Contacts of the helix formed by residues 335 - 353 (chain C) in PDB entry 3IO6
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 GLN 335 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C PHE* 3.3 33.2 - - + -
178C ILE* 3.5 31.4 - - + +
333C ILE* 3.2 11.7 - - + +
334C PRO* 1.3 99.1 - - - +
336C MET* 1.3 60.7 + - - +
337C SER 3.2 1.6 - - - -
338C ALA* 3.4 7.5 + - + +
339C PHE 3.3 13.7 + - - -
372C ALA* 3.5 21.7 + - + +
373C THR* 4.9 13.4 - - + +
376C LYS* 5.1 12.1 - - - +
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Residues in contact with MET 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ALA* 4.0 3.8 - - + -
169C PHE* 4.0 14.8 - - - -
258C PHE* 3.9 13.2 - - + -
330C MET* 4.3 5.4 - - + -
331C PRO* 3.7 55.2 - - + +
333C ILE* 3.2 19.8 + - + +
334C PRO 3.1 0.8 - - - -
335C GLN* 1.3 77.5 - - - +
337C SER* 1.3 63.5 + - - +
338C ALA 3.2 0.4 - - - -
339C PHE* 3.6 32.8 + - + +
340C TRP* 3.0 53.4 + - + +
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Residues in contact with SER 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ILE 4.5 0.4 + - - -
334C PRO* 3.3 19.4 + - - +
336C MET* 1.3 79.4 - - - +
338C ALA* 1.3 63.2 + - - +
340C TRP* 3.8 8.2 + - - +
341C TYR* 3.7 15.1 + - - +
372C ALA* 4.6 4.0 - - - -
375C GLU* 4.5 15.2 + - - -
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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
----------------------------------------------------------
335C GLN* 3.4 6.6 + - + +
336C MET 3.2 0.4 - - - -
337C SER* 1.3 74.2 - - - +
339C PHE* 1.3 58.5 + - - +
340C TRP 3.0 1.8 - - - -
341C TYR* 2.7 28.2 + - - +
342C ALA* 3.0 12.8 + - - +
368C ALA* 3.7 21.3 - - + +
371C MET* 3.7 16.8 - - + +
372C ALA* 3.2 37.0 - - + +
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Residues in contact with PHE 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C TRP* 3.8 35.0 - + - -
168C ALA* 3.7 26.9 - - + -
169C PHE* 4.3 13.9 - - + -
181C VAL* 5.2 3.4 - - + -
183C VAL* 3.6 32.3 - - + -
258C PHE* 4.1 3.4 - + - -
335C GLN 3.3 9.5 + - - +
336C MET* 3.6 32.1 - - + +
338C ALA* 1.3 77.9 - - - +
340C TRP* 1.3 83.3 + + - +
342C ALA* 3.5 6.5 + - + +
343C VAL* 3.0 42.3 + - + +
368C ALA* 4.6 6.4 - - + +
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Residues in contact with TRP 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C PRO* 3.7 26.0 - - + +
155C TYR* 3.8 36.1 - + + -
158C TRP* 5.4 0.4 - - + -
258C PHE* 3.5 27.4 - + - -
330C MET* 4.0 29.3 - - + -
336C MET* 3.0 47.0 + - + +
337C SER* 3.9 8.1 - - - +
338C ALA 2.8 4.4 + - - -
339C PHE* 1.3 93.1 - + - +
341C TYR* 1.3 56.8 + - - +
343C VAL 3.9 0.2 - - - -
344C ARG* 2.9 41.0 + - - +
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Residues in contact with TYR 341 (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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384B LEU* 5.3 16.8 - - + -
385B LYS* 5.3 5.6 - - - -
388B GLN* 3.0 48.3 + - + +
337C SER 3.7 7.9 + - - +
338C ALA 2.7 13.1 + - - +
340C TRP* 1.3 72.8 - - - +
342C ALA* 1.3 60.0 + - - +
344C ARG* 4.2 22.4 - - - +
345C THR* 2.8 39.2 + - - -
371C MET* 4.5 28.9 - - + -
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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
----------------------------------------------------------
338C ALA 3.0 9.8 + - - +
339C PHE* 3.7 12.6 - - - +
341C TYR* 1.3 78.1 - - - +
343C VAL* 1.3 59.3 + - + +
345C THR* 4.1 3.2 - - - -
346C ALA* 3.2 25.5 + - - +
364C ALA* 3.3 38.2 - - + +
367C ASN* 4.3 12.9 + - + +
368C ALA* 4.1 13.7 - - + +
371C MET* 5.8 0.8 - - - +
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Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C PRO* 3.9 17.5 - - + -
158C TRP* 4.3 19.1 - - + -
161C ILE* 4.9 2.2 - - + -
183C VAL* 3.8 22.2 - - + -
339C PHE* 3.0 45.5 + - + +
340C TRP 4.3 0.4 - - - +
342C ALA* 1.3 77.7 - - + +
344C ARG* 1.3 60.3 + - - +
345C THR 3.2 0.4 - - - -
346C ALA* 4.0 6.1 - - + -
347C VAL* 2.9 46.1 + - + +
361C LEU* 6.1 2.2 - - + -
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Residues in contact with ARG 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PRO* 3.5 30.1 - - - +
152C GLN 3.6 17.7 + - - +
153C GLU* 2.9 38.4 + - - -
154C PRO* 3.8 19.0 - - + +
340C TRP* 2.9 29.6 + - - +
341C TYR* 4.2 24.7 - - - +
343C VAL* 1.3 76.6 - - - +
345C THR* 1.3 59.8 + - - +
347C VAL* 4.2 2.4 - - - +
348C ILE* 3.0 35.2 + - + +
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Residues in contact with THR 345 (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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384B LEU* 5.5 10.5 - - + +
341C TYR* 2.8 32.4 + - - -
342C ALA 4.1 3.1 - - - -
343C VAL 3.2 0.2 - - - -
344C ARG* 1.3 77.8 - - - +
346C ALA* 1.3 55.9 + - - +
348C ILE* 3.8 4.9 - - + +
349C ASN* 2.6 63.3 + - - +
367C ASN* 5.7 6.3 - - - +
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Residues in contact with ALA 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C LEU* 4.3 3.5 - - - +
342C ALA 3.2 17.2 + - - +
343C VAL* 3.6 8.3 - - + +
345C THR* 1.3 79.3 - - - +
347C VAL* 1.3 59.2 + - + +
349C ASN* 4.6 0.9 - - - +
350C ALA* 3.1 31.4 + - - +
360C ALA* 3.3 36.2 - - - +
361C LEU* 4.6 12.6 - - + -
364C ALA* 3.8 7.9 - - + -
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Residues in contact with VAL 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LEU* 3.9 18.8 - - + +
152C GLN 6.1 0.4 - - - -
153C GLU 5.3 1.1 - - - +
154C PRO* 5.1 3.1 - - + -
157C THR* 3.7 26.2 - - + +
161C ILE* 3.8 26.9 - - + -
192C LEU* 4.5 12.3 - - + +
195C LEU* 4.3 13.9 - - + -
343C VAL* 2.9 30.6 + - + +
344C ARG* 4.3 3.6 - - - +
346C ALA* 1.3 75.7 - - + +
348C ILE* 1.3 59.5 + - + +
350C ALA* 4.3 0.7 - - - +
351C ALA* 3.1 29.3 + - + +
361C LEU* 6.3 0.9 - - + -
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Residues in contact with ILE 348 (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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391B GLN* 5.2 12.6 - - + +
151C LEU* 3.5 23.1 - - + +
152C GLN* 3.4 38.4 - - + +
206C ALA 5.3 3.1 - - - +
344C ARG* 3.0 25.5 + - + +
345C THR* 3.1 7.0 + - + +
347C VAL* 1.3 78.0 - - + +
349C ASN* 1.3 67.1 + - - +
351C ALA* 3.6 4.9 + - + +
352C SER* 3.2 27.0 + - - +
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Residues in contact with ASN 349 (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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345C THR* 2.6 44.0 + - - +
346C ALA* 4.1 3.5 - - - +
348C ILE* 1.3 77.0 - - - +
350C ALA* 1.3 62.3 + - - +
352C SER* 3.2 16.2 + - - -
354C ARG* 3.3 50.4 + - + +
355C GLN* 3.4 35.2 + - + +
360C ALA* 4.1 4.0 - - + +
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Residues in contact with ALA 350 (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 LEU* 3.8 23.3 - - + -
196C VAL* 3.8 27.1 - - + +
346C ALA 3.1 19.3 + - - +
347C VAL 4.3 2.0 - - - +
349C ASN* 1.3 77.3 - - - +
351C ALA* 1.3 60.7 + - - +
352C SER 3.5 0.2 + - - -
353C GLY* 3.6 7.4 + - - -
355C GLN 3.6 16.0 - - - +
356C THR* 5.7 0.2 - - - -
357C VAL 4.6 9.4 - - - +
360C ALA* 4.2 8.7 - - + +
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Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LEU* 6.1 3.8 - - + +
195C LEU* 5.5 2.2 - - + -
196C VAL* 4.4 7.7 - - + +
199C ILE* 3.7 46.6 - - + +
206C ALA* 3.9 15.2 - - + +
347C VAL* 3.1 24.7 + - + +
348C ILE* 4.1 8.1 - - + +
349C ASN 3.3 0.2 - - - -
350C ALA* 1.3 76.4 - - - +
352C SER* 1.3 59.4 + - - +
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Residues in contact with SER 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ALA* 5.1 7.2 - - - -
348C ILE* 3.2 17.4 + - - +
349C ASN* 3.2 13.5 + - - -
351C ALA* 1.3 79.5 - - - +
353C GLY* 1.3 55.0 + - - +
354C ARG* 3.4 16.0 + - - +
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Residues in contact with GLY 353 (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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53B THR* 4.4 13.0 - - - +
349C ASN 3.4 3.2 + - - -
350C ALA 3.6 7.3 + - - -
351C ALA 3.5 2.4 - - - -
352C SER* 1.3 78.1 - - - +
354C ARG* 1.3 63.9 + - - +
355C GLN* 3.2 11.0 + - - +
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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