Contacts of the strand formed by residues 551 - 557 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449C ARG* 3.6 53.7 - - + +
451C PRO* 4.8 6.7 - - + -
454C VAL* 4.9 1.6 - - + -
466D CYS* 3.6 40.2 - - + -
468D ALA* 3.6 5.4 - - - +
469D ALA* 3.3 24.0 + - - +
549D GLY 5.0 1.3 - - - +
550D ASP* 1.3 77.5 - - - +
552D VAL* 1.3 63.0 + - - +
570D VAL* 4.2 16.6 - - + -
571D LEU 3.4 14.6 - - - +
572D SER* 3.8 19.3 - - - -
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Residues in contact with VAL 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D ALA* 4.7 0.7 - - - -
469D ALA* 5.3 0.4 - - + -
470D ALA* 3.1 41.3 - - + +
472D ILE* 4.1 20.9 - - + -
537D ILE* 5.0 0.9 - - + -
546D LEU* 4.4 12.6 - - + -
550D ASP 4.2 0.2 + - - -
551D LEU* 1.3 74.7 - - - +
553D ILE* 1.3 63.6 + - - +
554D VAL* 3.8 23.1 - - + -
570D VAL* 3.7 3.3 - - - +
571D LEU* 2.6 42.5 + - + +
573D ILE* 4.1 22.7 - - + -
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Residues in contact with ILE 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D ALA* 3.9 18.6 - - + +
462D ALA* 3.8 18.2 - - + -
463D ALA* 3.9 27.6 - - + +
466D CYS* 4.3 11.4 - - - -
468D ALA* 4.0 7.0 - - + -
470D ALA 3.0 9.3 + - - +
471D ILE* 3.2 10.5 - - + +
472D ILE* 2.7 32.7 + - - +
552D VAL* 1.3 78.3 - - - +
554D VAL* 1.3 57.1 + - - +
555D VAL* 4.5 1.1 - - + -
568D MET* 3.7 28.3 - - + -
569D ARG 3.4 3.4 - - - +
570D VAL* 3.8 28.0 - - + -
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Residues in contact with VAL 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D ILE* 3.4 15.7 - - + +
474D LEU* 5.5 0.4 - - + -
533D VAL* 3.7 38.6 - - + -
552D VAL* 3.8 15.0 - - + -
553D ILE* 1.3 75.7 - - - +
555D VAL* 1.3 64.1 + - - +
556D THR* 3.9 8.3 + - + +
567D ILE 3.9 0.9 - - - +
568D MET* 3.5 2.1 - - - -
569D ARG* 2.8 58.1 + - + +
571D LEU* 3.6 31.0 - - + -
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Residues in contact with VAL 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D THR* 4.2 7.6 - - + -
456D ALA* 6.0 0.7 - - - +
459D ALA* 3.6 30.5 - - + -
471D ILE* 4.1 12.8 - - + -
472D ILE 2.8 10.9 + - - +
473D VAL* 3.5 21.5 - - + +
474D LEU 3.3 24.8 + - - +
480D SER* 5.4 0.7 - - - -
484D LEU* 4.5 6.7 - - + -
553D ILE* 4.5 0.7 - - + -
554D VAL* 1.3 76.2 - - - +
556D THR* 1.3 66.2 + - - +
565D THR* 3.4 28.5 - - + -
567D ILE 3.3 11.0 - - - +
568D MET* 4.5 4.9 - - + -
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Residues in contact with THR 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D LEU* 3.9 26.7 - - + -
529D VAL* 4.1 16.3 - - + +
533D VAL* 4.2 3.4 - - + -
554D VAL* 3.9 20.4 + - + -
555D VAL* 1.3 78.6 - - - +
557D GLY* 1.3 61.3 + - - +
565D THR* 3.3 12.5 - - - +
566D ASN 3.0 19.8 + - - -
567D ILE* 3.1 33.9 + - - +
569D ARG* 4.2 11.2 + - - +
580D FBP 4.0 9.0 - - - -
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Residues in contact with GLY 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525D TRP* 3.3 14.8 - - - -
529D VAL* 5.6 1.1 - - - +
556D THR* 1.3 83.8 + - - +
558D TRP* 1.3 64.3 + - - -
559D ARG 3.4 2.2 - - - -
564D TYR 3.5 11.2 - - - -
565D THR* 4.1 0.4 - - - -
566D ASN* 3.9 3.4 - - - -
567D ILE* 3.6 12.6 - - - +
580D FBP 2.9 22.9 + - - -
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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