Contacts of the helix formed by residues 384 - 392 (chain C) in PDB entry 6T8B
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 LEU 384 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377B LYS* 4.2 16.8 - - + +
347C LEU* 4.6 5.4 - - + -
350C PHE* 3.6 45.3 - - + +
352C VAL* 4.3 18.2 - - + -
380C ARG 3.3 21.5 - - - +
381C ILE* 3.3 12.3 + - - +
382C SER 3.0 2.6 + - - -
383C ASN* 1.3 80.5 - - + +
385C ALA* 1.3 58.5 + - - +
386C LYS 3.5 2.0 - - - -
387C ASP* 3.3 24.7 + - + +
388C LEU* 2.9 38.7 + - + +
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Residues in contact with ALA 385 (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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381C ILE 4.1 1.3 + - - -
382C SER 3.2 14.7 + - - +
383C ASN 3.4 2.0 - - - -
384C LEU* 1.3 77.2 - - - +
386C LYS* 1.3 63.5 + - + +
387C ASP 3.0 0.2 - - - -
388C LEU* 3.4 1.3 + - - -
389C ALA* 2.9 30.2 + - - +
397C VAL* 3.8 35.8 - - + +
398C ARG* 5.4 0.4 - - - -
399C VAL* 5.1 9.2 - - + +
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Residues in contact with LYS 386 (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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378B VAL* 4.5 2.7 - - + +
401B GLU* 2.5 47.8 + - + +
402B VAL* 3.3 41.5 - - + +
383C ASN 5.1 2.1 + - - +
384C LEU 3.5 0.2 - - - -
385C ALA* 1.3 78.8 - - + +
387C ASP* 1.3 67.3 + - - +
389C ALA* 4.0 7.6 - - + +
390C ARG* 4.2 3.6 + - - +
396C SER* 6.3 2.9 - - - -
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Residues in contact with ASP 387 (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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376B VAL 4.9 0.4 - - - -
377B LYS* 3.5 32.9 - - - +
378B VAL* 3.2 36.2 + - - +
350C PHE* 3.8 22.2 - - + -
383C ASN 4.7 1.7 - - - +
384C LEU* 3.3 20.1 + - + +
385C ALA 3.0 0.6 - - - -
386C LYS* 1.3 80.2 - - - +
388C LEU* 1.3 61.5 + - - +
389C ALA 3.0 1.5 + - - -
390C ARG* 3.3 10.0 + - - +
391C SER* 2.8 31.6 + - - -
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Residues in contact with LEU 388 (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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343C LEU* 3.8 24.7 - - + -
346C LYS* 4.3 16.8 - - + -
347C LEU* 3.7 37.5 - - + +
350C PHE* 5.2 4.9 - - + -
381C ILE* 4.8 7.4 - - + +
384C LEU* 2.9 28.8 + - + +
385C ALA* 4.0 1.1 - - - +
387C ASP* 1.3 75.3 - - - +
389C ALA* 1.3 62.3 + - - +
391C SER* 3.7 4.0 - - - +
392C LEU* 3.0 35.1 + - + +
397C VAL* 3.5 25.4 - - + +
399C VAL* 5.1 1.1 - - + -
411C ILE* 4.4 13.2 - - + -
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Residues in contact with ALA 389 (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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402B VAL* 3.6 31.6 - - + -
385C ALA 2.9 18.3 + - - +
386C LYS* 4.0 2.9 - - + +
387C ASP 3.0 0.4 - - - -
388C LEU* 1.3 79.7 - - - +
390C ARG* 1.3 61.2 + - - +
393C ALA* 3.2 11.4 + - - -
394C VAL* 3.0 22.8 + - - +
395C ILE 4.0 9.6 - - - +
396C SER* 4.2 2.0 - - - -
397C VAL* 3.5 19.5 - - - +
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Residues in contact with ARG 390 (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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371B GLN* 5.5 0.6 - - - +
372B PRO* 3.6 34.9 + - - +
373B ALA 4.8 2.8 + - - -
376B VAL 2.8 31.3 + - - +
378B VAL* 3.3 28.0 - - - +
401B GLU 4.2 12.6 - - - +
402B VAL* 4.5 9.1 - - + +
403B ILE 5.2 0.4 - - - +
406B LYS 3.5 8.5 - - - +
407B THR* 3.1 56.6 + - - +
408B THR 4.3 8.3 - - - +
409B VAL* 4.5 6.5 - - - -
350C PHE* 4.4 12.3 - - - -
386C LYS 4.2 3.3 + - - +
387C ASP* 3.3 12.8 + - - +
389C ALA* 1.3 77.5 - - - +
391C SER* 1.3 75.5 + - - +
393C ALA 3.2 6.1 + - - -
394C VAL 5.0 0.2 - - - -
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Residues in contact with SER 391 (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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407B THR* 4.1 16.1 + - - +
342C LEU* 4.1 13.7 - - - +
346C LYS* 3.7 43.1 - - - +
350C PHE* 4.3 10.7 - - - -
387C ASP 2.8 22.3 + - - -
388C LEU* 3.8 9.1 - - - -
389C ALA 3.3 0.2 - - - -
390C ARG* 1.3 87.2 + - - +
392C LEU* 1.3 62.8 + - - +
393C ALA* 3.4 1.0 + - - +
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Residues in contact with LEU 392 (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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339C MET* 3.9 34.8 - - + +
342C LEU* 4.6 15.8 - - + +
343C LEU* 3.7 47.6 - - + +
368C PHE* 5.0 0.7 - - + -
388C LEU* 3.0 29.3 + - + +
391C SER* 1.3 84.1 - - - +
393C ALA* 1.3 62.6 + - - +
394C VAL* 2.8 28.3 + - + +
397C VAL* 5.2 0.2 - - + -
413C ILE* 3.7 27.8 - - + -
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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