Contacts of the strand formed by residues 449 - 457 (chain C) in PDB entry 5U03
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 ARG 449 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436C MET 6.0 0.7 - - - +
437C PRO* 5.8 0.6 - - - +
438C GLU* 3.2 39.5 + - + +
447C THR 3.6 2.2 + - - -
448C MET* 1.3 70.1 - - - +
450C LEU* 1.3 61.3 + - - +
453C ARG* 3.3 37.2 - - - +
454C ARG 4.1 5.9 + - - +
478C HIS* 3.0 32.4 + - + -
479C ARG* 3.1 7.1 + - - -
480C HIS* 2.8 56.5 + - + +
481C ARG* 4.7 0.6 - - - +
503C ASP* 3.8 26.7 + - - +
504C VAL* 5.1 1.6 - - - +
505C GLU* 4.8 6.5 + - - -
508C ARG* 3.8 35.7 - - - +
510C GLU* 4.0 3.0 + - - -
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Residues in contact with LEU 450 (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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60C VAL* 4.0 11.4 - - + -
64C GLY* 3.2 37.4 - - - +
66C GLU* 3.5 19.5 - - + +
448C MET* 3.3 16.1 + - + +
449C ARG* 1.3 75.4 - - - +
451C GLY* 1.3 64.3 + - - +
453C ARG* 2.8 28.5 + - - +
478C HIS* 3.1 10.8 - - - +
479C ARG* 3.4 37.9 - - + +
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Residues in contact with GLY 451 (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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60C VAL* 3.8 17.7 - - - +
64C GLY* 4.1 9.9 - - - -
450C LEU* 1.3 82.9 - - - +
452C LYS* 1.3 63.5 + - - -
453C ARG* 3.3 8.2 + - - +
477C ARG* 4.5 0.7 - - - -
478C HIS* 2.7 36.7 + - - +
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Residues in contact with LYS 452 (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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60C VAL* 4.9 0.6 - - - +
61C LEU 4.7 2.0 + - - -
62C ASP* 4.3 30.0 + - + +
81C ARG* 5.9 1.2 - - - +
451C GLY* 1.3 68.7 - - - -
453C ARG* 1.3 66.5 + - - +
475C GLU* 3.4 43.1 + - + +
476C GLU 3.2 15.5 - - - +
477C ARG* 3.6 29.9 - - - +
530C LEU* 5.2 6.7 - - + +
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Residues in contact with ARG 453 (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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438C GLU* 2.7 42.0 + - - -
440C ASN* 5.6 1.8 - - - +
448C MET 4.9 0.4 + - - -
449C ARG* 3.3 31.3 - - - +
450C LEU 2.8 38.7 + - - +
451C GLY* 3.4 11.7 - - - +
452C LYS* 1.3 85.0 - - - +
454C ARG* 1.3 62.2 + - - +
455C THR 3.9 0.2 + - - -
475C GLU* 3.2 7.8 - - - -
476C GLU 3.0 28.4 + - - +
478C HIS* 3.5 22.9 + - + +
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Residues in contact with ARG 454 (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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449C ARG* 4.1 10.4 + - - +
453C ARG* 1.3 74.3 - - - +
455C THR* 1.3 64.0 + - - +
456C LEU* 3.9 20.6 - - + -
473C TYR* 3.5 50.0 + - + -
474C LEU 3.5 2.9 - - - -
475C GLU* 2.8 30.1 + - + +
503C ASP* 4.2 0.9 - - - -
504C VAL* 3.7 33.2 + - + +
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Residues in contact with THR 455 (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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453C ARG 3.9 0.4 + - - -
454C ARG* 1.3 72.4 - - - +
456C LEU* 1.3 67.6 + - - +
473C TYR* 3.3 5.0 - - - +
474C LEU* 2.8 56.6 + - + +
476C GLU* 5.2 1.7 - - - +
478C HIS* 3.5 27.9 + - - -
501C GLY* 4.0 4.7 - - - -
502C GLN 3.2 20.2 - - - +
503C ASP* 5.4 0.2 - - - -
510C GLU* 3.6 26.5 + - + +
511C ILE* 4.6 4.3 - - + -
525C TYR* 4.6 4.8 - - + -
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Residues in contact with LEU 456 (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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454C ARG* 3.9 17.3 - - + -
455C THR* 1.3 78.3 - - - +
457C PHE* 1.3 67.6 + - - +
458C GLN 3.7 0.3 + - - -
472C ASP 4.3 3.6 - - - +
473C TYR* 3.6 23.6 - - + -
474C LEU* 4.9 0.2 - - - -
501C GLY* 3.5 4.6 - - - -
502C GLN* 2.7 49.3 + - + +
503C ASP 4.3 1.8 - - - +
504C VAL* 3.9 40.2 - - + +
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Residues in contact with PHE 457 (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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456C LEU* 1.3 79.1 - - - +
458C GLN* 1.3 61.5 + - - +
459C THR 3.3 7.2 - - - +
462C SER* 4.3 3.1 - - - -
464C MET* 4.5 1.8 - - + -
465C ARG* 3.4 57.2 + - + +
468C TYR* 3.8 19.7 - + + -
471C ALA* 3.0 33.4 - - + -
472C ASP 3.3 20.2 + - - +
473C TYR* 3.9 7.4 - - - -
474C LEU* 3.7 22.2 - - + -
500C VAL* 3.6 19.5 - - + -
502C GLN* 5.3 1.6 + - - -
511C ILE* 4.2 18.6 - - + -
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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