Contacts of the helix formed by residues 376 - 383 (chain C) in PDB entry 5V2C
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 ASP 376 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369C LEU 3.0 17.3 + - - +
371C GLY* 4.3 9.5 - - - +
372C PRO* 5.8 0.7 - - - +
374C GLY 3.2 5.8 + - - +
375C LEU* 1.3 72.5 - - - +
377C LEU* 1.3 59.8 + - - +
378C ASN* 2.7 33.5 + - - +
379C LYS* 2.8 33.6 + - + +
380C ILE* 2.8 31.8 + - - +
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Residues in contact with LEU 377 (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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328C VAL* 4.2 9.6 - - + -
329C GLY* 3.7 37.7 - - - +
341C LEU* 3.8 17.5 - - + +
375C LEU 3.9 3.2 + - - -
376C ASP* 1.3 73.8 + - - +
378C ASN* 1.3 59.0 + - - +
380C ILE* 3.2 8.0 + - + +
381C LYS* 2.9 56.5 + - + +
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Residues in contact with ASN 378 (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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376C ASP* 2.7 15.1 + - - +
377C LEU* 1.3 72.1 - - - +
379C LYS* 1.3 64.6 + - + +
381C LYS* 3.4 13.7 + - - +
382C ASN* 3.0 43.9 + - - +
383C ASP* 4.6 0.8 - - - +
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Residues in contact with LYS 379 (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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368C PRO 3.5 19.9 + - - +
369C LEU* 4.0 21.6 - - + +
370C ARG 3.3 22.6 + - - -
371C GLY* 4.1 6.9 - - - -
372C PRO* 5.5 1.0 - - - +
376C ASP* 2.8 35.6 + - + +
378C ASN* 1.3 77.3 - - + +
380C ILE* 1.3 60.1 + - - +
383C ASP* 2.7 53.4 + - + +
384C ILE 3.6 2.8 + - - -
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Residues in contact with ILE 380 (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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315C MET* 5.3 0.9 - - + -
318C LEU* 3.5 33.4 - - + -
322C GLN* 3.1 24.3 + - - +
328C VAL* 4.0 8.7 - - + -
341C LEU* 4.1 25.8 - - + -
351C PHE* 5.3 1.8 - - + -
369C LEU* 4.4 22.2 - - + -
375C LEU* 4.1 27.4 - - + -
376C ASP 2.8 21.8 + - - +
377C LEU* 3.5 7.4 - - + +
378C ASN 3.2 0.2 - - - -
379C LYS* 1.3 79.1 - - - +
381C LYS* 1.3 61.3 + - - +
384C ILE* 3.2 21.0 - - + +
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Residues in contact with LYS 381 (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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322C GLN* 3.4 24.0 + - - +
326C ALA 5.5 0.4 + - - -
327C ASN* 3.9 31.3 + - - +
328C VAL 4.7 3.4 - - - +
329C GLY 5.0 0.8 - - - +
377C LEU* 2.9 50.1 + - + +
378C ASN* 3.8 17.7 - - - +
380C ILE* 1.3 74.3 - - - +
382C ASN* 1.3 72.2 + - - +
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Residues in contact with ASN 382 (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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378C ASN* 3.0 36.7 + - - +
381C LYS* 1.3 93.0 - - - +
383C ASP* 1.3 69.8 + - - +
384C ILE 3.7 3.2 + - - +
385C GLN* 5.0 2.1 + - - -
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Residues in contact with ASP 383 (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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368C PRO 5.8 1.3 - - - +
369C LEU* 4.6 6.4 - - + +
378C ASN 4.6 0.3 - - - +
379C LYS* 2.7 48.9 + - + +
382C ASN* 1.3 85.0 - - - +
384C ILE* 1.3 60.2 + - - +
385C GLN* 3.0 25.9 + - - +
388C GLN* 3.6 5.7 - - - +
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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
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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