Contacts of the strand formed by residues 538 - 543 (chain C) in PDB entry 6VSB
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 CYS 538 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320C VAL* 4.0 12.6 - - + +
321C GLN 4.4 1.7 - - - +
322C PRO* 3.2 16.3 - - + +
323C THR* 2.9 26.0 + - - +
537C LYS* 1.3 70.8 - - - +
539C VAL* 1.3 59.6 + - - +
549C THR* 4.4 5.2 - - - -
550C GLY 3.1 25.1 - - - -
551C VAL* 3.4 4.8 - - - +
590C CYS* 2.0 53.8 - - + -
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Residues in contact with VAL 539 (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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322C PRO* 3.5 10.5 - - - -
323C THR 3.2 16.6 - - - +
324C GLU 3.1 23.6 - - - +
325C SER* 3.6 12.1 - - - -
326C ILE* 3.7 19.1 - - + +
534C VAL* 3.6 25.4 - - + -
537C LYS* 3.2 19.3 - - + +
538C CYS* 1.3 73.6 - - - +
540C ASN* 1.3 72.2 + - - +
541C PHE* 3.7 5.9 + - + +
549C THR* 3.1 6.4 - - - -
550C GLY 2.8 28.9 + - - +
552C LEU* 6.2 3.6 - - + -
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Residues in contact with ASN 540 (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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322C PRO* 3.6 13.7 - - + +
323C THR 5.0 1.0 - - - +
325C SER* 3.1 33.6 + - - -
326C ILE 3.4 17.5 + - - +
539C VAL* 1.3 72.7 - - - +
541C PHE* 1.3 60.2 + - - +
547C THR* 6.2 3.4 - - + -
548C GLY 3.6 6.3 - - - +
549C THR* 4.0 13.9 - - + -
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Residues in contact with PHE 541 (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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326C ILE* 3.6 16.6 - - + -
539C VAL* 3.9 11.4 - - + +
540C ASN* 1.3 73.5 - - - +
542C ASN* 1.3 61.9 + - - +
543C PHE* 3.4 38.6 - + + -
546C LEU* 3.6 17.9 - - + -
547C THR* 3.1 27.5 - - - +
548C GLY* 3.0 45.4 + - - +
549C THR 3.4 17.5 - - - -
550C GLY* 3.8 4.5 - - - -
552C LEU* 4.7 9.2 - - + -
573C THR* 5.5 3.1 - - - -
587C ILE* 4.1 35.0 - - + -
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Residues in contact with ASN 542 (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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982A SER* 5.4 2.4 + - - -
326C ILE* 3.5 6.7 + - - +
327C VAL* 3.6 20.2 - - + +
328C ARG 3.0 27.3 + - - +
329C PHE* 3.9 14.4 - - - -
389C ASP* 4.4 19.4 + - - +
541C PHE* 1.3 77.0 - - - +
543C PHE* 1.3 60.0 + - - +
544C ASN 3.8 0.2 + - - -
545C GLY* 3.3 25.4 + - - -
546C LEU 2.9 3.8 - - - +
547C THR* 3.1 21.0 + - + +
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Residues in contact with PHE 543 (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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326C ILE* 4.0 9.9 - - + -
328C ARG* 3.5 41.3 - - + +
533C LEU* 4.7 3.1 - - + -
541C PHE* 3.4 40.2 - + + -
542C ASN* 1.3 69.1 - - - +
544C ASN* 1.3 61.1 + - - +
545C GLY 2.7 15.3 + - - -
546C LEU* 3.0 28.0 + - + +
552C LEU* 3.4 36.3 - - + -
576C VAL* 4.1 36.4 - - + +
578C ASP* 4.6 9.0 - - + -
579C PRO* 4.2 12.1 - - + -
585C LEU* 5.5 3.1 - - + -
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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