Contacts of the helix formed by residues 519 - 525 (chain B) in PDB entry 4EGA
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B PRO* 3.9 20.9 - - + -
515B ILE* 3.5 10.3 - - + +
516B GLY 3.6 16.4 - - - +
517B LYS 3.1 0.2 - - - -
518B ASP* 1.3 98.4 - - + +
520B LEU* 1.3 63.6 + - - +
521B LYS 3.4 1.8 - - - -
522B PHE* 3.4 24.9 + - + +
523B HIS* 2.9 50.5 + - + +
813B 0P8 3.9 37.2 - - + -
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Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ILE* 4.1 11.9 - - + -
432B ARG* 3.6 43.7 - - + +
435B GLU* 5.3 3.8 - - + +
436B VAL* 3.8 21.1 - - + -
515B ILE* 3.4 12.0 - - + +
517B LYS* 3.2 17.4 + - - +
518B ASP 3.5 0.4 - - - -
519B ILE* 1.3 74.3 - - - +
521B LYS* 1.3 62.7 + - - +
522B PHE 3.2 0.2 + - - -
523B HIS 3.2 0.9 + - - -
524B ALA* 2.8 47.5 + - + +
542B ILE* 4.0 24.7 - - + -
544B ALA* 4.4 5.6 - - + -
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Residues in contact with LYS 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B VAL* 5.5 3.1 - - - -
439B ALA* 5.9 4.3 - - + -
517B LYS 5.0 0.2 + - - -
518B ASP 5.2 2.6 + - - +
519B ILE* 3.4 0.4 - - - +
520B LEU* 1.3 78.9 - - - +
522B PHE* 1.3 80.2 + - + +
524B ALA* 5.0 0.7 - - - -
525B ILE* 3.0 58.3 + - + +
526B TYR* 3.5 30.0 + - + -
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Residues in contact with PHE 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B TRP* 3.6 24.2 - + - -
478B LEU* 3.9 4.4 - - + +
518B ASP 4.3 10.3 - - - -
519B ILE* 3.4 27.5 + - + +
520B LEU 3.1 0.8 - - - -
521B LYS* 1.3 105.1 - - + +
523B HIS* 1.3 62.9 + - - +
526B TYR* 3.5 30.7 + + + +
527B TRP* 3.0 28.1 + - - +
810B DMS 5.6 3.4 - - + -
813B 0P8 3.3 51.6 - - + -
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Residues in contact with HIS 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LEU* 3.8 11.0 - - + +
481B TYR* 2.7 45.1 + + - -
513B HIS* 4.7 9.0 - + + -
515B ILE* 3.5 24.7 - - + +
519B ILE* 2.9 51.3 + - + +
520B LEU 3.2 3.6 + - - +
522B PHE* 1.3 77.8 - - - +
524B ALA* 1.3 58.3 + - - +
525B ILE 3.6 0.2 - - - -
527B TRP* 3.6 15.5 - + + +
528B PRO* 3.3 16.5 - - - +
542B ILE* 3.1 26.2 - - + +
813B 0P8 3.6 17.8 - + + +
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Residues in contact with ALA 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B LEU* 4.3 0.7 - - - +
419B TRP* 5.1 0.7 - - - -
420B TYR* 2.8 27.9 + - - -
427B ILE* 3.8 28.0 - - + -
436B VAL* 3.9 12.8 - - + -
520B LEU* 2.8 28.0 + - + +
523B HIS* 1.3 77.0 - - - +
525B ILE* 1.3 56.9 + - + +
528B PRO* 3.4 14.5 - - - +
542B ILE* 3.8 8.7 - - + -
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Residues in contact with ILE 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B LEU* 4.2 3.1 - - + -
416B LEU* 3.8 20.7 - - + +
420B TYR* 3.8 11.2 - - - +
436B VAL* 4.1 11.9 - - + -
439B ALA* 4.6 12.1 - - + -
440B VAL* 3.4 19.3 - - + -
444B LEU* 4.0 26.2 - - + -
521B LYS* 3.0 39.9 + - + +
524B ALA* 1.3 82.3 - - - +
526B TYR* 1.3 81.8 + - + +
527B TRP 3.6 0.2 - - - -
528B PRO* 3.4 1.8 - - - +
529B ALA* 3.4 20.1 + - - +
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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