Contacts of the strand formed by residues 421 - 425 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C ARG* 1.3 86.3 - - + +
422C TRP* 1.3 60.3 + - - +
470C VAL* 4.4 3.6 - - + +
472C PHE* 3.7 22.4 - + - -
501C LEU* 3.8 45.5 - - + -
521C PHE* 3.1 25.1 - - - -
522C PRO 2.7 22.9 + - - -
523C PRO* 3.6 16.3 + - + -
524C GLY* 3.1 26.7 - - - -
525C ILE 4.1 0.4 - - - -
526C VAL* 3.6 27.6 - - + -
540C ARG 4.4 9.7 + - - +
541C PHE* 3.4 10.2 - - + -
542C VAL* 2.9 29.5 + - - +
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Residues in contact with TRP 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C VAL* 3.5 33.2 - - + -
407C ASP* 4.2 12.1 - - + -
408C PHE* 3.9 45.2 - + + -
411C CYS* 3.2 26.0 - - + +
420C ARG 3.3 16.4 - - - -
421C TYR* 1.3 76.8 - - - +
423C LEU* 1.3 60.1 + - - +
424C PHE* 4.3 8.5 - + + -
524C GLY 3.1 5.9 + - - -
525C ILE* 3.6 17.0 - - + +
526C VAL 3.0 25.1 + - - +
541C PHE* 3.7 5.9 - - - -
542C VAL* 4.0 10.5 - - + +
543C LYS* 3.5 44.0 - - + -
545C ILE* 3.5 19.5 - - + -
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Residues in contact with LEU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C TRP* 1.3 71.5 - - - +
424C PHE* 1.3 67.2 + - - +
425C LYS* 3.5 17.7 + - + -
526C VAL 3.2 15.9 - - - +
528C MET* 3.5 37.2 - - + -
533C VAL* 4.9 1.3 - - + -
538C GLN* 3.8 20.2 - - - +
541C PHE* 3.5 25.3 - - + -
543C LYS 2.9 16.4 + - - +
544C GLN* 3.5 34.8 - - + +
545C ILE* 2.8 30.1 + - - +
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Residues in contact with PHE 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C PHE* 6.3 0.2 - + - -
422C TRP* 4.3 11.4 - + + -
423C LEU* 1.3 76.8 - - - +
425C LYS* 1.3 58.5 + - - +
426C GLY 3.6 1.0 + - - -
432C LYS* 3.9 13.6 - - + +
435C LEU* 3.5 34.3 - - + -
436C ALA* 3.8 24.9 - - + -
439C LEU* 3.6 22.4 - - + -
525C ILE* 3.4 24.5 - - + -
526C VAL 3.0 8.5 + - - -
527C THR* 3.5 19.4 - - + -
528C MET 3.3 21.1 + - - +
545C ILE* 3.8 30.7 - - + -
547C PHE* 3.5 20.2 - + + -
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Residues in contact with LYS 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423C LEU* 3.4 17.4 + - + -
424C PHE* 1.3 73.4 - - - +
426C GLY* 1.3 59.9 + - - +
528C MET* 3.5 30.3 - - + -
530C GLU* 3.5 26.2 + - + +
531C TYR 3.0 27.9 + - - -
532C SER* 5.0 0.6 - - - +
533C VAL* 4.1 10.5 - - + +
538C GLN* 5.7 0.6 + - - -
544C GLN* 3.3 25.9 + - + +
545C ILE 3.4 4.3 + - - -
546C ASP* 3.1 35.5 - - - +
547C 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