Contacts of the strand formed by residues 408 - 413 (chain C) in PDB entry 2VZE
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 GLY 408 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C ILE* 3.5 13.2 - - - +
395C ILE 3.9 6.3 - - - -
396C ASP* 5.7 0.4 - - - -
402C LEU* 4.4 2.9 - - - -
407C GLU* 1.3 76.5 - - - +
409C ASP* 1.3 66.1 + - - -
447C ARG* 3.3 19.5 - - - -
448C GLY 2.9 31.5 + - - +
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Residues in contact with ASP 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C ILE* 3.4 2.7 - - - -
395C ILE* 2.8 41.3 + - - +
396C ASP 4.8 1.0 - - - -
397C ASP* 5.0 0.9 + - - -
408C GLY* 1.3 71.9 - - - -
410C ILE* 1.3 65.2 + - - +
411C GLY 3.4 1.0 + - - -
438C ARG* 2.6 35.5 + - - -
443C LEU* 4.1 21.3 - - + -
445C GLY* 6.2 1.8 - - - +
446C ASP 3.8 6.0 - - - +
447C ARG* 3.0 35.1 + - - -
462C ALA* 5.0 4.7 - - - +
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Residues in contact with ILE 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C TYR* 4.1 22.0 - - + +
383C MET* 4.0 24.5 - - + -
392C VAL* 4.0 24.0 - - + -
393C GLN 3.5 4.7 - - - +
394C ILE* 3.4 20.9 - - + -
409C ASP* 1.3 72.0 - - - +
411C GLY* 1.3 59.7 + - - +
443C LEU* 3.7 3.7 - - - +
444C LEU* 2.9 33.9 + - + +
445C GLY 4.6 0.3 + - - -
446C ASP* 2.8 30.4 + - + +
447C ARG 3.6 19.1 - - - +
448C GLY* 3.7 9.9 - - - +
456C PHE* 4.7 5.4 - - + -
457C GLN 5.1 0.4 - - - +
458C PHE* 4.9 4.3 - - + -
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Residues in contact with GLY 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C VAL* 3.3 7.1 - - - +
393C GLN 2.8 35.0 + - - -
395C ILE* 4.7 4.0 - - - -
409C ASP 3.4 2.3 + - - -
410C ILE* 1.3 75.5 - - - +
412C ILE* 1.3 63.7 + - - -
441C PHE* 3.8 15.9 - - - -
442C TRP 3.0 13.9 - - - -
443C LEU* 4.4 1.3 - - - -
444C LEU* 3.9 2.5 - - - -
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Residues in contact with ILE 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C THR* 3.7 31.6 - - + -
369C THR* 3.4 34.3 - - + -
390C TYR* 3.8 26.2 - - + -
391C ASP 3.5 9.4 - - - +
392C VAL* 4.2 5.2 - - + -
411C GLY* 1.3 76.5 - - - +
413C ARG* 1.3 75.3 + - - +
414C VAL* 3.2 4.1 + - + +
419C PRO* 4.1 4.5 - - + -
422C ILE* 3.7 22.2 - - + -
441C PHE* 3.4 5.1 - - - -
442C TRP* 2.9 31.0 + - + +
444C LEU* 3.9 7.6 - - + -
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Residues in contact with ARG 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C ASP* 2.9 48.2 + - + +
393C GLN* 5.5 0.2 - - - +
401C VAL* 4.1 12.1 - - - +
412C ILE* 1.3 71.1 - - - +
414C VAL* 1.3 59.4 - - - +
415C LYS 3.4 24.9 + - - +
416C PRO* 5.1 6.1 - - - +
417C ILE 3.9 3.7 - - - +
419C PRO* 3.2 23.6 - - - +
440C ASP* 3.5 33.7 + - - +
441C PHE* 3.4 31.4 - - + -
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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