Contacts of the helix formed by residues 296 - 309 (chain C) in PDB entry 6IY6
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 PRO 296 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256C PHE* 3.9 26.9 - - + +
260C ASN* 3.5 35.7 - - + +
294C THR 4.0 4.7 - - - +
295C VAL* 1.4 94.0 - - + +
297C ALA* 1.3 65.1 + - - +
298C ASN 3.6 0.2 - - - -
299C VAL* 3.6 21.1 - - + -
300C GLN* 3.4 21.5 + - - +
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Residues in contact with ALA 297 (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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260C ASN* 4.3 1.9 + - - +
296C PRO* 1.3 70.9 - - - +
298C ASN* 1.3 71.9 + - - +
300C GLN* 3.3 19.1 + - - +
301C ARG* 3.3 13.5 + - - +
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Residues in contact with ASN 298 (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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260C ASN* 2.6 44.7 + - - +
263C LEU* 3.8 15.0 - - + -
264C GLY* 3.2 20.9 - - - -
296C PRO 3.6 0.2 - - - -
297C ALA* 1.3 79.7 - - - +
299C VAL* 1.3 57.8 + - - +
301C ARG* 3.3 31.1 + - - +
302C TRP* 3.0 27.7 + - - +
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Residues in contact with VAL 299 (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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256C PHE* 4.1 19.5 - - + -
259C MET* 4.0 22.9 - - + -
260C ASN* 4.2 4.3 - - - +
263C LEU* 4.0 23.3 - - + -
295C VAL* 3.7 17.7 - - + -
296C PRO* 3.6 30.2 + - + +
297C ALA 3.3 0.2 - - - -
298C ASN* 1.3 72.2 - - - +
300C GLN* 1.3 55.5 + - - +
302C TRP* 3.3 7.9 + - + +
303C MET* 2.7 49.7 + - + +
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Residues in contact with GLN 300 (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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295C VAL* 3.8 31.7 + - + +
296C PRO 3.4 12.0 + - - +
297C ALA* 3.3 13.9 + - - +
299C VAL* 1.3 78.1 - - - +
301C ARG* 1.3 56.7 + - - +
303C MET* 3.5 10.2 + - - +
304C ARG* 3.2 41.3 + - - +
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Residues in contact with ARG 301 (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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263C LEU* 3.0 32.7 + - - +
266C SER 4.4 3.8 + - - -
267C PRO* 4.6 12.3 + - - +
297C ALA 3.3 8.3 + - - +
298C ASN* 3.3 37.4 + - - +
300C GLN* 1.3 75.9 - - - +
302C TRP* 1.3 59.2 + - - +
304C ARG* 3.6 23.4 + - - +
305C SER* 2.9 31.1 + - - -
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Residues in contact with TRP 302 (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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259C MET* 3.4 30.7 - - + -
263C LEU* 3.6 33.4 - - + +
267C PRO 4.3 5.2 - - - +
268C TRP* 3.6 24.9 - + - -
269C LEU* 4.2 10.1 - - + -
278C ASP* 3.3 43.9 + - - +
281C LEU* 4.2 2.9 - - + -
282C TRP* 3.4 35.2 - + + -
285C LEU* 3.8 14.6 - - + -
298C ASN 3.0 17.4 + - - +
299C VAL* 3.6 9.0 - - + +
301C ARG* 1.3 76.1 - - - +
303C MET* 1.3 72.0 + - + +
305C SER* 3.5 6.3 - - - -
306C CYS* 3.0 37.2 + - - -
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Residues in contact with MET 303 (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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256C PHE* 5.1 2.5 - - + -
282C TRP* 3.6 16.1 + - + +
285C LEU* 3.9 40.4 - - + +
286C GLN* 4.7 12.1 - - - +
295C VAL* 4.8 15.7 - - + -
299C VAL* 2.7 36.3 + - + +
300C GLN* 3.6 11.2 - - - +
302C TRP* 1.3 81.9 - - + +
304C ARG* 1.3 52.6 + - + +
306C CYS* 3.4 4.2 + - - +
307C GLU* 2.8 49.5 + - - +
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Residues in contact with ARG 304 (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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300C GLN* 3.2 20.6 + - - +
301C ARG* 3.9 28.8 - - - +
303C MET* 1.3 75.0 - - + +
305C SER* 1.3 56.1 + - - +
307C GLU* 3.8 15.0 - - - +
308C ASN* 2.7 37.1 + - - +
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Residues in contact with SER 305 (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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267C PRO 5.5 1.8 + - - -
268C TRP* 3.2 26.1 - - - -
301C ARG* 2.9 21.5 + - - -
302C TRP* 3.5 12.1 - - - -
304C ARG* 1.3 77.3 - - - +
306C CYS* 1.3 59.9 + - - +
308C ASN* 3.7 12.1 + - - +
309C LEU* 3.4 19.8 - - - +
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Residues in contact with CYS 306 (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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268C TRP* 3.9 12.1 - - - -
274C LEU* 4.8 2.7 - - - -
278C ASP* 4.8 1.1 - - - -
282C TRP* 3.6 17.0 - - + -
302C TRP* 3.0 49.0 + - - +
303C MET 3.5 8.5 - - - +
305C SER* 1.3 70.7 - - - +
307C GLU* 1.3 57.0 + - - +
308C ASN 3.1 1.3 - - - -
309C LEU* 2.9 38.1 + - - +
312C PHE* 3.2 36.4 - - + +
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Residues in contact with GLU 307 (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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282C TRP* 3.6 20.3 + - + -
286C GLN* 2.9 25.6 + - - -
303C MET* 2.8 35.0 + - - +
304C ARG* 3.3 15.2 + - - +
306C CYS* 1.3 72.6 - - - +
308C ASN* 1.3 59.8 + - - +
309C LEU 3.4 8.0 - - - +
312C PHE* 4.3 7.0 - - - -
313C ASN* 3.5 21.0 + - + +
316C LEU* 4.9 7.9 - - + -
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Residues in contact with ASN 308 (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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304C ARG 2.7 21.8 + - - +
305C SER* 3.7 10.9 + - - +
306C CYS 3.1 0.2 - - - -
307C GLU* 1.3 72.0 - - - +
309C LEU* 1.3 67.5 + - - +
310C ALA 3.8 0.9 + - - -
313C ASN* 4.0 5.7 + - - -
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Residues in contact with LEU 309 (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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268C TRP* 4.2 16.8 - - + -
274C LEU* 3.9 18.6 - - + -
305C SER 3.4 14.1 - - - +
306C CYS* 2.9 20.3 + - - +
307C GLU 3.4 5.4 - - - +
308C ASN* 1.3 81.9 - - + +
310C ALA* 1.3 58.8 + - - +
311C PRO* 4.1 5.8 - - + -
312C PHE* 3.5 32.2 + - + -
313C ASN* 2.9 24.4 + - - -
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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