Contacts of the strand formed by residues 421 - 425 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420I ARG* 1.3 86.1 - - + +
422I TRP* 1.3 59.5 + - - +
470I VAL* 4.4 3.2 - - + +
472I PHE* 3.7 22.4 - + - -
501I LEU* 3.8 46.9 - - + -
521I PHE* 3.1 25.5 - + - -
522I PRO 2.7 22.6 + - - -
523I PRO* 3.6 17.2 + - + -
524I GLY* 3.1 28.3 - - - -
525I ILE 4.5 0.4 - - - -
526I VAL* 3.6 26.9 - - + -
540I ARG 4.4 10.5 + - - +
541I PHE* 3.4 10.0 - - + -
542I VAL* 2.9 30.3 + - - +
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Residues in contact with TRP 422 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404I VAL* 3.5 32.8 - - + -
407I ASP* 4.2 12.6 - - + -
408I PHE* 3.9 44.6 - + + -
411I CYS* 3.2 25.3 - - + +
420I ARG 3.3 15.7 - - - -
421I TYR* 1.3 75.7 - - - +
423I LEU* 1.3 61.2 + - - +
424I PHE* 4.3 8.5 - + + -
524I GLY 3.1 6.3 + - - -
525I ILE* 3.6 17.5 - - + +
526I VAL 3.0 25.1 + - - +
541I PHE* 3.7 6.2 - - - -
542I VAL* 4.0 11.4 - - + +
543I LYS* 3.5 44.2 - - + +
545I ILE* 3.5 20.6 - - + -
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Residues in contact with LEU 423 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422I TRP* 1.3 70.3 - - - +
424I PHE* 1.3 66.4 + - - +
425I LYS* 3.5 18.3 + - + -
526I VAL 3.2 16.6 - - - +
528I MET* 3.5 36.1 - - + -
533I VAL* 4.9 1.3 - - + -
538I GLN* 3.8 20.4 - - - +
541I PHE* 3.5 24.6 - - + -
543I LYS 2.9 16.6 + - - +
544I GLN* 3.5 34.8 - - + +
545I ILE* 2.8 30.0 + - - +
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Residues in contact with PHE 424 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408I PHE* 6.3 0.2 - + - -
422I TRP* 4.3 11.9 - + + -
423I LEU* 1.3 77.9 - - - +
425I LYS* 1.3 60.3 + - - +
426I GLY 3.6 1.2 + - - -
432I LYS* 3.9 12.4 - - + +
435I LEU* 3.5 34.3 - - + -
436I ALA* 3.8 24.7 - - + -
439I LEU* 3.6 23.6 - - + -
525I ILE* 3.4 25.4 - - + -
526I VAL 3.0 8.3 + - - -
527I THR* 3.5 19.8 - - + -
528I MET 3.3 20.9 + - - +
545I ILE* 3.8 30.3 - - + -
547I PHE* 3.5 20.4 - + + -
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Residues in contact with LYS 425 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I LEU* 3.4 17.4 - - + +
424I PHE* 1.3 73.1 - - - +
426I GLY* 1.3 59.5 + - - +
528I MET* 3.5 31.0 - - + -
530I GLU* 3.5 26.9 + - + +
531I TYR 3.0 28.5 + - - +
532I SER* 5.0 0.8 - - - +
533I VAL* 4.1 10.9 - - + +
538I GLN* 5.7 0.4 + - - -
544I GLN* 3.3 25.5 + - + +
545I ILE 3.4 4.2 + - - -
546I ASP* 3.1 35.4 - - - +
547I 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