - + +
451A TYR* 2.8 35.7 + + - -
464A GLN* 4.4 1.2 - - - +
467A VAL* 3.7 24.1 - - + +
468A GLU* 2.5 32.6 + - + +
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Residues in contact with CYS 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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350A TYR* 2.7 38.0 + - + -
377A TYR* 3.6 36.3 - - + -
381A GLY* 3.4 23.3 - - - -
384A MET* 4.5 17.9 - - + +
385A ALA* 3.6 11.5 - - - +
386A ASP 3.5 7.4 + - - -
403A LEU* 5.2 0.2 - - - -
440A ARG* 2.9 17.9 + - + +
443A TYR* 1.3 78.5 - - - +
445A ARG* 1.4 58.9 + - - +
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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