Contacts of the strand formed by residues 542 - 550 (chain C) in PDB entry 3VI4
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 ASP 542 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486C PHE* 3.7 2.1 - - - +
487C CYS* 3.4 1.7 - - - -
488C LEU* 3.2 29.5 + - - +
533C LEU* 5.3 6.5 - - + +
534C LEU 4.2 15.6 - - - +
535C ILE* 4.0 27.2 - - + +
540C ARG 3.3 5.5 + - - +
541C GLU* 1.3 70.3 - - - +
543C CYS* 1.3 62.2 + - - +
544C ARG* 2.7 37.2 + - - +
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Residues in contact with CYS 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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485C SER* 5.7 3.1 - - - -
486C PHE 3.3 4.9 - - - +
487C CYS* 2.0 47.8 - - - -
541C GLU* 3.4 17.3 + - - -
542C ASP* 1.3 76.4 + - - +
544C ARG* 1.3 78.7 + - - +
545C GLU* 5.9 2.9 - - + -
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Residues in contact with ARG 544 (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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484C LEU 3.7 1.7 - - - +
485C SER* 3.3 19.2 - - - -
486C PHE* 3.2 31.8 + - + +
531C GLN* 4.4 15.6 - - - +
533C LEU* 3.8 36.3 - - - +
542C ASP* 2.7 41.4 + - - +
543C CYS* 1.3 86.4 + - - +
545C GLU* 1.3 65.2 + - - +
546C MET* 5.1 6.1 - - + +
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Residues in contact with GLU 545 (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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483C ASN* 4.3 20.1 + - + +
484C LEU 3.4 4.9 - - - +
485C SER* 3.6 21.1 + - - -
543C CYS* 5.9 2.5 - - + -
544C ARG* 1.3 76.0 - - - +
546C MET* 1.3 66.6 + - - +
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Residues in contact with MET 546 (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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482C ILE 3.6 0.9 - - - +
483C ASN* 3.6 6.2 + - - +
484C LEU* 2.8 51.0 + - + +
486C PHE* 4.9 10.8 - - + -
505C LEU* 4.6 7.2 - - - -
521C PHE* 3.7 31.6 - - + -
529C LEU* 3.9 26.2 - - + -
531C GLN* 4.0 13.5 - - - +
544C ARG* 5.1 7.2 - - + +
545C GLU* 1.3 79.4 - - - +
547C LYS* 1.3 66.5 + - - +
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Residues in contact with LYS 547 (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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472C CYS* 4.2 23.4 - - - -
481C CYS* 4.3 18.2 - - + +
482C ILE 3.3 14.4 - - - +
483C ASN* 3.7 26.5 - - - +
521C PHE* 3.9 2.8 - - - -
522C LEU* 2.9 39.9 + - + +
546C MET* 1.3 81.6 - - - +
548C ILE* 1.3 65.8 + - - +
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Residues in contact with ILE 548 (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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460C ILE* 5.3 7.6 - - + -
465C PHE* 3.6 21.5 - - + -
480C ALA 3.7 0.8 - - - +
481C CYS* 4.9 1.3 - - - -
482C ILE* 3.2 43.2 + - + +
484C LEU* 3.8 31.4 - - + -
507C LEU* 3.7 24.9 - - + -
519C ALA* 5.4 1.8 - - + +
520C LEU 3.2 12.1 - - - +
521C PHE* 3.5 34.5 - - + -
547C LYS* 1.3 73.1 - - - +
549C TYR* 1.3 60.4 + - - +
565C ILE* 5.4 7.0 - - + -
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Residues in contact with TYR 549 (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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465C PHE* 3.9 3.8 - - - -
474C LEU* 4.4 11.4 - - + +
479C VAL* 3.7 22.9 - - + -
480C ALA 3.2 15.3 - - - +
481C CYS* 5.2 1.1 - - - -
519C ALA* 3.5 5.0 - - - +
520C LEU* 2.8 81.4 + - + +
521C PHE 3.5 19.3 - - - -
522C LEU* 3.8 30.3 - - + -
525C ARG* 3.0 34.7 - - + +
547C LYS 4.3 0.2 - - - -
548C ILE* 1.3 73.8 - - - +
550C LEU* 1.3 72.8 + - - +
551C ARG* 4.5 9.4 - - + -
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Residues in contact with LEU 550 (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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465C PHE* 3.4 50.9 - - + +
466C ASN 5.3 5.2 - - - +
467C PRO* 5.7 3.8 - - + -
479C VAL* 2.9 25.7 - - - +
480C ALA* 3.7 8.4 + - + +
518C ARG* 3.7 20.4 - - + +
519C ALA* 3.9 14.6 - - + -
549C TYR* 1.3 77.7 - - - +
551C ARG* 1.3 70.9 - - - +
559C LYS* 4.8 16.8 - - - +
563C ILE* 5.9 4.7 - - + -
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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