Contacts of the strand formed by residues 529 - 535 (chain C) in PDB entry 6V3O
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 PHE 529 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304C THR* 4.3 4.7 - - + -
308C CYS* 4.1 18.4 - - - -
452C LYS* 3.7 18.6 + - - +
453C LEU* 3.5 13.0 - - + +
455C ILE* 4.1 17.7 - - + -
521C LEU* 3.9 38.4 - - + -
524C LEU* 3.7 42.0 - - + -
525C PRO 3.9 13.2 - - - -
526C PRO* 3.2 17.7 + - + +
527C ASP 3.3 0.2 - - - -
528C SER* 1.3 86.8 - - - +
530C GLY* 1.3 66.7 + - - +
559C LEU* 4.0 25.1 - - + -
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Residues in contact with GLY 530 (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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452C LYS* 4.1 9.6 - - - +
453C LEU 3.0 15.5 + - - +
454C ASP* 4.2 3.1 - - - -
529C PHE* 1.3 76.3 - - - +
531C PRO* 1.3 73.5 - - - +
559C LEU* 3.5 19.6 - - - +
560C PRO* 4.0 8.9 - - - +
669C ARG* 5.6 0.2 - - - -
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Residues in contact with PRO 531 (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 ASP* 3.3 21.7 - - - +
455C ILE* 3.0 26.9 + - - +
530C GLY* 1.3 88.4 - - - +
532C TYR* 1.3 57.9 + - - +
533C ILE* 4.1 8.3 - - + -
559C LEU* 4.0 2.7 - - - +
560C PRO* 3.5 13.9 - - + +
562C VAL* 3.5 27.1 - - + -
596C GLN* 3.9 12.8 - - - +
669C ARG* 3.5 27.6 - - - +
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Residues in contact with TYR 532 (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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293C ARG* 5.8 0.9 - - - -
455C ILE* 3.4 31.0 - - + -
457C GLN* 3.4 19.0 - - + +
462C HIS* 2.7 40.7 + + - -
514C VAL* 5.0 1.9 - - - +
517C ALA* 5.9 4.5 - - + -
518C PHE* 3.4 34.6 - + - -
521C LEU* 4.1 12.1 - - + -
531C PRO* 1.3 71.2 - - - +
533C ILE* 1.3 71.8 + - - +
534C ILE* 4.0 2.0 + - + -
546C VAL* 3.8 24.2 - - + -
550C GLN* 5.2 3.4 - - + +
559C LEU* 4.0 14.4 - - + +
560C PRO 3.0 11.0 + - - +
561C VAL* 3.6 5.6 - - - +
562C VAL 3.0 23.2 + - - +
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Residues in contact with ILE 533 (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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288C TRP* 4.0 13.5 - - + +
454C ASP* 4.0 19.1 - - + +
455C ILE 2.6 16.3 + - - +
456C ARG* 3.3 18.0 - - + +
457C GLN 3.1 26.3 + - - +
531C PRO* 4.1 14.1 - - + -
532C TYR* 1.3 80.6 - - - +
534C ILE* 1.3 62.5 + - - +
562C VAL* 3.3 18.2 - - + +
564C LEU* 4.1 11.7 - - + -
598C MET* 3.9 20.6 - - + -
638C PHE* 3.7 34.1 - - + -
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Residues in contact with ILE 534 (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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457C GLN 3.4 3.1 - - - +
459C SER* 3.7 25.1 - - - +
462C HIS* 4.3 6.3 - - + +
532C TYR* 4.4 3.1 - - + -
533C ILE* 1.3 73.0 - - - +
535C SER* 1.3 72.6 + - - +
537C ALA* 3.6 14.6 - - + +
542C ASP* 3.2 33.4 - - + +
543C VAL* 3.8 7.6 - - + -
546C VAL* 3.6 18.6 - - + -
561C VAL* 3.5 29.2 - - + -
562C VAL 2.8 15.5 + - - +
563C PRO* 4.5 0.4 - - + -
564C LEU* 2.9 29.7 + - - +
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Residues in contact with SER 535 (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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294C ASP* 2.7 29.4 + - - -
456C ARG* 3.3 28.3 + - - +
457C GLN 2.9 9.1 + - - -
458C GLU* 3.7 16.2 - - - -
459C SER* 3.0 24.0 + - - -
533C ILE 3.8 1.8 + - - -
534C ILE* 1.3 72.7 - - - +
536C MET* 1.3 72.0 + - - +
537C ALA 3.2 1.0 + - - -
564C LEU* 3.8 6.8 - - - +
566C GLU* 3.8 6.4 + - - -
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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