Contacts of the helix formed by residues 427 - 437 (chain A) in PDB entry 1EX0
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 427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ARG* 2.8 34.7 + - - -
402A ASN* 3.3 25.8 + - - +
403A SER* 4.6 7.3 + - - -
404A ASP* 5.6 1.0 - - - +
408A ARG 3.9 0.5 - - - +
409A CYS* 3.3 22.2 - - + -
410A GLY 2.8 19.0 + - - +
412A ALA* 4.6 0.9 - - - -
425A GLN* 4.4 2.0 - - - +
426A PHE* 1.3 70.7 - - - +
428A ALA* 1.3 64.9 + - - +
429A PRO* 3.3 6.7 - - - +
430A PHE* 3.1 24.4 + - + +
431A VAL* 3.4 10.8 + - + +
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Residues in contact with ALA 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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412A ALA* 4.0 18.4 - - + -
413A SER 5.8 0.7 - - - +
416A ALA* 5.6 3.8 - - + -
417A ILE* 4.3 9.2 - - + +
421A HIS 4.9 0.9 - - - +
422A VAL* 3.6 32.2 + - + +
424A PHE 3.6 14.3 + - - +
426A PHE 3.2 1.2 - - - -
427A ASP* 1.3 78.0 - - - +
429A PRO* 1.3 64.7 - - + +
430A PHE 3.2 0.2 + - - -
431A VAL* 3.3 2.6 + - - +
432A PHE* 2.9 30.0 + - - +
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Residues in contact with PRO 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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346A ALA* 3.9 23.6 - - + +
422A VAL* 3.3 30.5 - - + +
427A ASP* 3.3 7.6 - - - +
428A ALA* 1.3 90.9 - - - +
430A PHE* 1.3 64.8 + - + +
432A PHE* 3.6 6.3 - - + +
433A ALA* 3.0 28.6 + - - +
500A TYR 3.7 14.6 - - - +
501A GLY* 4.0 14.1 - - - +
502A ALA* 4.2 5.5 - - - +
425B GLN* 6.3 1.3 - - - +
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Residues in contact with PHE 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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344A ASN* 2.9 30.2 + - - -
345A ASP* 3.4 28.0 - - - -
346A ALA* 3.5 18.4 - - + -
400A GLN* 3.9 22.2 - - - +
401A GLU 3.4 25.4 - - - -
402A ASN* 3.5 20.9 - - + -
403A SER* 3.5 24.7 - - - -
409A CYS* 4.2 4.7 - - - -
427A ASP* 3.1 23.8 + - - +
429A PRO* 1.3 84.0 - - + +
431A VAL* 1.4 66.4 + - - +
433A ALA 3.3 1.9 + - - -
434A GLU* 3.0 8.9 + - - +
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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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375A TRP* 4.5 14.6 - - + -
394A ALA* 4.3 13.9 - - + +
396A ASP* 5.6 6.1 - - + -
400A GLN* 5.3 2.7 - - - +
409A CYS* 4.6 18.6 - - + +
412A ALA* 4.3 15.3 - - + -
417A ILE* 3.5 25.1 - - + -
427A ASP 3.4 11.0 + - - +
428A ALA 3.3 2.8 + - - +
430A PHE* 1.4 74.2 - - - +
432A PHE* 1.3 64.2 + - - +
434A GLU* 3.1 24.0 + - + +
435A VAL* 3.4 8.9 + - + +
481A TYR* 4.2 17.3 - - + -
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Residues in contact with PHE 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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348A LEU* 4.0 26.5 - - + -
417A ILE* 3.4 35.9 - - + +
418A LYS 5.2 0.7 - - - -
420A GLY* 4.0 12.8 - - - -
422A VAL* 4.0 18.6 - - + -
428A ALA 2.9 17.3 + - - +
429A PRO* 3.6 5.6 - - + +
431A VAL* 1.3 77.1 - - - +
433A ALA* 1.3 62.0 + - - +
435A VAL* 3.3 0.8 + - - -
436A ASN* 3.0 62.1 + - + +
493A ALA* 4.1 12.6 - - + -
494A LEU* 4.2 14.1 - - + -
497A ALA* 3.7 24.0 - - + -
502A ALA* 4.5 5.6 - - + -
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Residues in contact with ALA 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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341A ALA* 3.9 3.5 - - - +
344A ASN* 3.6 21.3 - - - +
346A ALA* 3.9 8.1 - - - +
347A ASN 3.5 24.2 - - - +
348A LEU* 3.6 18.2 - - + -
429A PRO 3.0 16.5 + - - +
430A PHE 3.3 0.2 + - - -
432A PHE* 1.3 72.9 - - + +
434A GLU* 1.3 64.8 + - - +
435A VAL 3.2 0.7 + - - -
437A SER* 2.7 26.3 + - - -
502A ALA* 6.4 0.2 - - + -
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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
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337A ASN* 3.6 5.9 + - - -
340A SER* 2.5 26.4 + - - +
341A ALA 3.2 41.0 + - - +
342A HIS* 2.5 52.2 + - - +
344A ASN* 3.6 0.2 - - - +
373A HIS* 3.4 8.8 - - - -
375A TRP* 3.6 19.7 - - + -
396A ASP* 4.3 1.4 - - - +
400A GLN* 3.6 11.1 + - - +
430A PHE 3.0 10.2 + - - +
431A VAL* 3.1 18.8 - - + +
433A ALA* 1.3 76.2 - - - +
435A VAL* 1.3 57.0 + - + +
460A ILE* 3.4 7.8 - - - +
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Residues in contact with VAL 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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337A ASN* 3.8 6.5 - - - +
375A TRP* 3.7 30.5 - - + -
417A ILE* 5.1 1.3 - - + -
431A VAL 4.0 9.6 - - - +
432A PHE* 3.3 4.2 + - - +
433A ALA 3.2 0.2 - - - -
434A GLU* 1.3 82.8 - - - +
436A ASN* 1.3 78.1 + - - +
437A SER 3.8 1.1 - - - -
460A ILE* 3.3 9.7 - - - +
461A GLY* 3.4 12.6 - - - -
464A ILE* 4.1 13.9 - - + -
481A TYR* 4.6 16.4 - - + +
482A LYS* 2.8 44.3 + - + -
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Residues in contact with ASN 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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348A LEU* 4.0 9.0 - - + +
417A ILE* 5.1 0.6 - - - +
432A PHE* 3.0 66.1 + - + +
435A VAL* 1.3 91.3 - - - +
437A SER* 1.3 62.4 + - - +
438A ASP* 3.7 2.1 + - - +
460A ILE* 5.1 0.2 - - - -
481A TYR 4.9 4.2 + - - -
482A LYS* 3.6 25.4 - - - +
490A GLU* 4.9 9.4 - - - +
494A LEU* 6.4 0.2 - - + -
504A LYS* 5.0 3.5 + - - -
1320A CA 2.8 20.8 - - - -
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Residues in contact with SER 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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341A ALA* 4.1 8.2 - - - +
344A ASN* 4.8 0.3 - - - +
347A ASN 3.6 6.9 + - - -
348A LEU* 3.3 30.2 - - - +
349A GLN* 4.5 0.9 - - - -
350A MET* 5.1 3.6 - - - -
433A ALA 2.7 24.4 + - - -
435A VAL 3.8 0.8 - - - -
436A ASN* 1.3 79.6 - - - +
438A ASP* 1.3 62.8 + - - +
439A LEU* 5.6 0.2 - - - +
456A ASP 4.7 1.4 - - - +
457A ALA 4.8 1.7 - - - +
460A ILE* 3.3 41.8 + - - +
1320A CA 3.7 5.2 - - - -
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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