Contacts of the helix formed by residues 519 - 525 (chain A) in PDB entry 4EG8
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 ILE 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A PRO* 3.9 26.7 - - + -
474A TRP* 3.4 30.7 - - + -
515A ILE* 4.0 10.1 - - + -
516A GLY 3.1 15.0 + - - +
518A ASP* 1.3 93.8 - - - +
520A LEU* 1.3 65.3 + - - +
521A LYS 3.4 2.4 + - - -
522A PHE* 3.5 13.7 + - + -
523A HIS* 3.0 44.2 + - + +
811A DMS 3.7 0.2 - - - -
815A MET* 3.7 24.0 - - + +
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Residues in contact with LEU 520 (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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427A ILE* 4.3 13.9 - - + -
432A ARG* 3.9 32.5 - - + +
435A GLU* 4.6 6.3 - - + +
436A VAL* 3.5 20.4 - - + -
515A ILE* 3.7 21.1 - - + +
517A LYS* 3.4 12.0 + - - +
519A ILE* 1.3 77.1 - - - +
521A LYS* 1.3 57.1 + - - +
523A HIS* 3.2 2.4 + - - -
524A ALA* 2.8 43.9 + - + +
542A ILE* 4.4 5.8 - - + -
544A ALA* 4.4 7.4 - - + -
810A DMS 3.5 24.7 - - + -
811A DMS 2.9 7.9 - - + +
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Residues in contact with LYS 521 (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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369A SER* 2.7 29.5 + - - +
370A PHE 3.0 6.3 + - - -
371A LEU* 4.4 0.8 - - - +
392A GLU* 4.1 10.4 + - - +
436A VAL* 6.0 0.2 - - - -
520A LEU* 1.3 76.3 - - - +
522A PHE* 1.3 90.0 + - + +
524A ALA* 5.2 0.4 - - - -
525A ILE* 3.0 38.2 + - + +
526A TYR* 3.2 29.4 + - - +
810A DMS 3.7 13.9 - - - +
811A DMS 3.3 28.2 - - + +
812A DMS 3.9 15.4 - - + +
813A DMS 3.0 23.4 - - - +
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Residues in contact with PHE 522 (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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367A ASP* 4.0 3.8 - - + -
368A GLU 4.2 0.2 - - - -
369A SER* 3.8 17.3 - - - -
472A TYR* 3.7 11.9 - - - -
474A TRP* 3.3 80.5 - + + -
478A LEU* 3.6 6.0 - - + +
518A ASP 4.3 5.4 - - - -
519A ILE* 3.6 25.4 - - + +
520A LEU 3.2 0.4 - - - -
521A LYS* 1.3 106.7 - - + +
523A HIS* 1.3 58.1 + - - +
526A TYR* 3.5 26.3 - + + +
527A TRP* 3.0 28.9 + - - +
811A DMS 4.3 3.4 - - + -
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Residues in contact with HIS 523 (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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474A TRP* 3.9 11.0 - + - -
478A LEU* 3.7 8.2 - - + +
481A TYR* 2.7 43.7 + + - -
513A HIS* 4.7 8.3 - + + -
515A ILE* 3.7 27.4 - - + +
519A ILE* 3.0 47.0 + - + +
520A LEU 3.2 5.5 + - - +
522A PHE* 1.3 79.0 - - - +
524A ALA* 1.3 57.5 + - - +
525A ILE 3.6 0.4 - - - -
527A TRP* 3.6 13.8 - + + +
528A PRO* 3.2 17.4 - - - +
542A ILE* 3.2 22.8 - - + +
815A MET* 3.7 11.1 - - - -
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Residues in contact with ALA 524 (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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419A TRP* 4.2 0.8 - - - -
420A TYR* 2.6 30.0 + - - -
427A ILE* 4.0 12.3 - - + -
436A VAL* 3.8 30.1 - - + -
520A LEU* 2.8 28.6 + - + +
523A HIS* 1.3 71.3 - - - +
525A ILE* 1.3 56.7 + - + +
528A PRO* 3.2 15.0 - - - +
542A ILE* 3.7 10.5 - - + -
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Residues in contact with ILE 525 (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 LEU* 4.1 7.2 - - + -
416A LEU* 3.8 7.2 - - + +
420A TYR* 3.6 8.3 - - - +
436A VAL* 4.0 10.8 - - + -
439A ALA* 4.6 4.9 - - + -
440A VAL* 3.6 28.5 - - + -
444A LEU* 3.9 28.9 - - + -
521A LYS* 3.0 21.7 + - + +
524A ALA* 1.3 78.8 - - - +
526A TYR* 1.3 82.3 + - + +
527A TRP 3.4 0.9 - - - -
528A PRO* 3.4 3.9 - - - +
529A ALA* 3.3 19.4 + - - +
810A DMS 4.6 5.2 - - - +
812A DMS 4.3 30.5 - - + +
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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
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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