Contacts of the strand formed by residues 524 - 528 (chain H) 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 GLY 524 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408H PHE* 4.3 3.7 - - - -
412H MET* 4.0 5.1 - - - +
420H ARG 3.9 2.8 - - - +
421H TYR* 3.1 33.0 - - - +
422H TRP 3.1 4.2 + - - -
469H LEU* 3.9 9.6 - - - -
470H VAL 3.1 13.5 - - - -
523H PRO* 1.3 81.0 - - - +
525H ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 525 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408H PHE* 3.5 28.0 - - + -
421H TYR* 4.0 0.4 - - - -
422H TRP* 3.6 11.9 - - + +
424H PHE* 3.4 41.1 - - + -
436H ALA* 4.6 7.2 - - + +
439H LEU* 3.5 35.7 - - + -
469H LEU* 6.0 1.1 - - + -
470H VAL 2.8 11.1 + - - +
471H VAL* 3.4 13.3 - - + +
472H PHE* 2.9 25.5 + - - +
524H GLY* 1.3 78.2 - - - +
526H VAL* 1.3 71.9 + - - +
527H THR* 4.2 7.4 - - + -
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Residues in contact with VAL 526 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421H TYR* 3.6 18.8 - - + -
422H TRP 3.0 6.1 + - - -
423H LEU* 3.2 9.9 - - - +
424H PHE 3.0 21.0 + - - -
472H PHE* 3.5 33.4 - - + -
475H VAL* 4.1 9.9 - - + -
494H LEU* 3.7 31.9 - - + -
501H LEU* 5.1 2.7 - - + -
525H ILE* 1.3 76.6 - - - +
527H THR* 1.3 64.9 + - - +
528H MET* 4.9 2.9 - - + -
541H PHE* 3.7 27.8 - - + -
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Residues in contact with THR 527 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424H PHE* 3.5 31.2 - - + -
432H LYS* 4.9 10.5 - - + -
433H THR* 6.1 0.7 - - - -
436H ALA* 3.7 25.6 - - + -
471H VAL* 5.1 1.6 - - + -
472H PHE 2.8 24.7 + - - +
473H GLU* 3.2 13.8 + - - +
474H ASP* 2.8 23.6 + - - -
475H VAL* 3.2 24.6 + - - +
525H ILE* 4.2 4.3 - - + -
526H VAL* 1.3 75.0 - - - +
528H MET* 1.3 63.6 + - - +
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Residues in contact with MET 528 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423H LEU* 3.5 22.0 - - + -
424H PHE 3.3 4.8 + - - +
425H LYS* 3.5 31.8 - - + -
426H GLY 3.0 21.7 + - - +
432H LYS* 3.9 1.0 - - - +
474H ASP* 4.3 3.1 - - - +
475H VAL* 3.5 26.9 - - + +
491H ILE* 3.6 25.8 - - + -
494H LEU* 4.9 3.4 - - + -
526H VAL* 4.9 5.4 - - + -
527H THR* 1.3 78.4 - - - +
529H ASN* 1.3 73.3 + - - +
531H TYR* 4.1 11.9 - - + +
533H VAL* 3.5 32.3 - - + -
537H LEU* 5.3 0.2 - - + -
541H PHE* 5.0 2.7 - - + -
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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
------------------------------------------------------------
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