Contacts of the strand formed by residues 551 - 557 (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 LEU 551 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466C CYS* 3.6 38.1 - - + -
467C CYS 5.8 0.2 + - - -
468C ALA* 3.6 3.7 - - - +
469C ALA 3.3 24.9 + - - +
549C GLY 5.0 1.1 - - - +
550C ASP* 1.3 77.7 - - - +
552C VAL* 1.3 63.9 + - - +
570C VAL* 4.2 17.3 - - + -
571C LEU 3.4 15.0 - - - +
572C SER* 3.7 20.4 - - - -
449D ARG* 3.4 57.4 - - + +
451D PRO* 4.7 6.1 - - + -
454D VAL* 4.8 1.6 - - + -
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Residues in contact with VAL 552 (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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468C ALA* 4.7 0.7 - - - -
469C ALA* 5.3 0.2 - - + -
470C ALA* 3.2 38.6 - - + +
472C ILE* 4.2 19.5 - - + -
537C ILE* 5.1 0.7 - - + -
546C LEU* 4.3 13.9 - - + -
551C LEU* 1.3 76.9 - - - +
553C ILE* 1.3 63.7 + - - +
554C VAL* 3.8 22.4 - - + -
570C VAL* 3.7 3.6 - - - +
571C LEU* 2.6 47.7 + - + +
573C ILE* 4.1 21.1 - - + -
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Residues in contact with ILE 553 (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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459C ALA* 4.0 17.5 - - + -
462C ALA* 3.9 17.9 - - + -
463C ALA* 4.0 17.9 - - + +
466C CYS* 4.4 8.1 - - - -
468C ALA* 4.0 16.4 - - + -
470C ALA 3.0 8.1 + - - +
471C ILE* 3.1 11.0 - - + +
472C ILE* 2.7 27.4 + - - +
552C VAL* 1.3 77.1 - - - +
554C VAL* 1.3 66.7 + - - +
568C MET* 3.7 29.2 - - + -
569C ARG 3.3 3.4 - - - +
570C VAL* 3.8 27.8 - - + -
454D VAL* 4.3 3.8 - - + -
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Residues in contact with VAL 554 (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 ILE* 3.3 15.0 - - + +
533C VAL* 3.7 30.1 - - + -
552C VAL* 3.8 14.6 - - + -
553C ILE* 1.3 76.6 - - - +
555C VAL* 1.3 63.6 + - - +
556C THR* 4.0 7.9 + - + +
567C ILE* 3.8 0.9 - - - +
568C MET* 3.5 3.1 - - - -
569C ARG* 2.8 69.8 + - + +
571C LEU* 3.5 32.1 - - + -
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Residues in contact with VAL 555 (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* 4.2 8.1 - - + +
456C ALA* 5.8 0.9 - - - +
459C ALA* 3.7 30.1 - - + -
471C ILE* 4.0 13.7 - - + -
472C ILE 2.8 11.3 + - - +
473C VAL* 3.5 21.6 - - + +
474C LEU 3.3 24.3 + - - +
480C SER* 5.4 0.4 - - - -
484C LEU* 4.6 6.1 - - + -
553C ILE* 4.6 0.7 - - + -
554C VAL* 1.3 76.1 - - - +
556C THR* 1.3 65.2 + - - +
565C THR* 3.4 31.4 - - + -
567C ILE 3.3 9.9 - - - +
568C MET* 4.5 4.9 - - + -
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Residues in contact with THR 556 (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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474C LEU* 3.9 26.2 - - + -
529C VAL* 4.2 12.9 - - + +
533C VAL* 4.1 7.6 - - + -
554C VAL* 4.0 19.6 + - + -
555C VAL* 1.3 79.6 - - - +
557C GLY* 1.3 62.1 + - - +
565C THR* 3.4 10.5 - - - +
566C ASN 3.0 20.1 + - - -
567C ILE* 3.1 34.8 + - - +
569C ARG* 4.3 10.1 + - - +
580C FBP 4.3 7.2 - - - -
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Residues in contact with GLY 557 (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* 3.4 14.7 - - - -
529C VAL* 5.6 1.2 - - - +
556C THR* 1.3 83.4 + - - +
558C TRP* 1.3 63.7 + - - -
559C ARG 3.4 2.9 - - - -
564C TYR 3.6 12.6 - - - -
565C THR* 4.0 1.3 - - - -
566C ASN* 3.9 2.7 - - - -
567C ILE* 3.7 13.0 - - - +
580C FBP 3.2 23.0 + - - -
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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