Contacts of the strand formed by residues 551 - 557 (chain C) in PDB entry 1UES
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 ASN 551 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527C ALA* 3.3 6.3 - - - -
528C SER* 3.0 49.5 + - - +
529C ASP* 5.7 1.1 - - - +
545C PRO* 5.1 0.2 - - - -
550C LEU* 1.3 75.2 + - - +
552C PRO* 1.3 71.9 - - - +
553C LEU* 3.3 1.6 + - + +
590C ARG* 2.8 27.4 - - - +
591C TYR* 5.2 0.7 - - - +
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Residues in contact with PRO 552 (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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476C LEU* 4.2 18.9 - - + +
525C TRP* 3.3 35.0 - - + -
526C LEU 4.2 3.1 - - - +
544C ASN* 4.4 0.7 - - - +
545C PRO* 4.1 11.2 - - + -
546C VAL* 3.8 20.0 - - + -
550C LEU 3.5 9.8 - - - +
551C ASN* 1.3 88.7 - - + +
553C LEU* 1.3 64.8 + - - +
554C LEU 3.8 0.4 - - - -
590C ARG* 3.7 19.2 + - - +
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Residues in contact with LEU 553 (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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493C LEU* 3.9 11.4 - - + -
526C LEU* 2.9 34.9 + - + +
528C SER* 3.6 16.4 - - - +
534C LEU* 3.6 21.3 - - + -
551C ASN* 3.9 7.2 - - - +
552C PRO* 1.3 76.6 - - - +
554C LEU* 1.3 61.7 + - - +
587C VAL* 3.7 14.5 - - + +
590C ARG* 3.1 56.9 + - + +
591C TYR* 3.5 37.9 - - + +
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Residues in contact with LEU 554 (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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480C GLN* 3.6 27.1 - - - +
507C PHE* 5.0 0.9 - - + -
511C PHE* 4.2 16.3 - - + -
524C VAL 3.9 0.2 - - - +
525C TRP* 3.5 6.3 - - - -
526C LEU* 2.9 37.9 + - + -
552C PRO 3.8 0.4 - - - -
553C LEU* 1.3 81.2 - - - +
555C THR* 1.3 71.2 + - - +
556C PHE* 3.8 18.4 - - + -
579C TRP* 4.0 26.7 - - + -
582C VAL* 4.1 21.5 - - + -
584C TRP* 4.0 15.3 - - + -
587C VAL* 4.1 12.8 - - + -
590C ARG* 4.1 1.1 - - - +
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Residues in contact with THR 555 (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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473C ASN 4.4 0.4 - - - +
476C LEU* 4.8 0.9 - - + -
477C TYR* 3.4 30.3 - - + +
480C GLN* 2.6 39.6 + - - +
511C PHE* 4.9 0.4 - - - -
523C TRP* 3.4 25.5 - - + +
524C VAL 3.0 14.2 + - - -
525C TRP* 3.4 38.3 - - + -
554C LEU* 1.3 79.0 - - - +
556C PHE* 1.3 65.8 + - - +
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Residues in contact with PHE 556 (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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477C TYR* 4.4 2.5 - - - -
480C GLN* 4.5 0.9 - - - -
481C PHE* 4.6 4.7 - + - -
511C PHE* 3.6 15.7 - + - -
512C ASN* 4.5 1.6 - - - -
523C TRP* 3.4 4.0 - - - -
524C VAL* 2.9 44.2 + - + +
554C LEU* 3.8 22.7 - - + -
555C THR* 1.3 84.2 - - - +
557C ASP* 1.3 61.5 + - - +
558C VAL* 3.5 2.1 + - + +
575C LEU* 3.8 33.2 - - + -
578C LEU* 3.7 34.5 - - + -
579C TRP* 3.6 54.5 - + - -
582C VAL* 4.0 7.6 - - + -
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Residues in contact with ASP 557 (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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427C HIS* 2.9 10.2 + - - -
474C HIS* 3.6 0.9 + - - -
477C TYR* 3.5 24.3 + - + -
522C GLY 3.6 0.8 - - - +
523C TRP* 3.4 27.2 - - + -
556C PHE* 1.3 73.0 - - - +
558C VAL* 1.3 60.7 + - - +
559C TRP* 3.1 32.4 + - - +
562C ALA* 3.5 19.9 - - + +
563C TYR* 4.5 2.1 - - - -
574C HIS* 4.5 11.1 + - - -
575C LEU* 4.9 0.2 - - - +
578C LEU* 5.3 0.4 - - - +
592C MN 2.1 34.8 + - - -
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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
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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