Contacts of the helix formed by residues 328 - 346 (chain C) in PDB entry 2IK8
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 ASP 328 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C GLN* 3.6 2.0 - - - -
172C GLN* 5.2 0.7 - - - +
325C CYS* 2.6 37.4 + - + +
326C ALA 3.2 0.8 - - - -
327C THR* 1.3 69.4 - - - +
329C THR* 1.3 63.7 + - - +
330C LYS* 3.8 7.4 + - - +
331C ASN* 3.2 22.3 + - + +
332C VAL* 3.0 21.1 + - - +
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Residues in contact with THR 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLN* 2.5 29.7 + - - +
55C ILE* 4.2 15.3 - - + +
56C ILE* 3.6 28.8 - - + +
171C GLN* 4.9 3.7 + - - +
172C GLN* 5.7 0.2 - - - +
175C LEU* 4.1 8.7 - - - +
327C THR 3.8 1.6 + - - -
328C ASP* 1.3 69.8 + - - +
330C LYS* 1.3 57.1 + - - +
332C VAL 2.9 1.4 + - - +
333C GLN* 2.7 37.9 + - - +
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Residues in contact with LYS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ASP* 3.5 8.1 + - - +
329C THR* 1.3 76.9 - - - +
331C ASN* 1.3 62.2 + - - +
333C GLN* 3.4 13.1 + - - +
334C PHE* 3.1 23.6 + - - +
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Residues in contact with ASN 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LYS* 3.9 19.4 - - - +
323C PHE 4.3 2.6 + - - -
324C THR* 3.5 9.4 - - - +
325C CYS* 3.0 31.9 + - + +
328C ASP* 3.2 24.1 + - + +
330C LYS* 1.3 79.8 - - - +
332C VAL* 1.3 58.9 + - - +
334C PHE* 3.3 5.4 + - - +
335C VAL* 3.0 39.2 + - - +
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Residues in contact with VAL 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 4.1 16.4 - - + -
52C GLN* 3.7 27.4 - - + -
53C MET* 4.0 15.9 - - + -
56C ILE* 4.2 0.9 - - + -
267C PHE* 5.5 4.9 - - + -
324C THR* 5.4 3.4 - - + -
325C CYS 3.6 11.4 - - - +
326C ALA* 3.5 29.6 - - - +
328C ASP 3.0 13.4 + - - +
329C THR 2.9 6.5 + - - +
331C ASN* 1.3 78.5 - - - +
333C GLN* 1.3 66.1 + - - +
335C VAL* 4.5 4.9 - - - -
336C PHE* 2.9 26.3 + - + +
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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
----------------------------------------------------------
56C ILE* 3.5 36.9 - - + +
57C HIS* 5.8 2.5 - - - +
191C PHE* 5.9 0.7 - - - -
329C THR* 2.7 22.6 + - - +
330C LYS* 3.4 13.1 - - - +
332C VAL* 1.3 73.7 - - - +
334C PHE* 1.3 55.8 + - - +
336C PHE* 3.9 2.6 - - - +
337C ASP* 2.9 28.8 + - + +
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Residues in contact with PHE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C LYS 3.1 14.1 + - - +
331C ASN* 3.8 7.4 - - - +
332C VAL 3.3 0.2 - - - -
333C GLN* 1.3 77.5 - - - +
335C VAL* 1.3 62.8 + - + +
337C ASP* 3.3 10.5 - - + +
338C ALA* 3.1 23.4 + - - +
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Residues in contact with VAL 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PHE* 3.5 36.1 - - + -
322C HIS* 3.7 22.7 - - + -
323C PHE 4.8 2.2 - - - +
324C THR* 3.9 20.0 - - + -
331C ASN* 3.0 35.9 + - - +
332C VAL* 4.0 4.3 - - - +
334C PHE* 1.3 74.5 - - + +
336C PHE* 1.3 55.0 + - - +
337C ASP 3.1 1.6 - - - -
338C ALA* 2.9 11.3 + - - +
339C VAL* 2.7 32.1 + - - +
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Residues in contact with PHE 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.8 21.1 - - + -
49C ILE* 5.6 1.6 - - + -
53C MET* 3.6 41.5 - - + -
57C HIS* 4.0 14.4 - + + -
189C PHE* 3.8 10.5 - + - -
191C PHE* 4.1 10.5 - + - -
196C PHE* 3.7 31.2 - + - -
198C MET* 4.6 0.7 - - + -
222C ILE* 4.3 16.6 - - + -
267C PHE* 5.2 4.7 - + + -
332C VAL* 2.9 19.8 + - + +
333C GLN* 4.2 3.4 - - - +
335C VAL* 1.3 75.1 - - - +
337C ASP* 1.3 58.5 + - - +
339C VAL* 3.8 13.9 - - + -
340C THR* 2.7 52.3 + - - -
343C ILE* 5.9 0.9 - - + -
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Residues in contact with ASP 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C PHE* 4.6 18.1 - - + -
333C GLN* 2.9 21.2 + - + +
334C PHE* 3.3 14.3 - - - +
336C PHE* 1.3 75.6 - - - +
338C ALA* 1.3 66.3 + - - +
340C THR* 3.1 6.1 + - - -
341C ASP* 3.0 38.4 + - - +
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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
----------------------------------------------------------
322C HIS* 3.9 22.9 - - + +
334C PHE 3.1 9.2 + - - +
335C VAL* 2.9 11.5 + - - +
337C ASP* 1.3 84.8 + - - +
339C VAL* 1.3 62.8 + - - +
341C ASP* 3.4 8.6 + - - +
342C VAL* 3.2 27.4 + - + +
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Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ILE* 4.7 11.7 - - + -
265C ILE* 4.1 26.2 - - + -
267C PHE* 3.9 31.6 - - + -
320C TYR* 6.5 0.2 - - + -
322C HIS* 4.0 13.4 + - + -
335C VAL 2.7 23.1 + - - +
336C PHE* 3.8 14.1 - - + +
338C ALA* 1.3 72.2 - - - +
340C THR* 1.3 60.1 + - - +
342C VAL* 3.0 12.0 + - - +
343C ILE* 3.0 43.8 + - + +
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Residues in contact with THR 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C PHE* 3.8 24.4 - - + -
192C LYS* 4.0 19.7 - - + -
194C LEU* 4.0 16.8 - - + -
196C PHE* 4.0 5.0 - - + -
336C PHE* 2.7 48.3 + - - -
337C ASP 3.1 4.0 + - - +
339C VAL* 1.3 75.3 - - - +
341C ASP* 1.3 67.5 + - - +
343C ILE* 3.3 10.5 + - - +
344C ILE* 3.1 22.4 + - + +
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Residues in contact with ASP 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C LYS* 5.1 10.0 - - - +
337C ASP* 3.0 32.6 + - - +
338C ALA* 3.5 9.9 - - - +
339C VAL 3.3 0.2 - - - -
340C THR* 1.3 76.6 - - - +
342C VAL* 1.3 59.3 + - + +
344C ILE* 2.9 25.2 + - - +
345C LYS* 3.0 12.9 + - - +
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Residues in contact with VAL 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C SER* 5.1 4.0 - - - +
265C ILE* 5.8 3.1 - - + -
320C TYR* 3.6 55.9 - - + +
322C HIS* 5.7 3.1 - - - +
338C ALA* 3.2 17.7 + - + +
339C VAL* 3.0 11.8 + - + +
341C ASP* 1.3 76.0 - - + +
343C ILE* 1.3 58.5 + - + +
345C LYS* 3.3 6.4 + - - +
346C ASN* 3.0 33.0 + - - +
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Residues in contact with ILE 343 (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 VAL* 4.5 31.9 - - + -
36C LEU* 4.8 3.6 - - + -
194C LEU* 5.1 6.3 - - + -
196C PHE* 4.7 10.1 - - + -
219C THR* 4.9 4.5 - - + +
220C ALA* 3.6 31.4 - - + -
263C SER* 4.8 9.4 - - - -
265C ILE* 5.1 1.6 - - + -
336C PHE* 5.9 0.2 - - + -
339C VAL* 3.0 32.7 + - + +
340C THR* 3.6 14.6 - - + +
341C ASP 3.2 0.2 - - - -
342C VAL* 1.3 75.7 - - + +
344C ILE* 1.3 60.0 + - + +
345C LYS 3.4 0.2 - - - -
346C ASN* 4.5 2.5 - - - -
347C ASN* 2.8 48.4 + - - +
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Residues in contact with ILE 344 (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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192C LYS* 4.8 12.1 - - + +
194C LEU* 3.3 43.3 - - + -
340C THR* 3.1 19.0 + - + +
341C ASP* 2.9 12.8 + - - +
343C ILE* 1.3 74.5 - - + +
345C LYS* 1.3 65.2 + - - +
347C ASN* 3.8 7.8 + - - +
348C LEU* 4.0 15.6 - - + +
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Residues in contact with LYS 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ASP 3.0 10.3 + - - +
342C VAL* 3.8 10.3 - - - +
344C ILE* 1.3 78.5 - - - +
346C ASN* 1.3 61.3 + - - +
347C ASN 3.2 1.4 + - - -
348C LEU 3.0 25.1 - - - +
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Residues in contact with ASN 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C THR 5.7 0.2 - - - -
263C SER* 2.8 31.8 + - - +
320C TYR* 3.2 29.8 + - - -
342C VAL* 3.0 18.9 + - - +
343C ILE 4.2 0.2 - - - +
344C ILE 3.4 0.2 - - - -
345C LYS* 1.3 79.3 - - - +
347C ASN* 1.3 66.6 + - - +
348C LEU 3.6 0.9 - - - -
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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