Contacts of the helix formed by residues 428 - 447 (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 PRO 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 3.3 37.0 - - + +
86A ASN* 4.3 17.5 - - + +
350A GLN* 5.6 2.7 - - - +
427A ARG* 1.3 89.0 - - + +
429A SER* 1.3 60.4 + - - +
430A ALA* 3.1 7.6 - - + +
431A VAL* 2.8 34.5 + - + +
432A LEU* 3.2 9.1 + - - +
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Residues in contact with SER 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ALA* 4.1 22.9 + - - +
354A GLY* 4.9 0.9 + - - -
357A VAL* 4.4 10.5 - - - +
427A ARG 3.6 2.2 + - - -
428A PRO* 1.3 70.4 - - - +
430A ALA* 1.3 55.5 + - - +
432A LEU* 3.8 9.1 - - - +
433A ASN* 2.7 51.7 + - - +
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A PRO* 3.1 5.6 + - + +
429A SER* 1.3 78.8 - - - +
431A VAL* 1.3 64.9 + - + +
433A ASN* 4.1 4.3 - - - +
434A GLU* 3.2 26.8 + - - +
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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
----------------------------------------------------------
74A LEU* 4.1 24.0 - - + +
76A LEU* 4.5 11.2 - - + -
84A ASP* 5.1 1.1 - - - +
427A ARG* 3.9 42.0 - - + +
428A PRO* 2.8 31.1 + - + +
430A ALA* 1.3 78.0 - - + +
432A LEU* 1.3 65.0 + - - +
434A GLU* 3.4 6.1 + - - +
435A ALA* 3.0 21.5 + - - +
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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
----------------------------------------------------------
76A LEU* 3.8 16.2 - - + -
354A GLY* 3.5 37.7 - - - +
357A VAL* 3.7 16.6 - - + -
358A TYR* 3.6 30.7 - - + +
424A THR 3.7 7.4 - - - +
425A VAL 4.0 6.7 - - - +
427A ARG* 3.7 29.6 - - + +
428A PRO 3.2 10.9 + - - +
429A SER* 3.8 6.1 - - - +
431A VAL* 1.3 77.2 - - - +
433A ASN* 1.3 53.0 + - - +
435A ALA* 2.9 5.2 + - - +
436A VAL* 2.8 37.2 + - + +
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Residues in contact with ASN 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL* 3.4 25.9 - - - +
360A ARG* 2.6 35.4 + - - +
429A SER* 2.7 32.3 + - - +
430A ALA* 4.1 5.1 - - - +
432A LEU* 1.3 72.5 - - - +
434A GLU* 1.3 62.1 + - - +
436A VAL 3.6 0.2 + - - -
437A ASP* 3.2 32.3 + - - +
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Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 4.2 5.2 + - - -
74A LEU* 3.9 17.1 - - + +
430A ALA 3.2 18.2 + - - +
431A VAL* 3.8 4.7 - - - +
433A ASN* 1.3 78.0 - - - +
435A ALA* 1.3 61.9 + - - +
437A ASP* 3.4 11.7 + - + +
438A ARG* 3.2 50.2 + - + +
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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
----------------------------------------------------------
74A LEU* 3.8 17.5 - - + -
76A LEU* 4.0 32.1 - - + -
407A VAL* 4.2 12.8 - - + +
431A VAL 3.0 15.9 + - - +
432A LEU 2.9 5.1 + - - +
434A GLU* 1.3 74.9 - - - +
436A VAL* 1.3 66.5 + - - +
438A ARG* 3.2 4.9 + - - +
439A ILE* 3.1 28.4 + - - +
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Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 6.0 0.2 - - + -
357A VAL* 3.9 26.5 - - + +
358A TYR* 4.2 25.4 - - + -
360A ARG* 3.8 28.9 - - + +
361A LEU* 3.9 20.0 - - + -
432A LEU 2.8 19.0 + - - +
433A ASN 3.9 3.8 - - - +
435A ALA* 1.3 74.5 - - + +
437A ASP* 1.3 64.9 + - - +
439A ILE* 3.2 10.0 + - + +
440A ILE* 2.9 32.1 + - + +
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Residues in contact with ASP 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ARG* 2.6 35.3 + - - -
433A ASN* 3.2 18.3 + - - +
434A GLU* 3.6 11.8 - - + +
435A ALA 3.2 0.2 - - - -
436A VAL* 1.3 75.2 - - - +
438A ARG* 1.3 59.8 + - + +
440A ILE* 3.3 9.3 + - - +
441A GLU* 3.0 29.8 + - - +
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Residues in contact with ARG 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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71A LYS* 3.2 16.9 - - - +
72A SER* 2.9 49.3 + - - +
74A LEU* 3.7 17.0 - - - +
405A GLU* 2.6 68.8 + - + +
406A ASN 4.0 2.6 + - - -
407A VAL* 4.0 8.9 - - + +
434A GLU* 3.2 33.6 + - + +
435A ALA 3.2 7.9 + - - +
437A ASP* 1.3 76.0 - - + +
439A ILE* 1.3 56.9 + - - +
441A GLU* 3.7 9.1 - - - +
442A PHE* 2.8 34.9 + - - +
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Residues in contact with ILE 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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76A LEU* 4.4 19.5 - - + -
358A TYR* 5.5 2.2 - - + -
361A LEU* 3.8 23.3 - - + -
368A ILE* 4.1 18.2 - - + -
381A LEU* 5.7 5.8 - - + -
397A PHE* 5.0 9.2 - - + -
401A LEU* 4.2 23.3 - - + -
407A VAL* 4.6 7.0 - - + -
409A VAL* 5.2 4.0 - - + -
435A ALA 3.1 20.8 + - - +
436A VAL* 3.5 15.0 - - + +
437A ASP 3.2 0.2 - - - -
438A ARG* 1.3 75.3 - - - +
440A ILE* 1.3 60.6 + - - +
442A PHE* 3.2 6.5 + - - +
443A CYS* 2.9 33.7 + - - -
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Residues in contact with ILE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ARG* 3.9 16.8 - - - +
361A LEU* 3.9 15.3 - - + -
364A HIS* 3.6 51.4 - - + +
366A ILE* 4.2 12.3 - - + +
436A VAL* 2.9 33.9 + - + +
437A ASP* 3.5 7.9 - - - +
439A ILE* 1.3 73.2 - - - +
441A GLU* 1.3 66.8 + - - +
443A CYS* 3.2 3.8 + - - +
444A GLU* 3.1 31.6 + - + +
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Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLU* 2.8 31.5 - - - +
437A ASP 3.0 17.5 + - - +
438A ARG* 3.8 5.8 - - - +
440A ILE* 1.3 78.6 - - - +
442A PHE* 1.3 62.6 + - - +
444A GLU* 3.5 6.9 + - - +
445A ARG* 3.2 35.7 + - - +
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Residues in contact with PHE 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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391A LEU* 4.0 12.3 - - + -
397A PHE* 3.7 42.2 - + - -
400A LYS* 3.8 12.6 - - + -
401A LEU* 3.6 42.6 - - + -
404A GLU* 3.6 5.8 - - - -
405A GLU* 4.1 6.5 - - + -
438A ARG 2.8 19.6 + - - +
439A ILE* 3.4 9.0 - - - +
440A ILE 3.1 0.2 - - - -
441A GLU* 1.3 78.4 - - - +
443A CYS* 1.3 64.3 + - - +
445A ARG* 3.4 27.0 + - - +
446A HIS* 3.2 58.7 + + - -
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Residues in contact with CYS 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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366A ILE* 3.5 42.2 - - + +
368A ILE* 4.0 23.1 - - - -
388A PHE* 4.1 12.9 - - + -
397A PHE* 4.0 20.2 - - - -
439A ILE* 2.9 19.8 + - - +
440A ILE 3.7 0.4 - - - +
442A PHE* 1.3 77.6 - - - +
444A GLU* 1.3 66.5 + - - +
446A HIS* 3.1 3.7 + - - +
447A LYS* 3.0 27.8 + - - +
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Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A HIS* 4.5 15.6 - - - +
365A ASP 5.1 1.7 + - - +
366A ILE* 3.7 19.6 - - + +
440A ILE* 3.1 21.9 + - + +
441A GLU* 3.9 6.1 - - - +
442A PHE 3.4 0.2 - - - -
443A CYS* 1.3 77.2 - - - +
445A ARG* 1.3 63.1 + - - +
447A LYS* 3.4 38.2 + - - +
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Residues in contact with ARG 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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404A GLU* 3.0 30.6 + - - +
405A GLU* 2.8 21.7 + - - +
441A GLU* 3.2 48.0 + - - +
442A PHE* 3.4 25.2 - - - +
443A CYS 3.1 0.4 - - - -
444A GLU* 1.3 81.9 - - - +
446A HIS* 1.3 66.0 + - + +
447A LYS 3.7 2.9 + - - +
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Residues in contact with HIS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PHE* 3.7 5.8 - - + -
389A GLN* 3.0 26.7 + - - +
390A ASP* 3.0 34.5 + - - +
391A LEU* 4.1 28.2 - - + +
400A LYS* 4.6 5.2 - - + -
404A GLU* 2.9 37.8 + - - -
442A PHE* 3.2 43.4 + + - +
443A CYS* 3.1 5.3 + - - +
445A ARG* 1.3 84.3 + - + +
447A LYS* 1.3 65.7 + - - +
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Residues in contact with LYS 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ASP* 2.6 38.6 + - - +
366A ILE* 4.4 5.8 - - - -
387A TYR* 3.4 27.8 - - + +
388A PHE* 4.3 9.2 - - + +
389A GLN* 4.2 4.9 - - - +
443A CYS 3.0 19.7 + - - +
444A GLU* 3.4 38.6 + - - +
445A ARG 3.4 4.7 - - - +
446A HIS* 1.3 82.6 - - - +
448A LYS* 1.3 72.5 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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