Contacts of the helix formed by residues 421 - 436 (chain A) in PDB entry 1XJD
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 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A PHE* 4.6 13.9 - - + +
416A VAL* 2.9 16.7 + - + +
419A ASP* 2.5 39.5 + - + +
420A ASP* 1.3 79.1 - - - +
422A VAL* 1.3 64.1 + - - +
423A GLU 3.3 2.7 - - - +
424A CYS* 3.7 27.2 - - + -
425A THR* 3.2 24.4 + - - +
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Residues in contact with VAL 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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416A VAL* 4.0 13.0 - - + +
417A LEU* 3.7 21.1 - - + -
420A ASP* 3.4 6.2 + - - -
421A ASP* 1.3 78.8 - - - +
423A GLU* 1.3 60.4 + - - +
425A THR* 2.7 23.8 + - - +
426A MET* 3.4 13.6 + - + +
690A MET* 4.0 28.5 - - + +
691A PHE* 3.5 40.8 - - + -
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Residues in contact with GLU 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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420A ASP 5.3 0.4 + - - -
421A ASP* 3.3 0.4 - - - +
422A VAL* 1.3 74.0 - - - +
424A CYS* 1.3 62.6 + - - +
425A THR 3.1 2.2 - - - -
426A MET* 3.0 16.6 + - - +
427A VAL* 2.8 39.0 + - + +
430A ARG* 2.5 34.2 + - - -
528A GLU* 4.6 0.2 - - - +
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Residues in contact with CYS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PHE* 3.1 28.9 - - + -
420A ASP 5.7 0.2 - - - -
421A ASP* 3.3 28.3 + - + +
422A VAL 3.3 0.4 - - - -
423A GLU* 1.3 79.5 - - - +
425A THR* 1.3 60.4 + - - +
427A VAL* 3.4 12.2 + - - +
428A GLU* 3.3 16.8 + - - +
524A GLY 4.2 15.9 - - - +
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Residues in contact with THR 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PHE* 3.1 28.9 - - + -
411A LEU* 4.1 11.0 - - + -
416A VAL* 4.0 19.0 - - + +
421A ASP* 3.2 16.4 - - + +
422A VAL* 2.7 20.4 + - - +
423A GLU 3.1 0.2 - - - -
424A CYS* 1.3 74.1 - - - +
426A MET* 1.3 72.4 + - - +
428A GLU* 3.5 0.7 + - - +
429A LYS* 3.2 21.8 + - - +
454A LEU* 4.2 17.6 - - + +
456A PHE* 3.7 13.0 - - - -
691A PHE* 5.1 1.0 - - - -
694A PHE* 4.6 3.8 - - - -
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Residues in contact with MET 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 VAL* 3.4 19.5 - - + +
423A GLU* 3.0 17.6 + - - +
425A THR* 1.3 81.7 + - - +
427A VAL* 1.3 66.4 + - - +
429A LYS* 3.3 21.9 + - + +
430A ARG* 2.9 48.6 + - - +
691A PHE* 6.3 4.0 - - - -
692A ARG 5.9 2.7 - - - +
693A ASN 5.6 2.2 - - - +
694A PHE* 4.1 28.0 - - + -
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Residues in contact with VAL 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 GLU* 2.8 31.3 + - + +
424A CYS* 3.5 12.6 - - - +
426A MET* 1.3 76.3 - - - +
428A GLU* 1.3 59.0 + - - +
430A ARG* 3.0 24.9 + - - +
431A VAL* 2.9 28.1 + - + +
523A PHE 3.9 13.5 - - - +
524A GLY 4.9 2.5 - - - +
526A CYS* 3.6 33.7 - - + +
528A GLU* 3.8 16.2 - - - +
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Residues in contact with GLU 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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200A STU 3.9 7.0 - - - -
391A PHE* 3.2 13.9 - - + -
409A LYS* 2.5 45.8 + - - +
424A CYS 3.3 10.5 + - - +
425A THR 3.9 7.0 - - - +
426A MET 3.3 0.2 - - - -
427A VAL* 1.3 79.5 - - - +
429A LYS* 1.3 58.4 + - - +
431A VAL* 3.3 1.0 + - - +
432A LEU* 2.8 48.5 + - + +
456A PHE* 4.0 6.2 - - + -
522A ASP* 3.7 5.5 + - - -
523A PHE* 3.3 30.4 + - + +
524A GLY* 4.0 14.9 + - - +
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Residues in contact with LYS 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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425A THR 3.2 12.7 + - - +
426A MET* 3.6 22.8 - - + +
427A VAL 3.3 0.2 - - - -
428A GLU* 1.3 78.0 - - - +
430A ARG* 1.3 58.8 + - - +
432A LEU* 3.5 3.9 + - - -
433A SER* 3.0 33.8 + - - +
444A MET* 3.6 15.5 - - + +
447A THR* 4.3 3.4 - - + +
456A PHE* 3.8 15.9 - - + -
693A ASN 3.6 15.6 + - - -
694A PHE* 3.0 42.7 + - + +
695A SEP 3.9 0.6 + - - -
696A PHE* 3.8 32.0 - - - +
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Residues in contact with ARG 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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423A GLU* 2.5 32.5 + - - -
426A MET* 2.9 41.1 + - - +
427A VAL* 3.3 14.3 - - - +
429A LYS* 1.3 75.3 - - - +
431A VAL* 1.3 59.4 + - - +
433A SER* 3.2 7.7 + - - -
434A LEU* 3.0 25.8 + - - +
528A GLU* 2.9 37.5 + - - +
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Residues in contact with VAL 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 VAL* 2.9 25.4 + - + +
430A ARG* 1.3 72.6 - - - +
432A LEU* 1.3 61.5 + - - +
434A LEU* 3.1 8.5 + - + +
435A ALA* 2.8 28.3 + - + +
495A LEU* 4.0 21.5 - - + -
500A ILE* 4.1 15.5 - - + -
523A PHE* 3.5 39.5 - - + -
526A CYS* 4.1 25.4 - - + -
528A GLU* 4.3 8.5 - - - +
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Residues in contact with LEU 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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200A STU 6.1 0.2 - - + -
428A GLU* 2.8 32.1 + - + +
429A LYS 3.7 3.6 - - - +
431A VAL* 1.3 77.2 - - - +
433A SER* 1.3 62.6 + - - +
435A ALA* 3.4 15.0 + - - +
436A TRP* 3.7 6.1 + - - +
442A THR* 3.6 24.0 - - - +
444A MET* 3.8 39.0 + - + +
456A PHE* 3.7 30.5 - - + -
458A MET* 4.1 29.6 - - + -
522A ASP 5.9 1.1 - - - +
523A PHE* 3.6 22.0 - - + -
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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 LYS* 3.0 18.6 + - - +
430A ARG* 3.5 11.1 - - - -
431A VAL 3.2 0.2 - - - -
432A LEU* 1.3 76.0 - - - +
434A LEU* 1.3 64.2 + - - +
436A TRP* 3.4 18.2 + - - +
444A MET* 3.3 16.6 - - - +
696A PHE* 3.7 21.1 - - - -
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Residues in contact with LEU 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 ARG 3.0 13.4 + - - +
431A VAL* 3.4 8.5 - - - +
433A SER* 1.3 78.9 - - - +
435A ALA* 1.3 57.1 + - - +
436A TRP* 2.9 8.2 + - - +
437A GLU* 3.0 28.1 + - - +
494A PHE* 4.0 16.0 - - + -
495A LEU* 4.6 7.4 - - + -
498A LYS* 3.8 40.2 - - + +
500A ILE* 3.3 33.9 - - + -
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Residues in contact with ALA 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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431A VAL 2.8 19.5 + - - +
432A LEU* 3.6 6.1 - - - +
433A SER 3.3 0.2 - - - -
434A LEU* 1.3 67.9 - - - +
436A TRP* 1.3 64.9 + - - +
437A GLU 2.9 3.4 - - - -
438A HIS* 2.9 15.8 + - - +
441A LEU* 3.4 32.8 - - + -
442A THR 3.4 24.9 - - - +
443A HIS* 2.9 15.1 - - - -
494A PHE* 4.7 0.7 - - - -
523A PHE* 4.7 4.5 - - + -
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Residues in contact with TRP 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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432A LEU 3.7 4.3 + - - +
433A SER* 3.4 17.0 + - - +
434A LEU 2.9 1.0 + - - +
435A ALA* 1.3 77.9 - - - +
437A GLU* 1.3 62.4 + - - +
438A HIS 3.4 1.0 + - - -
443A HIS* 3.6 47.1 + + + -
444A MET 3.6 25.8 - - - -
445A PHE* 3.9 32.3 - + - -
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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