Contacts of the strand formed by residues 418 - 423 (chain B) in PDB entry 2VJD
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 418 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319B ILE* 3.4 16.2 - - + +
321B LEU* 4.0 12.3 - - + -
408B VAL* 3.4 33.2 - - + -
411B TYR* 4.0 9.5 - - - -
412B THR* 2.9 25.4 + - - +
415B GLY* 5.6 0.3 - - - -
417B GLY* 1.3 76.7 + - - +
419B TYR* 1.3 63.6 + - - +
494B LEU* 3.6 9.4 - - - +
495B PHE* 2.7 48.8 + - + -
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Residues in contact with TYR 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ILE 3.0 16.7 + - - +
320B LEU* 3.3 10.3 - - + +
321B LEU* 2.9 30.6 + - - +
417B GLY* 4.3 7.6 - - - -
418B THR* 1.3 76.0 - - - +
420B LEU* 1.3 60.6 + - - +
476B PHE* 4.4 7.4 - + - -
480B GLY 3.6 15.2 + - - -
481B ASN* 3.3 25.5 + - - +
482B PRO* 3.6 36.8 - - + -
483B ASN* 4.4 0.4 - - - -
492B TRP* 3.6 47.3 - + + +
493B PRO 3.8 4.5 - - - -
494B LEU* 3.3 39.1 - - + +
495B PHE* 4.6 1.6 - - - +
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B LEU* 3.1 26.9 - - + +
322B GLY* 3.9 5.4 - - - -
404B LEU* 3.9 26.0 - - + -
405B MET* 3.5 34.8 - - + -
408B VAL* 4.7 4.9 - - + -
418B THR 4.2 1.0 - - - -
419B TYR* 1.3 72.6 - - - +
421B TYR* 1.3 66.1 + - - +
492B TRP* 3.3 17.6 + - - +
493B PRO 5.3 0.2 + - - -
495B PHE* 3.9 28.7 - - + +
501B LYS 4.2 1.4 + - - +
502B PHE* 3.4 24.9 - - + +
503B ILE 3.4 14.7 + - - -
516B LEU* 4.3 12.6 - - + -
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Residues in contact with TYR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B LEU 4.5 1.1 - - - -
225B GLN* 3.3 34.7 - - + +
226B SER* 4.1 1.0 + - - -
320B LEU* 3.9 10.1 - - + -
321B LEU* 2.8 26.6 + - - -
322B GLY* 3.0 50.4 + - - -
323B VAL* 3.2 16.4 + - - +
324B ASN* 4.5 1.6 + - - -
420B LEU* 1.3 79.7 - - - +
422B PHE* 1.3 63.1 + - - +
423B PHE* 3.7 17.9 - - + -
443B GLU* 4.5 9.2 - - + +
473B TRP* 3.7 30.0 - + - -
492B TRP* 3.6 15.9 - + + -
502B PHE* 4.7 2.9 - - - -
503B ILE* 3.5 9.2 - - + +
505B LEU* 3.8 20.9 - - + -
516B LEU* 4.6 1.4 - - - +
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Residues in contact with PHE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B VAL* 3.6 22.9 - - + -
324B ASN 4.5 0.7 - - - -
325B LYS* 3.8 35.2 - - + -
401B ILE* 4.8 7.0 - - + -
421B TYR* 1.3 74.8 - - - +
423B PHE* 1.3 61.0 + - - +
424B ASN* 3.5 28.4 + - + +
502B PHE* 3.6 24.9 - + + -
503B ILE 2.9 7.6 + - - +
504B ASP* 3.3 20.4 - - - +
505B LEU 2.8 24.2 + - - -
516B LEU* 3.9 26.7 - - + -
517B ARG* 5.3 4.5 - - + -
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Residues in contact with PHE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B VAL 2.7 10.3 + - - +
324B ASN* 3.1 21.6 - - - +
325B LYS 2.8 26.3 + - - -
421B TYR* 3.7 12.8 - + + -
422B PHE* 1.3 69.8 - - - +
424B ASN* 1.3 59.1 + - - +
425B HIS* 3.4 35.2 - + + -
438B VAL* 3.6 13.7 - - + +
442B TYR 4.4 5.4 - - - -
443B GLU* 3.7 37.5 - - + -
446B PHE* 4.1 17.5 - + - -
465B LEU* 4.4 5.4 - - + -
469B ILE* 4.0 23.6 - - + -
505B LEU* 3.7 29.4 - - + -
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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