Contacts of the helix formed by residues 327 - 342 (chain C) in PDB entry 2DB3
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 327 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C SER* 3.0 15.6 + - - -
326C PRO* 1.3 89.6 + - - +
328C ARG* 1.3 66.0 + - - +
329C GLU* 3.6 16.2 - - + +
330C LEU* 3.2 30.1 - - + +
331C ALA 3.1 8.5 + - - -
375C THR* 3.3 10.7 - - - +
547C SER 5.2 0.3 + - - -
548C VAL* 3.2 28.0 + - - +
551C ARG* 5.3 4.7 - - - +
553C LEU* 5.3 3.6 - - + -
4G U 3.7 12.3 + - - -
5G U 3.6 3.6 - - - +
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Residues in contact with ARG 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C THR* 1.3 69.7 - - - +
329C GLU* 1.3 70.3 + - - +
331C ALA* 2.9 21.0 + - - +
332C ILE* 2.9 17.9 + - - +
353C TYR* 3.9 16.2 - - + -
354C GLY* 3.3 29.9 + - - -
355C GLY* 3.8 9.1 - - - +
375C THR* 3.8 12.6 - - + -
523C ARG 5.8 0.6 + - - -
525C GLN* 2.7 46.3 + - - +
528C ARG* 3.8 14.4 - - - +
5G U 2.9 31.4 + - - +
6G U 2.9 31.8 + - - +
7G U 4.1 10.1 + - - -
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Residues in contact with GLU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C THR* 3.6 11.0 - - + +
328C ARG* 1.3 72.3 - - - +
330C LEU* 1.3 57.2 + - - +
332C ILE* 3.4 10.6 + - + +
333C GLN* 3.0 27.0 + - - +
519C ILE* 3.8 15.2 - - + +
525C GLN* 3.0 19.4 + - - +
528C ARG* 2.9 46.8 + - - +
529C GLU* 4.9 10.5 - - + -
532C LEU* 3.6 33.2 - - + -
548C VAL* 4.2 3.5 - - - +
553C LEU* 4.0 12.3 - - + +
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C THR* 6.2 0.2 - - - +
325C SER* 3.3 20.9 - - - +
326C PRO* 4.2 5.4 - - + -
327C THR* 3.2 17.5 - - + +
328C ARG 3.1 1.0 - - - -
329C GLU* 1.3 75.1 - - - +
331C ALA* 1.3 66.3 + - - +
333C GLN* 3.3 27.3 + - - +
334C ILE* 2.9 38.6 + - + +
399C ASP* 4.3 9.9 - - - +
400C GLU* 3.6 31.0 - - + +
551C ARG* 4.1 15.0 - - + +
552C GLY* 3.8 17.0 - - - -
553C LEU* 4.1 4.9 - - + +
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C SER* 3.7 9.1 + - - -
327C THR 3.1 13.1 + - - +
328C ARG* 2.9 11.1 + - - +
330C LEU* 1.3 78.4 - - - +
332C ILE* 1.3 63.0 + - - +
334C ILE* 3.2 1.8 + - - -
335C PHE* 2.9 23.9 + - - +
351C ILE* 3.6 13.5 - - + -
353C TYR* 4.9 3.6 - - + -
373C ILE* 3.4 25.3 - - + +
374C ALA* 4.6 5.4 - - - -
375C THR* 4.3 12.8 - - + +
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Residues in contact with ILE 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ARG 2.9 17.6 + - - +
329C GLU* 3.7 13.9 - - + +
330C LEU 3.3 0.2 - - - -
331C ALA* 1.3 75.7 - - - +
333C GLN* 1.3 63.8 + - - +
335C PHE* 3.1 8.9 - - + +
336C ASN* 2.9 37.2 + - - +
351C ILE* 3.5 9.4 - - + -
353C TYR* 3.4 41.7 - - + +
525C GLN* 4.8 0.7 - - - +
529C GLU* 3.5 26.5 - - + +
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Residues in contact with GLN 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C THR* 5.3 4.4 + - - -
329C GLU 3.0 18.7 + - - +
330C LEU* 3.5 17.1 - - - +
331C ALA 3.2 0.2 - - - -
332C ILE* 1.3 78.7 - - - +
334C ILE* 1.3 64.0 + - + +
336C ASN* 3.2 8.7 + - - +
337C GLU* 3.0 32.0 + - + +
536C LYS* 5.9 1.8 + - - +
552C GLY 2.9 24.4 + - - -
553C LEU* 3.5 11.8 - - + +
554C ASP* 2.8 39.4 + - - +
555C ILE* 5.1 1.9 - - - +
2903C ANP 4.5 5.7 + - - -
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Residues in contact with ILE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C THR* 4.8 11.4 - - + +
299C PHE* 4.6 10.8 - - + -
300C LEU* 4.3 7.5 - - + +
323C ILE* 4.2 25.4 - - + -
325C SER* 4.4 9.6 - - - -
330C LEU* 2.9 36.5 + - + +
331C ALA* 3.7 4.0 - - - +
333C GLN* 1.3 76.2 - - + +
335C PHE* 1.3 65.0 + - - +
337C GLU* 3.0 9.6 + - - +
338C ALA* 2.9 21.7 + - - +
373C ILE* 3.7 21.3 - - + -
399C ASP* 3.3 35.4 - - + +
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Residues in contact with PHE 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C PRO* 4.0 21.8 - - + -
331C ALA 2.9 12.7 + - - +
332C ILE* 3.1 15.3 - - + +
334C ILE* 1.3 78.3 - - - +
336C ASN* 1.3 76.2 + - - +
338C ALA* 3.2 3.8 + - - +
339C ARG* 3.0 46.3 + - - +
349C ILE* 3.3 42.4 - - + -
350C GLY* 4.0 9.0 - - - -
351C ILE* 3.7 38.6 - - + -
373C ILE* 4.0 12.5 - - + +
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Residues in contact with ASN 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C PRO* 4.0 16.8 - - - +
214C ILE* 5.1 2.8 - - - +
217C SER* 5.7 4.7 - - - +
332C ILE* 2.9 30.6 + - - +
333C GLN* 3.2 9.7 + - - +
335C PHE* 1.3 94.8 - - - +
337C GLU* 1.3 67.3 + - - +
339C ARG* 3.4 13.6 + - - +
340C LYS* 3.0 21.8 + - - +
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Residues in contact with GLU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C SER* 2.8 30.5 + - - -
265C TYR* 4.0 10.0 + - - -
296C THR* 4.2 16.1 - - + +
300C LEU* 3.8 15.5 - - + -
333C GLN* 3.0 25.2 + - + +
334C ILE* 3.0 9.7 + - - +
336C ASN* 1.3 74.5 - - - +
338C ALA* 1.3 66.8 + - - +
340C LYS* 3.1 30.7 + - - +
341C PHE* 3.1 33.7 + - + -
554C ASP* 6.2 0.4 - - - -
2903C ANP 4.4 7.6 + - - -
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Residues in contact with ALA 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C LEU* 3.7 24.4 - - + +
304C LEU* 3.9 9.8 - - + +
334C ILE 2.9 12.4 + - - +
335C PHE* 3.2 9.4 + - - +
337C GLU* 1.3 77.4 - - - +
339C ARG* 1.3 57.2 + - - +
340C LYS 3.1 0.2 + - - -
341C PHE* 3.2 1.6 + - - -
342C ALA* 2.8 34.5 + - - +
349C ILE* 3.8 26.2 - - + -
371C VAL* 5.2 1.6 - - + -
373C ILE* 4.7 4.9 - - + -
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Residues in contact with ARG 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C PRO* 3.6 26.6 + - - +
208C SER 3.1 29.4 + - - -
209C ASN* 3.2 20.4 + - - -
214C ILE* 3.6 28.8 - - + +
335C PHE* 3.0 44.7 + - + +
336C ASN* 3.7 17.4 + - - +
337C GLU 3.3 0.2 - - - -
338C ALA* 1.3 76.2 - - - +
340C LYS* 1.3 57.7 + - - +
342C ALA* 3.7 2.4 - - - -
343C PHE* 3.0 27.0 + - - +
349C ILE* 4.1 23.6 - - + +
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Residues in contact with LYS 340 (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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214C ILE* 3.6 30.9 - - + +
215C PHE* 3.5 31.1 - - + -
217C SER* 3.6 19.3 + - - +
218C GLY* 4.9 0.8 - - - +
259C ASN* 3.6 8.3 - - - +
263C SER* 3.4 25.5 + - - +
265C TYR* 4.1 9.1 + - - -
336C ASN 3.0 13.3 + - - +
337C GLU* 3.1 40.1 + - - +
338C ALA 3.0 0.4 - - - -
339C ARG* 1.3 78.2 - - - +
341C PHE* 1.3 70.9 + - - +
343C PHE* 3.2 17.8 - - - +
2903C ANP 4.5 4.4 + - - -
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Residues in contact with PHE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ILE* 3.4 18.6 - - + +
259C ASN* 2.9 25.6 + - + +
260C VAL* 4.6 10.8 - - + -
263C SER* 3.5 25.6 - - - -
265C TYR* 3.5 37.7 - + - -
296C THR* 5.5 0.7 - - + -
297C ALA* 3.9 24.2 - - + -
300C LEU* 4.0 20.2 - - + -
301C LEU* 3.6 26.0 - - + -
304C LEU* 3.7 16.8 - - + -
337C GLU* 3.1 32.8 + - + +
340C LYS* 1.3 80.7 - - - +
342C ALA* 1.3 58.0 + - - +
343C PHE 3.2 1.3 - - - -
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Residues in contact with ALA 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ILE* 4.8 2.7 - - - -
259C ASN* 4.0 0.2 - - - -
304C LEU* 4.1 11.2 - - + +
338C ALA 2.8 19.1 + - - +
339C ARG* 3.7 5.6 - - - +
341C PHE* 1.3 77.0 - - - +
343C PHE* 1.3 66.0 + - - +
344C GLU 3.2 0.5 + - - -
345C SER* 2.6 37.4 + - - +
347C LEU* 4.4 19.2 - - + +
349C ILE* 4.5 10.1 - - + -
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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
------------------------------------------------------------
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