Contacts of the helix formed by residues 295 - 305 (chain C) in PDB entry 3N6J
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 ASN 295 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B TYR* 3.7 1.9 + - - -
97C TYR* 3.6 29.3 - - + +
100C PHE* 5.5 2.0 - - - -
108C GLU* 3.7 14.7 + - - +
293C ALA 3.5 0.4 - - - -
294C THR* 1.3 94.0 + - - +
296C TRP* 1.3 58.5 + - - +
297C ARG* 3.3 10.7 + - - +
298C GLU* 2.8 43.1 + - - +
299C MSE 2.9 26.9 + - - +
318C TRP* 3.2 14.6 - - - -
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Residues in contact with TRP 296 (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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89C HIS* 6.3 0.9 - - - -
295C ASN* 1.3 72.1 - - + +
297C ARG* 1.3 66.3 + - - +
299C MSE 3.3 17.4 - - + +
300C CYS* 3.1 21.8 + - - +
318C TRP* 3.4 24.6 - + - -
322C GLY* 4.0 5.6 + - - -
325C ARG* 3.1 59.2 - - + +
326C VAL* 3.6 28.3 - - + -
329C LEU* 4.3 24.5 - - + -
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Residues in contact with ARG 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 3.9 13.4 - - - +
267B GLU* 5.5 3.2 + - - +
268B ASN* 6.0 1.4 - - - +
270B TYR* 3.3 40.6 - - + +
275B ILE* 4.2 6.7 - - - +
278B GLU* 2.9 43.9 + - + +
97C TYR* 3.4 44.9 - - - +
295C ASN* 3.4 8.5 - - - +
296C TRP* 1.3 78.7 - - - +
298C GLU* 1.3 62.3 + - - +
300C CYS* 3.3 19.9 + - - +
301C HIS* 3.7 11.3 + - - +
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Residues in contact with GLU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B TYR* 3.4 25.7 + - + +
100C PHE* 3.6 20.4 - - - -
273C ARG* 3.3 34.5 + - - +
291C MSE 4.6 1.0 - - - +
292C ILE 3.3 13.0 - - - +
293C ALA* 3.9 3.4 - - - -
294C THR* 2.5 47.7 + - - +
295C ASN* 2.8 27.2 + - - +
297C ARG* 1.3 72.5 - - - +
299C MSE 1.3 64.2 + - - +
301C HIS* 3.2 4.2 + - - -
302C ALA* 3.0 18.7 + - - +
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Residues in contact with MSE 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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293C ALA* 3.7 30.4 - - + +
295C ASN 2.9 15.0 + - - +
296C TRP* 3.3 32.5 - - + +
298C GLU* 1.3 75.8 - - - +
300C CYS* 1.3 62.0 + - - +
302C ALA* 3.2 5.3 + - - +
303C ILE* 3.1 57.1 + - + +
308C VAL* 5.4 2.2 - - - -
311C PRO* 3.8 32.1 - - + -
312C LEU 5.9 1.8 - - - +
313C ALA* 6.0 0.4 - - + -
318C TRP* 3.9 23.6 - - + -
326C VAL* 4.3 12.6 - - + -
329C LEU* 5.3 2.9 - - + -
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Residues in contact with CYS 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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281B ARG* 3.9 32.8 - - - -
296C TRP 3.1 11.4 + - - +
297C ARG* 3.5 11.4 - - - +
299C MSE 1.3 76.0 - - - +
301C HIS* 1.3 65.4 + - + +
303C ILE* 3.4 5.8 + - - +
304C MSE 3.0 41.0 + - - +
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Residues in contact with HIS 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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270B TYR* 3.8 19.7 - + - -
274B GLU* 3.6 42.0 - - + +
277B ALA* 4.4 9.3 - - + +
278B GLU* 2.8 35.8 + - + -
281B ARG* 4.6 9.9 + - - -
305B LEU* 3.8 22.6 - - + +
273C ARG* 3.9 9.4 - - - -
297C ARG* 3.8 17.2 + - - +
298C GLU* 3.2 6.3 + - - +
300C CYS* 1.3 80.9 - - - +
302C ALA* 1.3 56.5 + - - +
303C ILE 3.2 0.2 + - - -
304C MSE 3.2 3.3 + - - +
305C LEU* 2.8 35.0 + - + +
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Residues in contact with ALA 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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273C ARG* 3.7 17.2 - - + +
292C ILE* 4.8 1.3 - - + -
293C ALA* 4.3 13.5 - - + -
298C GLU 3.0 12.5 + - - +
299C MSE 3.2 10.0 + - - +
301C HIS* 1.3 76.4 - - - +
303C ILE* 1.3 59.0 + - + +
305C LEU* 4.6 0.2 - - - -
306C GLN* 3.0 4.3 + - - -
307C SER* 2.9 46.1 + - - +
308C VAL* 4.0 17.2 - - + +
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Residues in contact with ILE 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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299C MSE 3.1 46.6 + - + +
300C CYS* 4.0 4.7 - - - +
302C ALA* 1.3 77.1 - - + +
304C MSE 1.3 72.1 + - - +
305C LEU 3.3 0.2 - - - -
306C GLN* 3.2 31.4 + - - +
308C VAL* 5.3 4.9 - - + -
329C LEU* 4.4 19.1 - - + -
333C TRP* 4.3 26.5 - - + -
335C LEU* 4.6 21.8 - - + -
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Residues in contact with MSE 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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304A MSE 5.1 8.1 - - + +
306A GLN* 4.3 5.0 + - - -
281B ARG* 5.3 4.5 - - - +
304B MSE 3.3 42.0 - - - +
305B LEU* 3.9 25.6 - - + +
306B GLN* 4.9 8.5 - - + -
300C CYS* 3.0 40.7 + - - +
301C HIS* 3.3 11.0 - - - +
303C ILE* 1.3 82.1 - - - +
305C LEU* 1.3 60.6 + - - +
306C GLN* 3.2 5.5 + - - +
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Residues in contact with LEU 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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306A GLN* 4.1 7.2 + - - -
274B GLU* 3.8 7.6 - - - +
301B HIS* 3.8 36.1 - - + +
304B MSE 4.1 11.8 - - + +
305B LEU* 3.6 27.4 - - + -
273C ARG* 3.5 38.8 - - + +
274C GLU* 3.4 25.1 - - + -
277C ALA* 3.3 13.6 - - + +
281C ARG* 4.2 4.9 + - - -
301C HIS 2.8 18.9 + - - +
302C ALA 4.2 3.4 - - - +
304C MSE 1.3 72.7 - - - +
306C GLN* 1.3 69.2 + - - +
307C SER* 4.4 0.4 - - - +
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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