Contacts of the strand formed by residues 421 - 425 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420K ARG* 1.3 85.9 - - + +
422K TRP* 1.3 60.0 + - - +
470K VAL* 4.4 3.2 - - + +
472K PHE* 3.7 22.7 - + - -
501K LEU* 3.8 46.2 - - + -
521K PHE* 3.1 25.9 - + - -
522K PRO 2.7 23.0 + - - -
523K PRO* 3.6 16.1 + - + -
524K GLY* 3.1 26.9 - - - -
525K ILE 4.5 0.2 - - - -
526K VAL* 3.6 26.9 - - + -
540K ARG 4.4 10.5 + - - +
541K PHE* 3.4 10.9 - - + -
542K VAL* 2.9 29.1 + - - +
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Residues in contact with TRP 422 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404K VAL* 3.5 32.8 - - + -
407K ASP* 4.2 13.2 - - + -
408K PHE* 3.9 45.5 - + + -
411K CYS* 3.2 25.5 - - + +
420K ARG 3.3 15.9 - - - -
421K TYR* 1.3 76.2 - - - +
423K LEU* 1.3 60.8 + - - +
424K PHE* 4.3 7.6 - + + -
524K GLY 3.1 5.7 + - - -
525K ILE* 3.6 17.2 - - + +
526K VAL 3.0 25.5 + - - +
541K PHE* 3.7 5.7 - - - -
542K VAL* 4.0 10.5 - - + +
543K LYS* 3.5 44.4 - - + -
545K ILE* 3.5 20.2 - - + -
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Residues in contact with LEU 423 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422K TRP* 1.3 72.0 - - - +
424K PHE* 1.3 66.0 + - - +
425K LYS* 3.5 17.3 + - + -
526K VAL 3.2 16.8 - - - +
528K MET* 3.5 37.0 - - + -
533K VAL* 4.9 2.0 - - + -
538K GLN* 3.8 19.7 - - - +
541K PHE* 3.5 24.7 - - + -
543K LYS 2.9 16.2 + - - +
544K GLN* 3.5 34.5 - - + +
545K ILE* 2.8 30.3 + - - +
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Residues in contact with PHE 424 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408K PHE* 6.3 0.2 - + - -
422K TRP* 4.3 11.4 - + + -
423K LEU* 1.3 77.1 - - - +
425K LYS* 1.3 59.2 + - - +
426K GLY 3.6 1.4 + - - -
432K LYS* 3.9 13.9 - - + +
435K LEU* 3.5 35.0 - - + -
436K ALA* 3.8 24.2 - - + -
439K LEU* 3.6 22.4 - - + -
525K ILE* 3.4 25.6 - - + -
526K VAL 3.0 8.8 + - - +
527K THR* 3.5 19.5 - - + -
528K MET 3.3 21.0 + - - +
545K ILE* 3.8 29.8 - - + -
547K PHE* 3.5 20.6 - + + -
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Residues in contact with LYS 425 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423K LEU* 3.4 17.4 - - + +
424K PHE* 1.3 72.6 - - - +
426K GLY* 1.3 60.7 + - - +
528K MET* 3.5 30.1 - - + -
530K GLU* 3.5 26.2 - - + +
531K TYR 3.0 28.1 + - - +
532K SER* 5.0 0.8 - - - +
533K VAL* 4.1 10.9 - - + +
538K GLN* 5.7 0.4 + - - -
544K GLN* 3.3 24.6 + - + +
545K ILE 3.4 4.1 + - - -
546K ASP* 3.1 34.9 - - - +
547K 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