Contacts of the strand formed by residues 408 - 413 (chain B) in PDB entry 3VOQ
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 LYS 408 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B TYR* 5.8 0.5 - - - -
403B GLY 3.7 1.6 - - - +
404B ILE* 3.7 1.4 - - - -
405B SER* 3.0 33.6 + - - +
407B ASP* 1.3 88.9 - - + +
409B VAL* 1.3 63.3 + - - +
410B GLU* 4.3 24.5 + - + +
431B SER* 3.4 22.4 + - - +
432B ILE 3.3 16.6 - - - +
433B ASP* 4.1 14.4 - - - +
434B SER* 3.9 3.6 - - - +
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LEU* 3.7 27.1 - - + -
403B GLY 3.3 4.3 - - - +
404B ILE* 4.2 21.5 - - + -
405B SER 5.1 0.7 - - - +
408B LYS* 1.3 78.9 - - - +
410B GLU* 1.3 66.5 + - - +
411B ILE* 4.8 2.2 - - + -
430B ILE 4.0 0.2 - - - +
431B SER* 3.5 1.4 + - - -
432B ILE* 2.8 51.5 + - + +
437B LEU* 3.7 33.2 - - + -
455B LEU* 4.1 18.2 - - + -
482B VAL* 5.4 3.1 - - + -
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TYR* 4.0 22.7 - - - -
401B GLN 3.6 0.6 - - - +
402B LEU* 3.4 4.5 - - - +
403B GLY* 2.8 35.3 + - - +
408B LYS* 4.3 26.1 + - + +
409B VAL* 1.3 78.6 - - - +
411B ILE* 1.3 65.8 + - - +
412B ASP* 4.1 14.6 - - - +
430B ILE 3.3 7.6 - - - +
431B SER* 4.1 16.4 + - - +
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Residues in contact with ILE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B MET* 4.2 13.9 - - - -
400B VAL* 3.9 33.2 - - + -
401B GLN 3.4 2.7 - - - -
402B LEU* 3.7 18.6 - - + -
409B VAL* 4.8 2.5 - - + -
410B GLU* 1.3 79.6 - - - +
412B ASP* 1.3 64.3 + - - +
413B PRO* 4.3 1.0 - - + +
428B LYS 4.8 0.2 - - - +
429B PRO* 3.3 6.4 - - - +
430B ILE* 2.9 57.3 + - + +
432B ILE* 4.6 6.5 - - + -
455B LEU* 5.3 0.2 - - + -
466B LEU* 3.4 33.4 - - + -
468B PHE* 3.8 11.7 - - + -
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Residues in contact with ASP 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B VAL* 3.3 5.6 - - - -
401B GLN* 2.7 57.3 + - + +
410B GLU* 4.1 18.4 - - - +
411B ILE* 1.3 77.7 - - - +
413B PRO* 1.3 74.7 - - + +
429B PRO* 3.1 29.7 - - - +
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Residues in contact with PRO 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B THR* 6.5 1.3 - - - -
399B ASP 3.9 9.2 - - - +
400B VAL* 4.3 5.7 - - + -
401B GLN* 5.6 0.3 - - - +
411B ILE* 4.3 4.0 - - + +
412B ASP* 1.3 91.5 - - + +
414B VAL* 1.3 68.3 + - - +
427B GLN* 3.4 46.4 - - + +
428B LYS 4.9 0.7 - - - +
429B PRO* 4.5 11.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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