Contacts of the helix formed by residues 393 - 412 (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 ASN 393 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C GLU* 3.2 33.6 + - + +
325C THR 3.1 17.3 - - - +
326C SER* 4.0 5.8 - - - -
373C THR* 5.1 0.7 - - - -
388C ARG* 3.6 3.4 - - - +
391C TYR* 4.8 0.2 - - - -
392C LEU* 1.3 77.9 - - - +
394C THR* 1.3 65.5 + - - +
395C PHE* 2.9 17.8 + - - +
396C GLU* 2.9 49.3 + - - +
397C PHE* 2.9 21.7 + - - +
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Residues in contact with THR 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET* 4.5 6.7 - - + -
21C ILE* 5.9 1.1 - - + -
22C ILE* 4.3 21.3 - - + -
25C LEU* 4.9 11.7 - - + -
325C THR* 2.8 27.9 + - - -
326C SER* 3.8 1.4 - - - +
327C THR* 2.9 38.5 + - - +
329C PRO* 5.7 1.6 - - + +
373C THR* 5.2 0.4 - - - -
393C ASN* 1.3 75.5 + - - +
395C PHE* 1.3 69.8 + - + +
397C PHE* 3.4 5.2 + - - +
398C MET* 3.1 35.1 + - + +
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Residues in contact with PHE 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET* 5.6 1.1 - - + -
21C ILE* 4.6 12.1 - - + -
25C LEU* 3.6 32.5 - - + -
29C LYS* 5.4 0.6 - - - -
319C TYR* 4.0 32.1 - + - -
325C THR* 5.0 6.7 - - - -
393C ASN* 2.9 12.6 + - + +
394C THR* 1.3 85.7 - - + +
396C GLU* 1.3 65.9 + - + +
398C MET* 3.4 6.7 + - - +
399C ASP* 2.8 35.3 + - - +
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Residues in contact with GLU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ARG* 2.9 26.5 + - - -
392C LEU* 3.6 28.1 - - + +
393C ASN* 2.9 35.4 + - - +
395C PHE* 1.3 75.8 - - - +
397C PHE* 1.3 61.6 + - - +
399C ASP* 3.5 9.7 + - - +
400C LYS* 3.1 21.1 + - - +
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Residues in contact with PHE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ASN* 4.8 0.9 - - - -
329C PRO* 3.6 37.0 - - + -
330C ILE* 4.1 11.4 - - + -
366C THR* 4.2 11.9 - - + -
367C ILE* 4.1 18.4 - - + -
371C PHE 3.1 28.7 - - - -
372C MET* 3.7 18.6 - - - -
373C THR* 4.0 15.5 - - + -
376C LEU* 5.5 1.3 - - + -
392C LEU* 3.9 13.6 - - + +
393C ASN 2.9 17.0 + - - +
394C THR 3.7 2.9 - - - +
396C GLU* 1.3 75.6 - - - +
398C MET* 1.3 59.9 + - - +
400C LYS* 3.1 4.2 + - + +
401C LEU* 2.9 55.3 + - + +
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Residues in contact with MET 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 5.3 1.8 - - + +
25C LEU* 3.6 52.9 - - + +
26C ILE* 3.8 9.0 - - + +
29C LYS* 4.1 19.0 - - + +
30C LEU* 3.8 27.0 - - + +
329C PRO* 3.8 33.2 - - + -
333C ILE* 4.6 0.9 - - - -
394C THR* 3.1 25.0 + - + +
395C PHE* 3.4 6.7 + - - +
397C PHE* 1.3 74.8 - - - +
399C ASP* 1.3 58.0 + - - +
401C LEU* 3.4 12.5 + - - +
402C GLY* 2.9 24.8 + - - -
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Residues in contact with ASP 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 2.8 37.5 + - - +
395C PHE* 2.8 28.9 + - - +
396C GLU* 3.6 9.1 - - - +
398C MET* 1.3 77.4 - - - +
400C LYS* 1.3 56.6 + - - +
402C GLY* 3.1 2.8 + - - -
403C GLU* 2.9 46.0 + - - +
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Residues in contact with LYS 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C THR* 3.9 20.4 - - + -
371C PHE* 3.6 51.2 - - + -
392C LEU* 4.2 9.4 - - + -
396C GLU 3.1 14.1 + - - +
397C PHE* 3.1 10.1 + - + +
399C ASP* 1.3 76.7 - - - +
401C LEU* 1.3 62.2 + - - +
403C GLU* 3.4 21.3 + - - +
404C ASN* 3.1 44.9 + - - +
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Residues in contact with LEU 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 4.3 12.3 - - + -
330C ILE* 4.6 0.7 - - + -
333C ILE* 3.7 28.0 - - + -
359C LEU* 6.0 2.2 - - + -
362C VAL* 3.8 6.8 - - + +
363C SER* 3.7 32.5 - - - +
366C THR* 3.7 23.6 - - - +
397C PHE* 2.9 49.3 + - + +
398C MET* 3.6 17.5 - - - +
400C LYS* 1.3 76.3 - - - +
402C GLY* 1.3 58.7 + - - +
404C ASN* 3.2 2.3 + - - -
405C LEU* 2.8 30.7 + - - +
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Residues in contact with GLY 402 (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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29C LYS* 4.8 9.6 - - - -
30C LEU* 3.8 17.0 - - - +
34C TYR* 4.3 3.8 + - - -
398C MET 2.9 15.1 + - - -
399C ASP* 3.1 3.7 + - - -
401C LEU* 1.3 75.8 - - - +
403C GLU* 1.3 62.0 + - - +
405C LEU* 3.4 3.6 + - - +
406C LYS* 3.1 23.4 + - - +
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Residues in contact with GLU 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ASP* 2.9 35.3 + - - +
400C LYS* 3.8 24.2 + - - +
402C GLY* 1.3 77.8 - - - +
404C ASN* 1.3 64.9 + - - +
406C LYS* 3.4 7.8 + - - +
407C ILE* 3.3 31.1 + - + +
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Residues in contact with ASN 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C VAL* 3.6 19.1 - - + +
366C THR* 3.0 33.5 + - - +
371C PHE* 5.3 1.6 - - - -
400C LYS* 3.1 35.6 + - - +
403C GLU* 1.3 79.1 - - - +
405C LEU* 1.3 58.0 + - - +
407C ILE* 3.5 13.4 + - - +
408C LYS* 3.0 29.3 + - - +
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS 4.7 0.2 - - - +
30C LEU* 3.6 34.1 - - + +
34C TYR* 3.6 25.8 - - + -
355C PHE* 4.4 6.5 - - + -
358C ALA* 4.6 2.9 - - + +
359C LEU* 4.3 20.9 - - + +
362C VAL* 3.7 26.8 - - + +
401C LEU 2.8 17.9 + - - +
402C GLY* 3.8 4.7 - - - +
403C GLU 3.3 0.2 - - - -
404C ASN* 1.3 75.0 - - - +
406C LYS* 1.3 64.3 + - - +
408C LYS* 3.7 3.9 - - + +
409C LEU* 3.0 52.5 + - + +
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Residues in contact with LYS 406 (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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34C TYR* 3.4 28.6 + - + +
402C GLY 3.1 14.3 + - - +
403C GLU* 3.7 7.6 - - - +
405C LEU* 1.3 77.2 - - - +
407C ILE* 1.3 64.1 + - + +
409C LEU* 3.5 1.9 + - - +
410C ALA* 3.1 24.0 + - + +
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Residues in contact with ILE 407 (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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403C GLU* 3.3 22.3 + - + +
404C ASN* 3.9 12.6 - - - +
405C LEU 3.3 0.2 - - - -
406C LYS* 1.3 76.3 - - + +
408C LYS* 1.3 66.7 + - - +
410C ALA* 3.2 7.0 + - + +
411C GLN* 3.1 48.5 + - + +
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Residues in contact with LYS 408 (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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354C PHE* 5.7 5.4 - - + -
358C ALA* 4.2 39.3 - - + +
361C GLU* 4.1 6.5 - - + +
362C VAL* 4.3 9.4 - - + +
365C GLU* 2.7 40.1 + - - -
404C ASN 3.0 18.3 + - - +
405C LEU* 3.7 8.5 - - + +
406C LYS 3.4 0.2 - - - -
407C ILE* 1.3 78.1 - - - +
409C LEU* 1.3 64.9 + - + +
411C GLN* 3.4 12.4 + - - +
412C ALA* 3.3 19.6 + - - +
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Residues in contact with LEU 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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5C ILE* 6.0 3.6 - - + -
34C TYR* 3.5 43.3 - - + -
354C PHE* 4.1 16.2 - - + -
355C PHE* 4.2 16.4 - - + -
358C ALA* 4.1 26.5 - - + -
405C LEU* 3.0 31.8 + - + +
406C LYS 4.0 3.4 - - - +
408C LYS* 1.3 76.2 - - + +
410C ALA* 1.3 63.3 + - - +
412C ALA* 3.3 16.7 + - - +
413C LYS* 3.5 18.2 - - - +
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Residues in contact with ALA 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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406C LYS* 3.1 18.6 + - + +
407C ILE* 3.2 7.4 + - - +
409C LEU* 1.3 78.2 - - - +
411C GLN* 1.3 63.7 + - + +
412C ALA 3.2 1.0 + - - -
413C LYS* 3.4 36.0 + - - +
414C LEU* 4.9 4.0 - - - +
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Residues in contact with GLN 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C ILE* 3.1 39.4 + - + +
408C LYS* 3.4 10.3 + - - +
410C ALA* 1.3 76.6 - - + +
412C ALA* 1.3 60.2 + - - +
413C LYS 3.3 0.7 - - - -
414C LEU* 3.5 28.0 - - + +
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Residues in contact with ALA 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C PHE* 3.5 37.5 - - + -
408C LYS 3.3 10.8 + - - +
409C LEU 3.5 12.3 - - - +
410C ALA 3.1 1.2 - - - -
411C GLN* 1.3 75.1 - - - +
413C LYS* 1.3 56.8 + - + +
414C LEU 3.0 16.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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