Contacts of the helix formed by residues 384 - 397 (chain C) in PDB entry 5I94
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 GLY 384 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380C GLU 3.4 18.4 + - - -
381C ARG 4.2 3.0 + - - -
382C GLU 3.7 2.0 - - - -
383C SER* 1.3 75.4 - - - +
385C ASP* 1.3 61.6 + - - -
386C ARG 3.3 2.9 - - - -
387C ASN* 3.3 26.4 + - - +
388C PHE* 3.0 27.2 + - - -
414C PHE* 4.4 3.8 - - - -
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Residues in contact with ASP 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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392B TYR* 3.4 31.5 - - + +
395B LYS* 2.8 48.1 + - - +
396B GLU* 3.7 26.0 - - + +
382C GLU 5.1 4.4 - - - +
383C SER* 3.1 14.2 + - - +
384C GLY* 1.3 76.2 - - - +
386C ARG* 1.3 62.5 + - - +
388C PHE* 3.3 3.1 + - - +
389C ALA* 3.0 18.2 + - - +
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Residues in contact with ARG 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B TYR* 4.4 16.7 + - + -
396B GLU* 3.4 39.6 - - + +
397B LYS* 5.4 5.9 - - - +
318C ASN 4.8 8.3 + - - -
319C LYS* 4.4 11.7 + - - +
321C PHE* 3.5 33.8 - - + -
334C ASN* 5.3 10.9 - - - +
384C GLY* 3.3 1.2 - - - -
385C ASP* 1.3 78.3 - - - +
387C ASN* 1.3 67.7 + - - +
389C ALA* 3.2 10.1 + - + +
390C ILE* 3.0 36.9 + - + +
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Residues in contact with ASN 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ASN* 3.3 29.2 + - - +
338C ILE* 4.1 7.6 - - + +
380C GLU* 5.4 4.8 + - - +
384C GLY* 3.3 17.8 + - - +
385C ASP 3.2 1.0 - - - -
386C ARG* 1.3 80.5 - - - +
388C PHE* 1.3 58.4 + - - +
390C ILE* 3.3 9.2 + - - +
391C GLY* 2.9 24.1 + - - -
410C LEU* 3.8 16.0 - - + +
413C TYR* 3.8 13.0 + - + -
414C PHE* 3.8 32.2 - - + -
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Residues in contact with PHE 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B TYR* 3.8 31.9 - + + -
381C ARG* 4.3 15.9 - - + -
384C GLY 3.0 25.1 + - - -
385C ASP* 3.6 8.3 - - - +
386C ARG 3.2 0.4 - - - -
387C ASN* 1.3 77.4 - - - +
389C ALA* 1.3 66.0 + - - +
391C GLY* 3.1 0.7 + - - -
392C TYR* 3.0 46.7 + + - -
406C MET* 5.5 0.2 - - - -
407C VAL* 4.6 17.9 - - + -
410C LEU* 3.4 27.6 - - + -
411C ASP* 5.5 4.0 - - - -
414C PHE* 3.9 23.8 - + - -
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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
----------------------------------------------------------
389B ALA* 3.6 16.9 - - - +
392B TYR* 3.7 7.9 - - - +
393B TYR* 3.8 38.8 - - + +
321C PHE* 4.6 6.0 - - + -
385C ASP 3.0 13.5 + - - +
386C ARG* 3.2 13.7 + - + +
388C PHE* 1.3 76.8 - - - +
390C ILE* 1.3 57.1 + - - +
392C TYR 3.6 0.2 + - - -
393C TYR* 3.0 29.0 + - - +
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Residues in contact with ILE 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C PHE* 3.5 43.9 - - + -
334C ASN* 4.0 26.2 - - + -
335C ALA* 3.8 23.3 - - + +
338C ILE* 3.8 18.8 - - + -
386C ARG* 3.0 32.2 + - + +
387C ASN* 3.5 10.8 - - - +
388C PHE 3.2 0.2 - - - -
389C ALA* 1.3 72.9 - - - +
391C GLY* 1.3 66.3 + - - +
393C TYR* 3.4 2.5 + - - +
394C LEU* 2.9 32.8 + - + +
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Residues in contact with GLY 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C ILE* 5.0 1.8 - - - -
387C ASN 2.9 14.5 + - - -
388C PHE 3.1 3.3 + - - -
390C ILE* 1.3 78.4 - - - +
392C TYR* 1.3 57.8 + - - +
394C LEU* 3.0 12.6 + - - +
395C LYS* 2.9 27.0 + - - +
400C PHE* 3.8 4.5 - - - -
406C MET* 3.9 24.2 - - - -
410C LEU* 4.8 6.3 - - - -
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Residues in contact with TYR 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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385B ASP* 3.7 31.8 - - + +
388B PHE* 4.0 27.7 - + + -
389B ALA* 3.7 20.4 - - - +
392B TYR* 4.0 31.0 + + - -
388C PHE* 3.0 36.4 + + - +
391C GLY* 1.3 71.4 - - - +
393C TYR* 1.3 66.2 + - - +
395C LYS* 3.8 7.6 - - + +
396C GLU* 2.9 25.6 + - - +
406C MET* 3.5 25.5 - - + +
407C VAL* 4.1 14.8 - - + +
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Residues in contact with TYR 393 (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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319B LYS* 4.4 6.9 + - - +
321B PHE* 3.8 34.3 - + - -
386B ARG* 5.3 11.0 - - + -
389B ALA* 3.7 10.2 - - + +
601B 69V 3.3 43.5 + - - -
321C PHE* 4.0 24.0 - + + -
322C LEU* 3.7 34.1 - - + -
389C ALA 3.0 18.6 + - - +
390C ILE 3.6 5.2 - - - +
391C GLY 3.3 0.2 - - - -
392C TYR* 1.3 76.8 - - - +
394C LEU* 1.3 64.9 + - + +
396C GLU* 3.2 8.0 + - + +
397C LYS* 3.1 41.8 + - + +
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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
----------------------------------------------------------
321C PHE* 5.7 2.0 - - + -
322C LEU* 3.8 19.3 - - + -
328C PRO* 4.0 5.4 - - + -
335C ALA* 3.9 7.6 - - + +
338C ILE* 3.6 30.5 - - + -
339C VAL* 3.7 21.1 - - + -
390C ILE* 2.9 34.9 + - + +
391C GLY 3.4 5.2 - - - +
393C TYR* 1.3 75.4 - - + +
395C LYS* 1.3 65.8 + - - +
397C LYS 3.1 1.6 + - - -
398C LYS 2.9 18.7 + - - -
399C CYS* 3.0 40.4 + - + -
400C PHE* 3.6 14.6 - - + -
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Residues in contact with LYS 395 (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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382B GLU* 6.0 0.2 + - - -
385B ASP* 3.1 33.9 + - + +
391C GLY 2.9 15.2 + - - +
392C TYR* 3.8 11.3 - - - +
394C LEU* 1.3 74.5 - - - +
396C GLU* 1.3 65.1 + - - +
398C LYS* 3.2 17.1 + - - +
400C PHE* 3.8 16.1 - - + -
404C THR 5.5 6.1 - - - +
406C MET* 4.3 28.6 - - + +
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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
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383B SER 5.7 0.9 - - - +
385B ASP* 4.0 11.4 - - + +
386B ARG* 3.4 52.9 - - + +
392C TYR 2.9 18.4 + - - +
393C TYR* 3.4 7.8 - - + +
395C LYS* 1.3 80.3 - - - +
397C LYS* 1.3 79.5 + - - +
398C LYS* 3.3 9.4 + - - +
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Residues in contact with LYS 397 (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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319B LYS* 3.0 29.8 - - - +
386B ARG* 6.2 2.2 - - - +
322C LEU* 3.8 25.8 - - + -
326C ASP* 3.9 26.5 + - - +
393C TYR* 3.1 40.9 + - + +
394C LEU 3.1 0.4 + - - -
396C GLU* 1.3 91.1 - - - +
398C LYS* 1.3 72.2 + - - +
399C CYS* 3.4 9.1 + - - -
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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