Contacts of the helix formed by residues 374 - 379 (chain C) in PDB entry 6UZA
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 VAL 374 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C LEU* 3.8 28.3 - - + -
301C SER* 4.8 2.2 - - - +
326C LYS* 3.9 39.3 - - + +
329C VAL* 5.5 2.9 - - + -
330C VAL* 4.6 5.4 - - + -
369C ALA* 3.0 16.2 + - + +
372C TYR* 4.1 16.2 - - + +
373C GLU* 1.3 73.8 - - - +
375C LYS* 1.3 62.9 + - - +
376C LYS 4.9 0.4 - - - +
377C PHE* 3.7 24.9 - - + +
378C VAL* 3.3 25.3 + - - +
744C PHE* 4.3 1.0 - - - -
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Residues in contact with LYS 375 (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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326C LYS* 5.4 1.4 - - - +
373C GLU* 3.6 39.3 + - - +
374C VAL* 1.3 74.0 - - - +
376C LYS* 1.3 60.5 + - + +
378C VAL* 3.4 2.6 + - - +
379C ALA* 2.9 30.0 + - - +
740C VAL* 3.7 19.9 - - + +
741C GLU* 4.8 17.6 - - + +
744C PHE* 3.9 40.4 - - + -
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Residues in contact with LYS 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C MET* 4.3 19.1 - - + +
327C ASP* 5.0 11.7 - - - +
330C VAL* 3.7 32.3 - - + +
374C VAL* 4.9 0.4 - - - +
375C LYS* 1.3 76.2 - - + +
377C PHE* 1.3 63.5 + - - +
378C VAL 3.3 0.2 - - - -
379C ALA* 3.9 4.2 - - - +
380C HIS* 3.4 23.6 + - - +
736C ASP* 6.0 3.4 - - - -
737C ASP* 5.3 11.1 - - - +
740C VAL* 3.9 31.2 - - + +
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Residues in contact with PHE 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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294C VAL* 5.2 0.7 - - + -
298C LEU* 5.9 2.9 - - + -
329C VAL* 3.6 38.1 - - + -
330C VAL* 3.5 9.5 - - + +
333C LEU* 3.7 31.3 - - + +
345C ILE* 3.9 28.3 - - + -
346C LEU* 3.7 21.1 - - + -
365C ARG* 5.0 10.1 - - + -
366C LEU* 3.8 24.5 - - + -
369C ALA* 3.7 24.2 - - + -
374C VAL* 3.7 24.3 + - + +
375C LYS 3.3 0.4 - - - -
376C LYS* 1.3 80.0 - - - +
378C VAL* 1.3 58.4 + - - +
380C HIS* 4.0 1.3 - - - +
383C CYS* 3.5 17.5 - - - +
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Residues in contact with VAL 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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366C LEU* 4.6 6.7 - - + -
369C ALA* 3.9 25.8 - - + +
370C ILE* 4.1 18.8 - - + -
374C VAL 3.3 18.2 - - - +
375C LYS 3.4 1.0 + - - -
376C LYS 3.3 0.2 - - - -
377C PHE* 1.3 81.7 - - + +
379C ALA* 1.3 56.0 + - - +
380C HIS 3.3 4.6 + - - -
383C CYS* 4.0 17.7 - - - +
384C GLN* 2.9 21.8 - - - +
387C LEU* 4.6 4.0 - - + -
743C LYS 5.2 1.1 - - - +
744C PHE* 4.0 18.6 - - + -
747C ALA* 3.7 28.4 - - + +
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Residues in contact with ALA 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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375C LYS 2.9 19.2 + - - +
376C LYS* 3.8 4.5 + - - -
377C PHE 3.5 0.2 - - - -
378C VAL* 1.3 75.5 - - - +
380C HIS* 1.3 59.3 + - - +
381C PRO* 4.1 4.7 - - - +
384C GLN* 4.5 4.4 - - - +
740C VAL* 3.9 29.6 - - + +
743C LYS* 3.7 39.7 + - + +
744C PHE 4.6 1.8 - - - +
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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