Contacts of the strand formed by residues 504 - 508 (chain C) in PDB entry 4BUR
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 THR 504 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C PRO* 3.6 27.0 - - + +
347C TYR* 4.3 3.5 + - - -
500C SER* 5.5 3.1 - - - +
502C LEU 3.2 9.8 + - - +
503C PRO* 1.3 74.2 - - - +
505C VAL* 1.3 69.8 + - - +
514C GLN 4.7 0.2 - - - -
515C ASP* 3.8 2.8 - - - +
516C ASN* 3.3 33.4 + - - +
565C ILE* 3.8 11.0 - - + -
566C PHE 3.1 6.7 - - - -
567C TYR* 3.4 46.9 - - + -
568C LEU* 4.9 0.2 - - - -
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Residues in contact with VAL 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C THR* 1.3 80.1 - - - +
506C GLY* 1.3 61.7 + - - +
507C VAL* 4.6 11.7 - - + -
513C ALA* 5.2 8.1 - - + -
514C GLN 3.6 6.5 - - - +
515C ASP* 3.7 24.7 - - - +
565C ILE* 3.4 3.4 - - - -
566C PHE* 2.7 43.2 + - + +
568C LEU* 3.7 23.8 - - + -
601C LEU* 3.9 30.5 - - + -
602C ASN* 5.4 2.9 - - - +
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Residues in contact with GLY 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C TYR* 3.8 7.9 + - - -
505C VAL* 1.3 74.2 - - - +
507C VAL* 1.3 61.9 + - - -
508C PHE* 3.3 22.5 - - - -
513C ALA* 3.3 3.0 - - - -
514C GLN 2.8 41.0 + - - -
564C VAL 3.4 7.4 - - - -
565C ILE* 4.1 5.2 - - - -
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Residues in contact with VAL 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C VAL* 4.6 11.2 - - + -
506C GLY* 1.3 76.6 - - - -
508C PHE* 1.3 65.8 + - - +
513C ALA* 4.4 9.6 - - + +
563C GLY* 3.2 2.6 - - - -
564C VAL 2.9 30.4 + - - +
566C PHE* 4.3 13.5 - - + -
601C LEU 4.5 5.2 - - - +
602C ASN* 3.7 29.8 - - - +
605C ALA* 3.8 31.2 - - + -
610C ILE* 3.6 11.4 - - + +
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Residues in contact with PHE 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C TYR* 3.7 29.6 - + - -
348C LEU* 4.4 5.6 - - + -
506C GLY* 3.3 31.4 - - - -
507C VAL* 1.3 79.4 - - - +
509C ALA* 1.3 65.0 + - - +
510C LYS 3.5 0.9 - - - +
511C ALA* 3.5 30.9 - - + +
512C THR 4.2 11.1 + - - -
514C GLN* 4.6 0.4 - - + -
559C ASP 4.7 2.5 - - - +
560C TYR* 3.7 48.7 - + + -
562C LYS 3.6 3.6 - - - +
563C GLY* 3.8 19.3 - - - -
564C VAL 5.1 0.2 - - - -
565C ILE* 4.0 21.5 - - + -
579C TRP* 4.4 8.5 - + - -
610C ILE* 3.9 5.8 - - - +
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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
------------------------------------------------------------
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