Contacts of the strand formed by residues 323 - 328 (chain B) in PDB entry 6VSB
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 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B GLN 4.4 4.9 + - - +
322B PRO* 1.3 79.7 - - - +
324B GLU* 1.3 79.1 - - - +
325B SER 3.4 2.0 - - - -
537B LYS* 3.9 21.9 + - - -
538B CYS 3.5 10.7 + - - -
539B VAL* 3.2 14.9 - - - +
540B ASN* 3.3 6.4 - - - +
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Residues in contact with GLU 324 (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 THR* 1.3 84.3 - - - +
325B SER* 1.3 68.7 + - - +
326B ILE* 3.2 13.9 + - - +
534B VAL* 3.2 30.4 - - + +
537B LYS* 2.3 39.2 + - - +
539B VAL* 3.9 8.5 - - + -
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Residues in contact with SER 325 (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 THR 3.3 0.8 + - - -
324B GLU* 1.3 75.5 - - - +
326B ILE* 1.3 59.9 + - - +
327B VAL* 4.8 8.2 - - - +
531B THR* 3.9 11.8 - - - +
540B ASN* 3.1 37.5 + - - -
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Residues in contact with ILE 326 (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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324B GLU* 3.2 16.4 - - - +
325B SER* 1.3 72.6 - - - +
327B VAL* 1.3 66.4 + - - +
328B ARG* 5.7 4.0 - - + -
531B THR* 4.0 4.5 - - - -
532B ASN 3.7 18.6 - - - +
533B LEU* 4.5 14.6 - - + -
534B VAL* 4.0 26.9 - - + +
539B VAL* 4.3 11.0 - - + -
540B ASN 3.0 6.6 + - - +
541B PHE* 3.5 22.4 - - + -
542B ASN* 3.1 20.6 + - - +
543B PHE* 5.3 6.7 - - + -
552B LEU* 3.6 31.9 - - + -
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Residues in contact with VAL 327 (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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325B SER* 4.7 9.9 - - - +
326B ILE* 1.3 83.2 - - - +
328B ARG* 1.3 64.3 + - - +
329B PHE* 4.6 4.3 - - + -
528B LYS* 3.3 44.0 - - + +
529B LYS* 5.7 1.6 - - + -
530B SER* 3.2 15.3 - - - +
531B THR* 2.8 53.3 + - + +
542B ASN* 4.2 18.6 - - + +
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Residues in contact with ARG 328 (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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326B ILE* 5.5 4.5 - - + -
327B VAL* 1.3 78.1 - - - +
329B PHE* 1.3 62.3 + - - +
530B SER* 4.5 1.8 - - - +
531B THR 3.2 20.8 + - - +
532B ASN* 4.5 3.0 + - - +
533B LEU* 3.2 53.9 - - + +
542B ASN 4.1 4.9 + - - -
543B PHE* 4.7 18.6 - - + +
544B ASN 2.9 27.9 + - - -
578B ASP* 4.0 15.5 + - + +
579B PRO* 3.2 22.9 - - + +
580B GLN* 3.9 30.4 + - - +
581B THR* 2.9 31.3 + - - -
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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