Contacts of the helix formed by residues 393 - 406 (chain A) in PDB entry 4IX8
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 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A LEU* 4.5 11.1 - - - +
391A LEU 3.4 2.0 - - - -
392A LYS* 1.3 83.8 + - - +
394A ASP* 1.3 69.5 + - - +
395A MET* 3.5 11.4 + - - +
396A GLU* 2.9 24.4 + - - +
397A PHE* 2.9 22.5 + - - +
413A GLU* 5.5 1.8 - - - -
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Residues in contact with ASP 394 (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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383A LEU* 3.8 16.2 - - + +
385A LEU* 4.7 3.0 - - - +
393A SER* 1.3 77.4 - - - +
395A MET* 1.3 64.8 + - - -
397A PHE* 3.4 3.1 + - - +
398A TYR* 3.0 22.9 + - - +
411A PRO* 3.4 6.1 - - - +
412A GLY* 3.0 25.0 + - - +
413A GLU* 3.0 19.8 + - - +
418A SER* 3.6 15.1 + - - -
419A GLY* 3.4 24.9 + - - +
420A PHE 3.3 22.4 - - - +
421A LEU* 3.8 4.9 - - - +
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Residues in contact with MET 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.7 11.2 - - + -
393A SER* 3.0 8.9 - - - +
394A ASP* 1.3 82.8 + - - +
396A GLU* 1.3 62.1 + - - +
398A TYR* 3.1 31.4 + - - +
399A GLU* 3.0 39.7 + - - +
411A PRO* 3.6 26.2 - - + -
413A GLU* 3.8 36.8 - - + +
414A ILE* 5.0 6.7 - - + -
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP 3.4 20.5 - - - +
391A LEU* 4.4 2.2 - - + -
392A LYS* 2.8 36.0 + - - +
393A SER* 2.9 21.3 + - - +
395A MET* 1.3 77.1 - - - +
397A PHE* 1.3 61.6 + - - +
399A GLU* 3.8 14.9 - - - +
400A LYS* 3.0 58.5 + - + +
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Residues in contact with PHE 397 (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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368A ILE* 4.8 5.2 - - + -
383A LEU* 4.0 35.0 - - + -
385A LEU* 6.1 0.9 - - + -
388A PHE* 4.2 19.7 - + - -
391A LEU* 3.6 32.2 - - + +
393A SER 2.9 12.3 + - - +
394A ASP 3.5 9.4 - - - +
396A GLU* 1.3 74.9 - - - +
398A TYR* 1.3 59.3 + - - +
401A LEU* 3.0 42.1 + - + +
409A VAL* 5.2 0.2 - - + -
421A LEU* 3.6 26.0 - - + -
439A ILE* 5.0 5.2 - - + -
442A PHE* 3.7 31.3 - + - -
443A CYS* 4.0 13.5 - - - -
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Residues in contact with TYR 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.6 36.0 - - + +
64A MET* 3.3 33.8 - - + +
394A ASP 3.0 13.5 + - - +
395A MET* 3.1 26.0 + - - +
397A PHE* 1.3 76.1 - - - +
399A GLU* 1.3 78.2 + - + +
401A LEU* 3.8 2.5 - - - +
402A LEU* 3.1 35.1 + - + +
407A VAL 4.8 0.5 - - - +
408A GLN* 4.0 16.2 + - + -
409A VAL* 3.1 50.2 - - + +
411A PRO* 3.9 15.9 - - + -
421A LEU* 4.6 0.4 - - + -
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Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A MET* 3.0 32.8 + - - +
396A GLU* 3.8 20.6 - - - +
397A PHE 3.3 0.2 - - - -
398A TYR* 1.3 93.7 - - + +
400A LYS* 1.3 60.3 + - + +
402A LEU* 3.3 8.0 + - - +
403A ASP* 2.9 30.7 + - - +
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Residues in contact with LYS 400 (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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390A ASP* 3.1 45.9 + - - +
391A LEU* 3.8 8.1 - - + +
396A GLU* 3.0 40.9 + - + +
399A GLU* 1.3 75.5 - - + +
401A LEU* 1.3 60.9 + - - +
403A ASP* 4.4 5.6 - - - +
404A GLU* 2.9 52.5 + - - +
442A PHE* 3.8 17.0 - - + -
446A HIS* 4.6 1.8 - - + -
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Residues in contact with LEU 401 (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 PHE* 3.0 30.7 + - + +
398A TYR 3.8 3.1 - - - +
400A LYS* 1.3 76.1 - - - +
402A LEU* 1.3 53.7 + - - +
405A GLU* 2.8 50.5 + - + +
406A ASN 3.5 0.9 + - - -
407A VAL* 3.5 33.7 - - + +
409A VAL* 4.2 25.4 - - + -
439A ILE* 4.2 21.1 - - + -
442A PHE* 3.6 34.9 - - + -
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Residues in contact with LEU 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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64A MET* 4.2 16.8 - - + -
65A LYS* 3.6 26.2 - - + +
67A SER* 2.7 32.1 + - - +
73A ASN* 4.5 5.2 - - - +
398A TYR* 3.1 41.0 + - + +
399A GLU* 3.5 5.8 - - - +
401A LEU* 1.3 77.4 - - - +
403A ASP* 1.3 53.5 + - - +
406A ASN* 2.9 31.0 + - - +
407A VAL 3.4 14.6 - - - +
408A GLN* 4.0 27.1 - - + +
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Residues in contact with ASP 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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65A LYS* 6.2 0.5 - - - +
66A PRO 4.6 2.6 - - - +
67A SER* 3.1 19.4 + - - +
68A ARG* 3.1 50.4 + - - +
399A GLU 2.9 17.5 + - - +
400A LYS* 3.9 7.4 - - + +
401A LEU 3.3 0.2 - - - -
402A LEU* 1.3 78.2 - - - +
404A GLU* 1.3 65.8 + - + +
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Residues in contact with GLU 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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68A ARG 4.9 1.5 - - - +
69A SER* 3.5 14.1 + - - -
400A LYS* 2.9 31.9 + - - +
403A ASP* 1.3 88.7 - - + +
405A GLU* 1.3 66.7 + - + +
406A ASN 3.8 0.4 - - - -
442A PHE* 3.6 2.1 - - + -
445A ARG* 3.0 31.2 + - - +
446A HIS* 2.9 40.4 + - - -
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Residues in contact with GLU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER* 4.2 4.5 - - - -
71A LYS* 5.1 1.6 - - - -
401A LEU* 2.8 31.7 + - + +
404A GLU* 1.3 81.3 - - + +
406A ASN* 1.3 60.7 + - - +
407A VAL* 3.1 2.3 + - + -
438A ARG* 2.6 81.9 + - + +
441A GLU* 2.8 27.4 - - - +
442A PHE* 4.1 1.3 - - + -
445A ARG* 2.8 26.5 + - - +
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Residues in contact with ASN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 3.7 23.9 + - - +
69A SER* 4.1 9.3 + - - +
71A LYS 3.0 25.4 + - - +
72A SER 3.4 7.1 - - - +
73A ASN* 2.6 46.1 + - - +
74A LEU 2.9 24.4 + - - +
401A LEU 3.5 0.2 + - - -
402A LEU* 2.9 21.1 + - - +
404A GLU 3.8 0.6 - - - -
405A GLU* 1.3 79.8 - - - +
407A VAL* 1.3 59.0 + - - +
408A GLN 4.2 0.2 - - - -
438A ARG* 4.2 0.2 - - - +
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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