Contacts of the helix formed by residues 391 - 408 (chain C) in PDB entry 2A19
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 ALA 391 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390C LEU* 1.3 84.5 - - + +
392C LEU* 1.3 57.8 + - - +
393C GLU* 3.2 4.5 - - - +
394C LEU* 3.3 39.3 + - + +
395C PHE 3.9 0.3 + - - -
481C LEU* 3.5 20.4 - - + +
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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
----------------------------------------------------------
390C LEU* 2.7 18.1 + - + +
391C ALA* 1.3 73.1 - - - +
393C GLU* 1.3 59.4 + - - +
394C LEU 3.1 1.6 - - - -
395C PHE* 3.3 8.8 + - + +
396C GLU* 2.9 29.2 + - - +
478C LEU* 4.1 25.6 - - + -
481C LEU* 4.7 7.4 - - + +
482C LEU* 4.4 19.3 - - + -
511C GLU* 5.7 2.9 - - - +
536C LEU* 3.9 20.3 - - + +
539C TRP* 3.8 33.7 - - + -
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Residues in contact with GLU 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU 3.5 11.1 + - - +
391C ALA* 4.8 2.0 - - - -
392C LEU* 1.3 77.9 - - - +
394C LEU* 1.3 60.9 + - + +
396C GLU* 3.5 23.5 - - - +
397C GLN* 3.2 55.1 + - - +
400C LYS* 5.9 0.3 + - - -
426C LYS* 4.8 9.2 - - + +
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Residues in contact with LEU 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C LEU* 4.4 14.4 - - + -
391C ALA* 3.3 28.2 + - + +
392C LEU 3.1 0.4 - - - -
393C GLU* 1.3 78.5 - - + +
395C PHE* 1.3 65.1 + - - +
397C GLN* 3.4 9.1 + - - +
398C ILE* 3.3 29.4 + - + +
422C LEU* 5.0 8.3 - - + -
425C THR 5.1 3.8 - - - +
426C LYS* 3.2 33.0 - - - +
428C VAL* 3.8 26.0 - - + +
481C LEU* 4.8 11.2 - - + -
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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
----------------------------------------------------------
391C ALA 3.9 1.8 + - - -
392C LEU* 3.3 16.0 + - + +
394C LEU* 1.3 75.2 - - - +
396C GLU* 1.3 67.1 + - - +
398C ILE* 3.3 9.2 + - + +
399C THR* 3.1 41.9 + - - -
474C LEU* 3.4 39.7 - - + -
475C GLY* 5.6 0.2 - - - -
477C ILE* 4.4 12.8 - - + -
478C LEU* 3.5 54.7 - - + -
481C LEU* 4.4 11.5 - - + +
514C LEU* 5.4 1.3 - - + -
532C ILE* 3.7 22.7 - - + -
536C LEU* 3.9 17.3 - - + -
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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
----------------------------------------------------------
392C LEU 2.9 14.2 + - - +
393C GLU* 3.5 29.1 - - - +
395C PHE* 1.3 76.7 - - - +
397C GLN* 1.3 62.5 + - + +
399C THR* 3.5 5.6 + - - -
400C LYS* 3.1 55.4 + - - +
533C LEU* 4.2 9.4 - - + +
536C LEU* 3.7 34.2 - - + +
537C THR* 5.5 4.7 + - - -
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Residues in contact with GLN 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ASN* 3.2 34.6 + - - +
393C GLU* 3.2 40.6 + - - +
394C LEU* 3.6 7.7 - - - +
395C PHE 3.1 0.6 - - - -
396C GLU* 1.3 76.1 - - + +
398C ILE* 1.3 67.4 + - - +
400C LYS* 2.8 13.1 + - + +
401C GLY 2.8 19.1 + - - -
426C LYS 3.0 18.3 - - - +
427C GLN* 3.4 16.4 - - - +
428C VAL* 3.0 37.2 - - + +
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Residues in contact with ILE 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ASN* 5.2 1.6 - - - -
374C LEU* 4.1 26.0 - - + -
394C LEU* 3.3 21.7 + - + +
395C PHE* 3.3 10.7 + - + +
397C GLN* 1.3 73.3 - - - +
399C THR* 1.3 57.7 + - - +
401C GLY* 2.9 6.0 + - - +
402C VAL* 2.9 29.5 + - + +
415C LEU* 5.3 2.7 - - + -
420C ILE* 4.2 25.8 - - + -
428C VAL* 3.9 15.7 - - + -
429C LYS 6.5 0.2 - - - -
430C ILE* 3.8 18.8 - - + +
474C LEU* 4.2 15.9 - - + -
477C ILE* 4.4 15.7 - - + -
481C LEU* 4.3 8.5 - - + -
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Residues in contact with THR 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C PHE* 3.1 43.8 + - - -
396C GLU* 3.6 5.2 - - - -
398C ILE* 1.3 76.4 - - - +
400C LYS* 1.3 52.5 + - - +
402C VAL* 3.3 3.2 + - - +
403C ASP* 2.7 32.2 + - - +
474C LEU* 3.5 13.8 - - + +
529C THR* 3.6 27.3 - - + +
532C ILE* 3.8 15.3 - - + -
533C LEU* 3.5 22.0 - - + -
536C LEU* 6.3 0.2 - - - -
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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
----------------------------------------------------------
317C HIS* 3.8 10.8 + - + +
319C ASN* 4.0 13.9 - - - +
393C GLU* 5.9 0.4 + - - -
396C GLU* 3.1 45.2 + - - +
397C GLN* 2.8 12.4 + - + +
399C THR* 1.3 71.9 - - - +
401C GLY* 1.3 61.6 + - - +
403C ASP* 3.2 8.3 + - + +
404C TYR* 2.9 30.1 + - - +
533C LEU* 4.1 19.5 - - + -
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Residues in contact with GLY 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C HIS* 3.8 18.2 - - - -
319C ASN* 4.0 5.8 - - - -
320C ILE* 4.3 3.7 - - - +
397C GLN 2.8 12.3 + - - -
398C ILE 2.9 5.1 + - - -
400C LYS* 1.3 76.5 - - - +
402C VAL* 1.3 60.9 + - - +
404C TYR* 3.2 4.2 + - - +
405C ILE* 3.1 24.5 + - - +
430C ILE* 3.8 17.9 - - - -
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Residues in contact with VAL 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C ILE* 2.9 18.9 + - + +
399C THR 3.5 6.1 - - - +
401C GLY* 1.3 74.3 - - - +
403C ASP* 1.3 57.3 + - - +
405C ILE* 2.9 27.7 + - + +
406C HIS* 2.9 43.4 + - + +
415C LEU* 3.8 31.4 - - + -
430C ILE* 3.9 3.3 - - + +
470C ASP* 4.2 9.2 - - + +
474C LEU* 3.8 25.1 - - + -
529C THR* 3.6 11.7 - - + -
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Residues in contact with ASP 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C THR 2.7 20.8 + - - +
400C LYS* 3.2 6.9 + - + +
402C VAL* 1.3 71.9 - - - +
404C TYR* 1.3 57.9 + - - +
406C HIS* 4.0 3.1 - - - +
407C SER* 3.0 27.4 + - - -
529C THR* 2.6 33.0 + - - +
530C SER* 3.3 17.2 + - - -
533C LEU* 3.4 19.4 - - + +
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Residues in contact with TYR 404 (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 LYS 4.1 5.5 + - - -
315C LEU* 3.7 23.3 - - + -
316C ASP* 2.8 48.8 + - - +
317C HIS* 3.4 34.1 - + + -
320C ILE* 4.2 2.0 - - + -
400C LYS 2.9 12.2 + - - +
401C GLY 3.5 8.5 - - - +
403C ASP* 1.3 74.3 - - - +
405C ILE* 1.3 56.7 + - - +
406C HIS 3.2 0.2 - - - -
407C SER* 2.9 11.6 + - - -
408C LYS* 2.8 51.9 + - + +
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Residues in contact with ILE 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU* 4.4 9.9 - - + -
320C ILE* 3.8 14.8 - - + -
401C GLY 3.1 19.4 + - - +
402C VAL* 2.9 21.0 + - + +
404C TYR* 1.3 76.7 - - - +
406C HIS* 1.3 62.7 + - + +
408C LYS* 3.5 4.9 + - - +
410C LEU* 2.9 53.4 + - + +
411C ILE* 4.0 0.9 - - - +
412C ASN* 3.8 27.6 - - + +
415C LEU* 5.0 0.9 - - + -
430C ILE* 4.1 12.1 - - + -
433C PHE* 3.9 28.0 - - + -
436C VAL* 5.2 0.9 - - + -
470C ASP* 5.2 0.2 - - - +
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Residues in contact with HIS 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C VAL* 2.9 41.9 + - + +
403C ASP* 4.2 4.7 - - - +
405C ILE* 1.3 75.8 - - + +
407C SER* 1.3 58.5 + - - +
409C LYS* 2.7 26.4 + - - +
410C LEU 3.4 17.9 - - - -
467C LYS* 4.0 29.2 - - + +
470C ASP* 3.4 25.2 + - + +
471C LEU* 4.0 21.0 - - + +
528C ASN* 6.1 0.8 + - - -
529C THR* 4.0 14.4 + - - +
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Residues in contact with SER 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ASP* 3.0 23.5 + - - -
404C TYR* 2.9 16.9 + - - -
406C HIS* 1.3 76.7 - - - +
408C LYS* 1.3 67.5 + - - +
409C LYS* 3.3 3.6 + - - +
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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
----------------------------------------------------------
314C LYS* 4.2 26.1 - - + +
315C LEU* 4.4 11.2 - - + -
404C TYR* 2.8 47.6 + - + +
405C ILE 3.6 2.5 - - - +
406C HIS 3.2 0.2 - - - -
407C SER* 1.3 80.5 - - - +
409C LYS* 1.3 68.0 + - - +
410C LEU* 3.3 17.7 + - + +
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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
------------------------------------------------------------
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