Contacts of the strand formed by residues 565 - 572 (chain C) in PDB entry 2VGB
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 THR 565 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451C PRO* 3.9 3.8 - - - +
452C THR* 3.8 42.1 + - + +
455C THR* 4.4 8.5 - - - -
474C LEU 4.4 3.3 + - - -
480C SER* 2.9 24.1 + - - -
555C VAL* 3.4 33.0 - - + -
556C THR* 3.4 13.2 + - - +
557C GLY* 4.0 3.1 - - - -
563C GLY 3.7 2.0 - - - -
564C TYR* 1.3 78.0 - - - +
566C ASN* 1.3 66.8 + - - +
580C FBP 3.8 16.5 + - - -
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Residues in contact with ASN 566 (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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451C PRO* 4.3 10.1 - - + -
455C THR* 3.3 19.1 + - - +
556C THR 3.0 4.9 + - - -
558C TRP* 3.3 38.2 + - + +
564C TYR 3.8 1.6 - - - +
565C THR* 1.3 77.1 - - - +
567C ILE* 1.3 75.6 + - - +
568D MET 3.8 0.3 - - - +
569D ARG* 3.1 10.1 - - - +
570D VAL 2.6 52.1 + - - +
571D LEU* 3.8 14.6 - - - +
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Residues in contact with ILE 567 (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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455C THR* 3.5 9.5 - - - +
554C VAL 4.4 0.4 - - - +
555C VAL* 3.3 6.8 - - - +
556C THR* 3.1 40.8 + - - +
557C GLY 3.7 26.5 - - - +
558C TRP* 4.1 5.8 - - + +
566C ASN* 1.3 94.6 - - - +
568C MET* 1.3 65.5 + - - +
569C ARG* 4.0 14.8 - - + +
567D ILE* 3.7 27.8 - - + -
568D MET 3.3 2.9 - - - +
569D ARG* 3.6 19.7 - - + -
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Residues in contact with MET 568 (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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455C THR* 3.9 12.8 - - + -
458C GLY 4.3 6.3 - - - +
459C ALA* 4.0 20.2 - - + +
462C ALA* 4.0 24.5 - - + -
553C ILE* 3.7 18.2 - - + -
554C VAL 3.5 2.9 - - - +
555C VAL* 4.5 0.9 - - + -
567C ILE* 1.3 77.1 - - - +
569C ARG* 1.3 70.4 + - - +
570C VAL* 3.7 29.4 - - + +
455D THR* 4.6 15.9 - - + -
458D GLY* 4.9 4.9 - - - -
567D ILE* 3.3 3.5 - - - -
568D MET* 2.7 58.5 + - + +
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Residues in contact with ARG 569 (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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529C VAL* 5.1 2.6 - - - +
530C ASP* 4.5 13.2 + - - -
533C VAL* 4.2 14.5 - - - +
553C ILE* 3.3 6.4 - - - +
554C VAL* 2.8 63.4 + - + +
556C THR* 4.3 16.4 + - - +
567C ILE* 4.0 8.8 - - + +
568C MET* 1.3 83.1 - - - +
570C VAL* 1.3 65.6 + - - +
571C LEU* 3.7 30.3 + - + +
558D TRP* 6.2 2.8 - - - +
566D ASN* 3.2 11.9 - - - +
567D ILE* 3.7 34.3 - - + -
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Residues in contact with VAL 570 (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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551C LEU* 4.2 21.5 - - + -
552C VAL 3.7 6.3 - - - +
553C ILE* 3.8 8.1 - - + -
568C MET* 3.7 21.1 - - + -
569C ARG* 1.3 72.1 - - - +
571C LEU* 1.3 62.2 + - - +
451D PRO* 3.8 33.6 - - + +
454D VAL* 3.7 33.7 - - + -
455D THR* 4.0 9.4 - - - +
566D ASN* 2.7 37.4 + - + +
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Residues in contact with LEU 571 (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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533C VAL* 4.6 10.1 - - + -
534C GLN* 5.6 2.9 - - - +
537C ILE* 4.8 9.9 - - + -
551C LEU* 3.4 7.4 - - - +
552C VAL* 2.6 50.3 + - + +
554C VAL* 3.5 29.4 - - + -
569C ARG* 3.7 29.1 + - + +
570C VAL* 1.3 84.8 - - - +
572C SER* 1.3 62.4 + - - +
573C ILE* 5.6 1.3 - - + -
451D PRO* 6.3 0.2 - - - -
558D TRP* 6.0 3.6 - - + -
566D ASN* 3.7 12.6 - - - +
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Residues in contact with SER 572 (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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549C GLY* 5.3 3.6 - - - -
550C ASP 3.4 7.4 - - - -
551C LEU* 3.7 17.0 - - - +
571C LEU* 1.3 78.0 - - - +
573C ILE* 1.3 68.6 + - - +
451D PRO* 6.1 2.0 - - - +
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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