Contacts of the strand formed by residues 408 - 413 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A TYR* 5.8 1.2 - - + -
403A GLY 3.8 1.4 - - - +
404A ILE* 3.7 2.3 - - - -
405A SER* 3.0 31.0 + - - +
407A ASP* 1.3 92.6 - - + +
409A VAL* 1.4 63.2 + - - +
410A GLU* 3.6 32.5 - - + +
431A SER* 3.6 16.9 + - - +
432A ILE 3.2 17.7 - - - +
433A ASP* 4.3 2.9 - - - +
434A SER* 3.7 5.6 - - - +
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Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU* 3.6 28.3 - - + -
403A GLY 3.4 4.5 - - - +
404A ILE* 4.2 25.1 - - + -
405A SER 5.2 1.1 - - - +
408A LYS* 1.4 77.0 - - - +
410A GLU* 1.3 61.0 + - - +
411A ILE* 4.1 7.6 - - + +
430A ILE 3.9 0.3 - - - +
431A SER* 3.6 1.6 - - - -
432A ILE* 2.8 44.4 + - + +
437A LEU* 3.8 36.3 - - + -
455A LEU* 4.1 19.3 - - + -
482A VAL* 5.1 4.3 - - + -
485A ILE* 6.2 0.2 - - + -
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Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TYR* 4.0 23.9 + - - -
401A GLN 3.4 1.4 - - - +
402A LEU* 3.3 7.1 - - - +
403A GLY* 2.8 38.7 + - - +
408A LYS* 3.6 26.2 - - + +
409A VAL* 1.3 75.6 - - - +
411A ILE* 1.3 61.3 + - - +
412A ASP* 3.9 15.7 - - - +
430A ILE 3.3 7.4 - - - +
431A SER* 3.9 17.9 + - - +
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Residues in contact with ILE 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A MET* 4.1 16.2 - - - -
400A VAL* 3.7 34.5 - - + -
401A GLN 3.4 2.9 - - - -
402A LEU* 3.8 14.1 - - + -
409A VAL* 4.1 17.5 - - + -
410A GLU* 1.3 77.7 - - - +
412A ASP* 1.3 65.6 + - - +
413A PRO* 4.4 1.1 - - + -
428A LYS 4.6 0.5 - - - +
429A PRO* 3.3 5.5 - - - +
430A ILE* 2.8 65.8 + - + +
432A ILE* 4.4 3.8 - - + -
455A LEU* 5.2 0.4 - - + -
466A LEU* 4.0 18.2 - - + -
468A PHE* 3.8 11.0 - - + -
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Residues in contact with ASP 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A VAL* 3.2 4.6 - - - -
401A GLN* 2.7 56.1 + - + +
410A GLU* 3.9 18.9 - - - +
411A ILE* 1.3 77.4 - - - +
413A PRO* 1.3 70.3 - - + +
429A PRO* 3.4 24.2 - - - +
430A ILE 5.2 0.2 - - - +
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Residues in contact with PRO 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A THR* 6.0 2.2 - - - +
399A ASP 3.8 7.6 - - - +
400A VAL* 4.2 8.0 - - + -
411A ILE* 4.2 5.2 - - + +
412A ASP* 1.3 89.3 - - + +
414A VAL* 1.3 66.1 + - - +
424A TRP* 6.0 3.6 - - + -
427A GLN* 3.6 36.8 - - + +
428A LYS 4.6 2.5 - - - +
429A PRO* 4.2 19.7 - - + -
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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
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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