Contacts of the helix formed by residues 401 - 418 (chain A) in PDB entry 5IXC
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 SER 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A LEU 3.8 1.1 + - - -
398A GLU* 2.6 43.5 + - - +
400A PHE* 1.3 73.0 - - - +
402A PRO* 1.4 67.1 - - - +
403A GLU* 2.9 26.6 + - - +
404A ARG* 2.9 28.9 + - - +
405A LEU* 3.0 10.4 + - - +
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Residues in contact with PRO 402 (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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400A PHE 4.0 2.6 - - - +
401A SER* 1.4 85.2 - - - +
403A GLU* 1.3 64.0 + - + +
404A ARG 3.4 0.2 - - - -
405A LEU* 3.9 17.4 - - + +
406A ALA* 2.9 29.3 + - - +
588A ALA* 6.2 1.3 - - + -
284B PHE* 5.4 10.8 - - + +
285B ASN* 5.9 1.3 - - - +
662B PRO* 5.4 13.0 - - + -
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Residues in contact with GLU 403 (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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398A GLU* 4.6 10.4 - - - +
401A SER* 2.9 24.8 + - - +
402A PRO* 1.3 84.1 - - + +
404A ARG* 1.3 61.2 + - + +
406A ALA* 3.6 5.0 - - - +
407A SER* 3.3 19.4 + - - -
410A ARG* 4.8 2.1 + - - -
284B PHE 5.6 0.3 - - - +
285B ASN* 3.4 33.1 - - - +
662B PRO* 4.6 5.4 - - - +
663B GLY* 4.1 19.8 + - - -
665B ARG* 6.0 2.8 - - - -
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Residues in contact with ARG 404 (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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394A LYS* 4.0 26.8 - - - +
398A GLU* 3.4 35.4 + - - +
399A VAL* 3.3 36.5 - - - +
401A SER* 2.9 9.7 + - - +
403A GLU* 1.3 77.5 - - + +
405A LEU* 1.3 60.9 + - - +
406A ALA 3.2 0.4 - - - -
407A SER* 2.6 25.7 + - - +
408A TYR* 2.8 31.7 + - + +
434A SER* 3.7 22.2 + - - -
438A GLY* 4.5 16.2 + - - -
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Residues in contact with LEU 405 (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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399A VAL 3.9 7.0 - - - +
400A PHE* 3.9 30.1 - - - +
401A SER 3.0 18.0 + - - +
402A PRO* 3.9 12.8 - - + +
404A ARG* 1.3 75.2 - - - +
406A ALA* 1.3 63.2 + - - +
408A TYR* 3.2 14.7 + - + +
409A ARG* 3.0 25.9 + - - +
584A ALA* 3.4 30.5 - - + +
585A LEU* 3.4 27.4 - - + -
588A ALA* 3.5 21.5 - - + -
589A PHE* 3.8 6.6 - - + -
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Residues in contact with ALA 406 (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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402A PRO 2.9 21.2 + - - +
403A GLU* 3.6 7.4 - - - +
405A LEU* 1.3 76.4 - - - +
407A SER* 1.3 57.3 + - - +
409A ARG* 3.5 9.3 - - - +
410A ARG* 2.9 44.9 + - - +
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Residues in contact with SER 407 (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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403A GLU 3.3 7.0 + - - -
404A ARG* 2.6 31.8 + - - +
406A ALA* 1.3 78.7 - - - +
408A TYR* 1.3 67.2 + - - +
410A ARG* 3.5 25.9 + - - +
411A GLU* 3.2 24.9 + - - +
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Residues in contact with TYR 408 (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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399A VAL* 3.4 28.1 + - - +
404A ARG* 2.8 35.7 + - + +
405A LEU* 3.6 20.6 - - + +
406A ALA 3.2 0.4 - - - -
407A SER* 1.3 79.5 - - - +
409A ARG* 1.3 53.9 + - - +
411A GLU* 2.9 7.3 + - - +
412A LEU* 2.7 36.0 + - - +
427A LEU* 4.3 14.1 - - + -
430A LEU* 3.5 50.2 + - + +
431A VAL* 4.3 12.3 - - + -
434A SER* 3.0 32.4 + - - -
585A LEU* 5.4 0.4 - - + -
589A PHE* 4.2 11.0 - + + -
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Residues in contact with ARG 409 (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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405A LEU 3.0 10.2 + - - +
406A ALA* 3.5 14.4 - - - +
408A TYR* 1.3 75.9 - - - +
410A ARG* 1.3 60.6 + - + +
412A LEU* 3.6 5.9 - - - +
413A GLU* 2.5 73.9 + - - +
588A ALA 4.5 7.2 - - - -
589A PHE* 3.5 30.9 - - + -
591A GLY 5.6 1.0 + - - -
592A PHE* 3.5 32.3 - - + -
154B LYS* 4.1 22.9 - - - +
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Residues in contact with ARG 410 (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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403A GLU 4.8 1.8 + - - -
406A ALA* 2.9 24.5 + - - +
407A SER* 3.5 34.2 + - - +
409A ARG* 1.3 80.7 - - + +
411A GLU* 1.3 56.9 + - - +
413A GLU* 3.4 34.7 - - - +
414A LEU* 3.6 10.4 + - - +
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Residues in contact with GLU 411 (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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407A SER 3.2 14.7 + - - +
408A TYR* 2.9 9.8 + - - +
410A ARG* 1.3 76.1 - - - +
412A LEU* 1.3 60.0 + - + +
413A GLU 3.3 1.1 - - - -
414A LEU* 3.4 15.4 + - + +
415A ARG* 2.8 30.0 + - + +
430A LEU* 3.8 17.6 - - + +
440A VAL* 5.8 1.2 - - - +
519A ARG* 2.7 43.9 + - - -
522A PHE* 4.1 8.7 - - + -
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Residues in contact with LEU 412 (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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408A TYR 2.7 20.6 + - - +
409A ARG* 3.6 8.1 - - - +
411A GLU* 1.3 71.7 - - + +
413A GLU* 1.3 53.4 + - - +
415A ARG* 3.2 16.2 + - - +
416A ALA* 2.5 38.7 + - - +
422A THR* 4.7 13.9 - - + +
423A THR 5.3 4.3 - - - +
426A ASP* 4.3 21.3 - - + +
427A LEU* 4.7 14.4 - - + +
430A LEU* 3.6 24.5 - - + -
522A PHE* 5.3 0.9 - - + -
589A PHE* 3.6 26.0 - - + -
592A PHE* 4.6 15.9 - - + -
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Residues in contact with GLU 413 (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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409A ARG* 2.5 57.8 + - - +
410A ARG* 3.4 27.9 - - - +
412A LEU* 1.3 70.1 - - - +
414A LEU* 1.3 66.2 + - + +
416A ALA* 3.6 6.5 - - - +
417A GLU* 2.8 39.5 + - + +
592A PHE* 5.0 4.0 - - + -
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Residues in contact with LEU 414 (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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410A ARG 3.6 13.7 + - - +
411A GLU* 3.4 17.2 + - + +
412A LEU 3.3 0.4 - - - -
413A GLU* 1.3 82.9 - - + +
415A ARG* 1.3 60.9 + - - +
417A GLU* 3.3 6.9 + - + +
418A GLN* 2.5 40.2 + - - +
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Residues in contact with ARG 415 (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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411A GLU* 2.8 21.3 + - + +
412A LEU* 3.3 21.5 - - - +
414A LEU* 1.3 76.9 - - - +
416A ALA* 1.3 57.3 + - - +
418A GLN* 2.8 30.1 + - - +
420A HIS* 3.1 56.9 + - + +
421A PRO 5.0 2.4 + - - +
422A THR* 5.4 5.2 - - + +
426A ASP* 2.9 29.4 + - - -
518A PRO* 4.0 16.2 - - - +
522A PHE* 3.7 45.3 - - - +
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Residues in contact with ALA 416 (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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412A LEU 2.5 21.3 + - - +
413A GLU* 3.7 7.4 - - - +
415A ARG* 1.3 69.2 - - - +
417A GLU* 1.3 61.7 + - - +
418A GLN 2.8 12.6 - - - +
420A HIS 4.3 11.7 - - - +
422A THR* 3.6 21.3 - - + -
592A PHE* 5.9 3.4 - - + -
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Residues in contact with GLU 417 (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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413A GLU* 2.8 34.4 + - + +
414A LEU* 3.6 10.1 - - + +
416A ALA* 1.3 68.5 - - - +
418A GLN* 1.3 70.4 + - - +
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Residues in contact with GLN 418 (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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414A LEU* 2.5 38.2 - - - +
415A ARG* 2.8 23.0 + - - +
416A ALA 2.8 14.7 - - - +
417A GLU* 1.3 82.5 - - - +
419A GLY* 1.3 61.4 + - - +
420A HIS* 3.0 18.2 + - + +
515A ILE* 6.3 0.4 - - + -
516A PRO* 5.9 8.1 - - + -
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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