Contacts of the strand formed by residues 421 - 425 (chain E) in PDB entry 4E2I
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 TYR 421 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420E ARG* 1.3 85.3 - - + +
422E TRP* 1.3 59.4 + - - +
470E VAL* 4.4 3.2 - - + +
472E PHE* 3.7 22.4 - + - -
501E LEU* 3.8 46.0 - - + -
521E PHE* 3.1 26.1 - + - -
522E PRO 2.7 22.7 + - - -
523E PRO* 3.6 15.7 + - + -
524E GLY* 3.1 26.7 - - - -
525E ILE 4.5 0.4 - - - -
526E VAL* 3.6 26.5 - - + -
540E ARG 4.3 10.3 + - - +
541E PHE* 3.4 11.0 - - + -
542E VAL* 2.9 30.2 + - - +
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Residues in contact with TRP 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E VAL* 3.5 33.2 - - + -
407E ASP* 4.2 13.0 - - + -
408E PHE* 3.9 43.5 - + + -
411E CYS* 3.2 25.0 - - + +
420E ARG 3.3 15.9 - - - -
421E TYR* 1.3 76.5 - - - +
423E LEU* 1.3 61.1 + - - +
424E PHE* 4.3 8.3 - + + -
524E GLY 3.1 6.1 + - - -
525E ILE* 3.6 17.9 - - + +
526E VAL 3.0 25.1 + - - +
541E PHE* 3.7 5.6 - - - -
542E VAL* 4.0 10.3 - - + +
543E LYS* 3.5 42.8 - - + +
545E ILE* 3.5 20.9 - - + -
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Residues in contact with LEU 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422E TRP* 1.3 72.2 - - - +
424E PHE* 1.3 66.7 + - - +
425E LYS* 3.5 19.0 + - + -
526E VAL 3.2 17.5 - - - +
528E MET* 3.5 36.6 - - + -
533E VAL* 4.9 1.6 - - + -
538E GLN* 3.8 20.4 - - - +
541E PHE* 3.5 24.4 - - + -
543E LYS 2.9 15.8 + - - +
544E GLN* 3.5 34.1 - - + +
545E ILE* 2.8 29.8 + - - +
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Residues in contact with PHE 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E PHE* 6.3 0.4 - + - -
422E TRP* 4.3 11.2 - + + -
423E LEU* 1.3 76.9 - - - +
425E LYS* 1.3 59.2 + - - +
426E GLY 3.6 0.9 + - - -
432E LYS* 3.9 14.6 - - + +
435E LEU* 3.5 34.3 - - + -
436E ALA* 3.8 24.7 - - + -
439E LEU* 3.6 22.7 - - + -
525E ILE* 3.4 25.4 - - + -
526E VAL 3.0 8.5 + - - -
527E THR* 3.5 19.9 - - + -
528E MET 3.3 21.9 + - - +
545E ILE* 3.8 29.4 - - + -
547E PHE* 3.5 20.6 - + + -
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Residues in contact with LYS 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E LEU* 3.4 17.1 + - + +
424E PHE* 1.3 73.6 - - - +
426E GLY* 1.3 59.7 + - - +
528E MET* 3.5 30.1 - - + -
530E GLU* 3.5 26.2 + - + +
531E TYR 3.1 28.7 + - - +
532E SER* 5.0 0.8 - - - +
533E VAL* 4.1 9.9 - - - +
538E GLN* 5.7 0.2 + - - -
544E GLN* 3.3 25.9 + - + +
545E ILE 3.4 4.7 + - - -
546E ASP* 3.1 35.5 - - - +
547E PHE 4.3 0.4 - - - -
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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