Contacts of the helix formed by residues 373 - 382 (chain C) in PDB entry 6B0Z
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 THR 373 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326C SER* 3.4 20.4 - - - +
327C THR 3.6 22.4 - - - +
328C ASN* 3.6 17.8 + - - +
372C MET* 1.3 80.0 - - - +
374C LYS* 1.3 68.4 + - - +
375C ASP* 2.5 22.8 + - - -
376C LEU* 3.3 6.7 + - - +
377C ALA 3.2 16.6 + - - -
391C TYR* 3.6 3.5 - - - +
392C LEU 3.7 6.1 - - - +
393C ASN 4.8 1.8 - - - +
394C THR* 5.2 0.2 - - - -
397C PHE* 4.0 30.1 - - + -
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Residues in contact with LYS 374 (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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314C ARG* 5.3 9.1 - - - +
326C SER* 2.8 28.5 + - - +
373C THR* 1.3 73.7 - - - +
375C ASP* 1.3 63.8 + - - +
377C ALA* 3.2 4.2 + - - +
378C ALA* 2.9 22.6 + - + +
386C VAL* 4.2 19.3 - - + +
391C TYR* 3.4 48.2 - - + +
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Residues in contact with ASP 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C GLY* 4.1 15.0 - - - +
287C SER* 5.3 0.3 - - - -
289C GLY* 4.4 6.9 + - - -
290C MET* 5.3 0.9 - - - +
326C SER 4.7 1.9 + - - +
328C ASN* 3.1 30.6 + - - +
373C THR* 2.5 30.7 + - - -
374C LYS* 1.3 74.4 - - - +
376C LEU* 1.3 66.2 + - - +
378C ALA* 3.2 9.4 + - - +
379C CYS* 3.1 26.5 + - - -
383C LEU* 6.3 0.7 - - - -
501C NDP 3.9 22.4 - - + +
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Residues in contact with LEU 376 (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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117C ILE* 3.8 25.2 - - + +
286C GLY 5.6 1.3 - - - +
287C SER* 6.0 1.3 - - - -
290C MET* 3.7 30.7 - - + -
328C ASN* 3.8 20.2 - - - +
330C ILE* 5.3 0.2 - - + -
367C ILE* 3.7 41.5 - - + -
372C MET* 3.7 26.2 - - + -
373C THR* 3.3 7.1 + - - +
374C LYS 3.3 0.2 - - - -
375C ASP* 1.3 83.9 + - - +
377C ALA* 1.3 65.8 + - - +
379C CYS* 3.2 19.6 + - - +
380C ILE* 3.5 15.1 + - - +
397C PHE* 5.5 1.3 - - + -
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Residues in contact with ALA 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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372C MET* 3.5 11.3 - - - -
373C THR 3.2 11.9 + - - +
374C LYS 3.5 7.6 - - - +
376C LEU* 1.3 76.9 - - - +
378C ALA* 1.3 61.3 + - - +
380C ILE* 3.3 6.7 + - - +
381C LYS* 3.1 27.3 + - + +
386C VAL* 4.1 11.3 - - + +
390C ASP* 3.8 36.6 - - + +
391C TYR* 4.2 3.1 - - + -
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Residues in contact with ALA 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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374C LYS* 2.9 13.4 + - + +
375C ASP* 3.4 12.1 - - - +
376C LEU 3.1 0.6 - - - -
377C ALA* 1.3 75.9 - - - +
379C CYS* 1.3 58.9 + - - +
382C GLY* 2.7 34.9 + - - -
383C LEU* 3.5 33.6 + - + +
386C VAL* 3.6 19.7 - - + +
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Residues in contact with CYS 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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117C ILE* 4.1 24.7 - - + -
118C PRO* 3.6 21.1 - - + +
285C TYR* 4.0 24.6 + - + -
286C GLY* 3.3 28.0 - - - -
287C SER* 4.9 6.1 - - - -
375C ASP 3.1 14.5 + - - -
376C LEU* 3.2 13.0 + - - +
378C ALA* 1.3 77.4 - - - +
380C ILE* 1.3 61.9 + - - +
382C GLY* 4.7 0.7 + - - -
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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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116C ASN* 3.5 30.5 - - + +
117C ILE* 4.1 5.8 - - + -
118C PRO* 4.3 8.0 - - + +
372C MET* 4.0 31.9 - - + -
376C LEU 3.7 8.3 - - - +
377C ALA* 3.3 6.9 + - - +
378C ALA 3.1 0.4 - - - -
379C CYS* 1.3 81.6 - - - +
381C LYS* 1.3 71.6 + - + +
382C GLY 3.7 0.3 + - - -
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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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377C ALA* 3.1 14.6 + - + +
380C ILE* 1.3 88.7 - - + +
382C GLY* 1.3 57.9 + - - +
385C ASN* 3.4 44.5 + - + +
386C VAL* 5.2 0.9 - - + -
387C GLN* 4.6 12.9 - - + +
390C ASP* 3.9 32.0 + - + +
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Residues in contact with GLY 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 ALA* 2.7 24.8 + - - +
379C CYS 4.5 0.6 + - - -
380C ILE 3.5 2.0 + - - -
381C LYS* 1.3 74.6 - - - +
383C LEU* 1.3 67.5 + - - +
384C PRO* 3.3 6.5 - - - -
385C ASN* 2.8 22.2 + - - -
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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
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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