Contacts of the helix formed by residues 436 - 447 (chain A) in PDB entry 1XC5
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 GLU 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A LYS 4.0 9.7 - - - +
425A ASP* 2.8 23.7 - - - +
427A GLN* 5.6 2.6 - - - +
428A VAL* 3.4 11.8 - - + +
431A MET 4.5 2.0 - - - +
433A SER* 3.0 33.7 + - - +
435A GLN* 1.3 90.2 - - - +
437A LYS* 1.3 53.1 + - - +
438A GLU 2.6 14.8 + - - -
439A THR* 2.7 18.0 + - - -
440A PHE* 2.8 35.1 - - + -
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Residues in contact with LYS 437 (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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432A TRP* 3.0 35.7 - - + +
433A SER* 2.6 28.0 + - - +
434A GLU* 3.5 25.2 + - - +
436A GLU* 1.3 70.1 - - - +
438A GLU* 1.3 51.5 + - - +
439A THR 3.1 0.2 - - - -
440A PHE* 2.8 12.8 - - - -
441A ARG* 2.6 56.9 + - + +
469A TYR* 3.7 11.7 - - + +
473A THR* 3.2 39.8 + - + +
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Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLU 3.5 8.9 + - - +
435A GLN* 2.8 51.7 + - - +
436A GLU 2.6 4.9 + - - -
437A LYS* 1.3 76.2 - - - +
439A THR* 1.3 55.6 + - - +
441A ARG* 4.6 2.0 - - - +
442A GLU* 2.9 37.2 + - - +
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Residues in contact with THR 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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421A LYS* 3.0 52.1 - - + +
425A ASP* 3.7 14.7 + - - +
435A GLN 4.7 3.5 + - - -
436A GLU 2.7 16.1 + - - -
438A GLU* 1.3 72.6 - - - +
440A PHE* 1.3 65.5 + - + +
441A ARG 3.2 0.2 - - - -
442A GLU* 3.2 6.8 + - - +
443A LYS* 3.1 29.2 + - + +
457A PHE* 3.2 16.6 - - + -
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Residues in contact with PHE 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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425A ASP* 3.0 31.4 - - + -
428A VAL* 3.0 25.8 - - + -
432A TRP* 3.1 32.1 - + + -
436A GLU* 2.8 37.7 - - + -
437A LYS* 2.8 22.2 - - - -
439A THR* 1.3 75.5 - - + +
441A ARG* 1.3 59.9 + - - +
444A PHE* 3.1 6.8 + - - +
454A ILE* 3.0 36.4 - - + +
457A PHE* 3.9 9.2 - - - -
458A LEU* 3.2 30.7 - - + -
461A LYS* 5.2 1.1 - - + -
469A TYR* 3.3 13.2 - + + -
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Residues in contact with ARG 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LYS* 2.6 40.7 + - - +
438A GLU* 4.6 2.2 - - - +
440A PHE* 1.3 74.1 - - - +
442A GLU* 1.3 50.0 + - - +
444A PHE* 4.1 4.0 - - + +
445A MET* 2.7 73.3 + - + +
469A TYR* 2.7 26.6 + - - +
473A THR* 5.8 3.1 - - - +
479A TYR* 3.3 41.8 + - - -
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Residues in contact with GLU 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 GLU* 2.9 27.7 + - - +
439A THR* 3.2 7.6 + - - +
441A ARG* 1.3 78.4 - - - +
443A LYS* 1.3 68.1 + - - +
445A MET* 3.5 5.3 - - - +
446A GLN* 2.6 56.9 + - - +
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Residues in contact with LYS 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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421A LYS* 5.8 4.0 - - + +
439A THR* 3.1 13.7 + - - +
442A GLU* 1.3 96.8 + - - +
444A PHE* 1.3 56.8 + - - +
446A GLN* 4.1 14.2 + - - +
447A HIS* 2.6 48.1 + - + +
453A LEU* 3.3 20.0 - - + -
454A ILE* 3.8 6.3 - - + -
457A PHE* 3.0 57.2 - - + -
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Residues in contact with PHE 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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440A PHE 3.1 19.6 + - - +
441A ARG* 4.1 5.4 - - + +
443A LYS* 1.3 76.7 - - - +
445A MET* 1.3 66.9 + - + +
447A HIS 2.9 19.4 - - - +
448A PRO* 3.7 2.9 - - - +
449A LYS* 4.1 39.7 - - + -
450A ASN* 3.7 16.8 - - - -
451A PHE* 3.2 42.4 - + + -
454A ILE* 3.5 10.7 - - + +
469A TYR* 5.6 9.2 - + + +
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Residues in contact with MET 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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441A ARG* 2.7 60.4 + - + +
442A GLU* 3.5 6.5 - - - +
444A PHE* 1.3 82.3 - - + +
446A GLN* 1.3 64.8 + - - +
448A PRO* 3.7 9.9 - - - +
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Residues in contact with GLN 446 (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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442A GLU* 2.6 43.5 + - - +
443A LYS* 3.6 16.5 + - - +
445A MET* 1.3 73.9 - - - +
447A HIS* 1.3 69.0 + - + +
448A PRO* 2.8 17.2 - - - +
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Residues in contact with HIS 447 (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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443A LYS* 2.6 34.8 + - - +
444A PHE 2.9 8.7 - - - +
446A GLN* 1.3 86.1 + - + +
448A PRO* 1.3 65.5 - - - +
450A ASN* 2.5 52.2 + - + +
453A LEU* 2.9 51.8 - - + +
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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