Contacts of the strand formed by residues 522 - 528 (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 GLY 522 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518C LEU* 4.0 5.4 - - - -
521C SER* 1.3 77.6 - - - +
523C TRP* 1.3 66.1 + - - -
539C GLU 3.1 13.0 - - - -
540C PRO* 4.0 1.1 - - - -
541C ASN 3.5 6.3 - - - -
557C ASP* 3.6 0.2 - - - +
558C VAL* 2.9 34.1 + - - +
559C TRP* 3.3 17.2 - - - -
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Residues in contact with TRP 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C GLN* 2.9 25.3 + - - -
473C ASN* 3.2 32.7 - - + +
474C HIS* 3.4 46.7 - + - -
477C TYR* 3.9 20.4 - + + -
518C LEU* 3.5 7.2 - - - +
522C GLY* 1.3 76.3 - - - -
524C VAL* 1.3 61.3 + - - +
525C TRP* 3.4 21.1 - + + +
537C GLU 3.6 0.3 - - - +
539C GLU* 2.7 39.1 + - - +
541C ASN 3.0 20.2 + - - -
543C GLY 3.9 6.7 - - - -
555C THR* 3.4 18.6 - - + +
556C PHE 3.4 4.9 - - - -
557C ASP* 3.4 40.6 - - + -
558C VAL* 4.5 0.2 - - - -
559C TRP* 3.7 2.6 - - - +
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Residues in contact with VAL 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C PHE* 3.2 47.3 - - + +
514C ALA* 3.8 29.4 - - + +
515C GLY* 4.5 15.9 - - - -
518C LEU* 4.6 2.4 - - + +
523C TRP* 1.3 74.3 - - - +
525C TRP* 1.3 62.9 + - - +
536C ILE* 4.0 7.4 - - + -
537C GLU 3.5 5.6 - - - +
538C LYS* 4.7 2.0 - - + +
555C THR* 3.0 5.9 + - - -
556C PHE* 2.9 45.0 + - + +
558C VAL* 5.0 2.3 - - + +
575C LEU* 5.6 0.4 - - + -
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Residues in contact with TRP 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C ASN* 3.5 18.8 - - + -
476C LEU* 3.6 21.1 - - + -
511C PHE* 3.7 4.8 - - - -
523C TRP* 3.4 17.4 - - + +
524C VAL* 1.3 73.8 - - - +
526C LEU* 1.3 61.4 + - - +
527C ALA 3.7 0.3 + - - -
535C SER 3.5 1.2 - - - +
536C ILE* 3.4 4.2 - - - -
537C GLU* 2.7 46.3 + - + +
539C GLU* 3.5 25.6 - - + -
543C GLY 3.2 17.6 + - - -
544C ASN* 3.1 26.9 - - - -
545C PRO* 3.4 22.3 - - + +
552C PRO* 3.3 33.0 - - + -
554C LEU* 3.5 12.6 - - - -
555C THR* 3.4 36.8 - - + -
590C ARG* 5.8 1.3 - - - -
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Residues in contact with LEU 526 (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* 4.8 7.6 - - + -
497C ILE* 5.1 3.6 - - + -
501C PHE* 4.9 0.9 - - + -
507C PHE* 3.7 34.1 - - + -
511C PHE* 3.6 17.1 - - + -
525C TRP* 1.3 73.0 - - - +
527C ALA* 1.3 62.8 + - - +
534C LEU* 4.1 24.9 - - + -
535C SER 3.5 11.9 - - - +
536C ILE* 4.9 0.7 - - + -
552C PRO* 4.2 1.2 - - - +
553C LEU* 2.9 51.5 + - + +
554C LEU* 2.9 28.7 + - + +
584C TRP* 4.7 12.8 - - + -
587C VAL* 4.8 1.6 - - + -
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Residues in contact with ALA 527 (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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525C TRP 3.7 0.4 + - - -
526C LEU* 1.3 76.3 - - - +
528C SER* 1.3 61.1 + - - +
534C LEU* 3.3 6.8 - - - +
535C SER* 2.8 46.8 + - - +
537C GLU* 4.1 9.9 - - + -
545C PRO* 4.1 13.9 - - + -
550C LEU* 3.9 21.5 - - + -
551C ASN 3.3 11.9 - - - +
553C LEU* 4.3 3.8 - - - -
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Residues in contact with SER 528 (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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527C ALA* 1.3 75.0 - - - +
529C ASP* 1.3 65.4 + - - +
532C GLY 4.8 0.2 - - - -
533C LYS 3.3 9.0 - - - -
534C LEU* 4.1 0.4 - - - -
550C LEU* 3.3 8.7 - - - +
551C ASN* 3.0 48.6 + - - +
553C LEU* 3.6 15.1 - - - +
591C TYR* 3.8 35.1 + - - -
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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