Contacts of the helix formed by residues 428 - 438 (chain A) in PDB entry 2E3O
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 THR 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A VAL* 1.3 74.6 - - - +
429A GLY* 1.3 59.4 + - - +
430A HIS 3.5 3.7 + - - -
431A GLU* 3.0 21.5 + - - +
432A VAL* 2.9 29.8 + - - +
531A THR* 3.9 11.9 - - + -
547A ILE* 3.7 10.1 - - + -
549A CYS* 3.9 3.6 - - - -
596A ILE* 3.4 33.0 - - + -
597A LEU 2.6 22.6 + - - +
598A PHE* 3.9 20.6 - - + -
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Residues in contact with GLY 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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428A THR* 1.3 68.0 - - - +
430A HIS* 1.3 60.2 + - - +
432A VAL* 3.9 0.4 - - - +
433A CYS* 2.9 35.0 + - - +
500A TRP* 3.9 11.0 - - - -
529A CYS* 3.5 27.4 - - - -
531A THR* 2.8 20.7 + - - -
549A CYS* 3.6 6.4 - - - -
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Residues in contact with HIS 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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428A THR* 3.3 1.8 + - - -
429A GLY* 1.3 75.5 - - - +
431A GLU* 1.3 58.6 + - - +
433A CYS* 3.9 0.9 - - - +
434A ASN* 2.9 51.7 + - - -
500A TRP* 3.4 58.4 - + + +
597A LEU* 3.7 25.0 - - + +
598A PHE 2.8 37.0 + - - -
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 3.5 2.9 - - - -
428A THR* 3.0 36.9 + - - +
430A HIS* 1.3 74.3 - - - +
432A VAL* 1.3 66.6 + - - +
434A ASN* 3.2 7.6 + - - +
435A TYR* 3.0 35.0 + - + -
544A ARG* 2.7 45.5 + - - -
587A VAL* 4.4 3.4 - - + -
591A THR* 3.8 20.8 - - + +
595A PRO 4.0 0.7 - - - +
597A LEU* 3.0 36.0 + - + +
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Residues in contact with VAL 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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424A VAL* 5.7 0.7 - - + -
427A VAL* 3.6 26.0 - - + -
428A THR 2.9 22.5 + - - +
429A GLY 3.9 3.4 - - - +
431A GLU* 1.3 71.9 - - - +
433A CYS* 1.3 64.4 + - - +
435A TYR 3.3 0.5 + - - -
436A PHE* 3.0 19.6 + - - +
527A MET* 3.5 27.1 - - - -
529A CYS* 3.6 15.7 - - - -
549A CYS* 4.0 9.0 - - - -
551A ILE* 4.1 12.3 - - + -
583A PHE* 3.4 15.7 - - + -
584A THR* 6.0 1.8 - - + -
587A VAL* 4.0 17.0 - - + -
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Residues in contact with CYS 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 GLY 2.9 19.5 + - - +
430A HIS 4.0 1.6 - - - +
432A VAL* 1.3 77.1 - - - +
434A ASN* 1.3 63.4 + - - +
436A PHE* 3.3 3.0 + - - -
437A TRP* 2.9 27.7 + - - +
486A ILE* 3.7 19.3 - - + -
500A TRP* 3.5 38.6 - - + -
501A ILE* 3.8 4.9 - - - -
502A VAL* 3.6 17.8 - - + +
527A MET* 4.0 6.5 - - - -
529A CYS* 3.9 13.5 - - - -
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Residues in contact with ASN 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 HIS* 2.9 32.0 + - - +
431A GLU* 3.2 6.0 + - - +
433A CYS* 1.3 76.5 - - - +
435A TYR* 1.3 62.6 + - + +
437A TRP* 3.9 3.6 - - - +
438A ASN* 2.9 37.0 + - + +
486A ILE* 3.5 18.3 - - - +
500A TRP* 5.0 0.2 - - - -
597A LEU* 3.3 31.1 - - - +
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Residues in contact with TYR 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 GLU* 3.0 33.2 + - + +
432A VAL 3.9 0.2 - - - +
434A ASN* 1.3 80.1 - - + +
436A PHE* 1.3 62.0 + - - +
438A ASN* 4.0 2.9 + - + +
441A VAL* 3.5 30.0 - - + +
445A TRP* 3.3 17.8 + - - -
583A PHE* 3.8 4.9 - - + -
586A TYR* 3.6 24.0 - + + -
587A VAL* 3.7 30.1 - - + -
590A LYS* 3.6 40.6 + - + +
591A THR* 3.9 20.3 - - + +
594A LYS* 4.9 3.5 + - - +
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Residues in contact with PHE 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 VAL 3.0 16.8 + - - +
433A CYS* 3.8 4.7 - - - +
435A TYR* 1.3 79.1 - - - +
437A TRP* 1.3 57.2 + - - +
442A ARG* 3.0 20.6 + - - -
445A TRP* 3.6 33.1 - + - -
502A VAL* 3.6 31.8 - - + +
504A ASN* 3.7 24.2 - - - +
525A VAL* 4.5 3.4 - - + -
527A MET* 3.5 47.6 - - + -
553A TYR* 4.2 6.3 - + - -
579A PHE* 3.8 11.0 - + - -
583A PHE* 3.5 13.8 - + + -
600A 16C 3.5 22.7 - - - -
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Residues in contact with TRP 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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433A CYS 2.9 16.9 + - - +
434A ASN* 4.1 3.8 - - - +
436A PHE* 1.3 79.6 - - - +
438A ASN* 1.3 77.7 + - + +
439A VAL* 3.1 8.9 + - - +
442A ARG* 3.4 11.3 + - - +
460A ASP 3.5 21.1 - - - -
461A ASN* 3.6 23.8 + - - -
462A ALA 3.9 2.7 - - - -
463A ILE* 4.2 28.2 - - + +
484A SER* 3.0 48.0 + - - -
485A VAL 4.0 1.6 - - - -
486A ILE* 3.7 31.9 - - + -
502A VAL* 4.0 14.4 - - + -
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Residues in contact with ASN 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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434A ASN* 2.9 20.5 + - + +
435A TYR* 4.0 2.4 + - - +
436A PHE 3.6 0.4 - - - -
437A TRP* 1.3 89.5 - - + +
439A VAL* 1.3 65.0 + - - +
440A ASP* 2.9 35.5 + - - +
441A VAL* 3.2 32.1 + - + +
442A ARG* 3.6 7.4 + - - +
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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