Contacts of the helix formed by residues 301 - 310 (chain C) in PDB entry 1DNU
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 LEU 301 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297C LEU* 2.9 21.9 + - + +
300C VAL* 1.3 84.6 - - + +
302C GLY* 1.3 69.2 + - - +
305C ALA* 3.4 24.6 + - + +
306C MET* 4.0 31.0 - - - +
309C TYR* 5.0 0.4 - - + -
310C LEU* 4.1 16.8 - - + -
486C LYS* 3.9 17.7 - - - +
489C GLY* 4.0 1.6 - - - -
491C VAL* 4.5 4.6 - - + +
496C ALA* 3.7 34.7 - - + +
499C ILE* 4.2 13.5 - - + -
500C GLY* 4.0 18.4 - - - +
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Residues in contact with GLY 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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298C PRO 3.0 17.6 + - - -
300C VAL 3.5 1.8 - - - -
301C LEU* 1.3 79.3 - - - +
303C PRO* 1.3 70.8 - - - +
304C THR 3.4 2.4 + - - -
306C MET* 2.9 28.8 + - - +
486C LYS* 5.3 0.4 - - - -
487C ARG 3.5 12.8 - - - -
488C LYS 3.5 7.9 - - - -
489C GLY* 3.7 1.6 - - - -
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Residues in contact with PRO 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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16C ACY 3.8 39.0 - - + +
298C PRO* 4.4 2.2 - - + +
302C GLY* 1.3 82.3 - - - +
304C THR* 1.3 58.2 + - - +
306C MET* 3.4 8.1 + - + +
307C ARG* 3.0 40.6 + - - +
487C ARG* 3.4 34.1 - - - +
488C LYS* 3.8 13.9 - - + +
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Residues in contact with THR 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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302C GLY 3.4 0.8 - - - -
303C PRO* 1.3 78.5 - - - +
305C ALA* 1.3 64.2 + - - +
307C ARG* 3.5 16.2 + - - +
308C LYS* 3.2 23.8 + - + +
486C LYS* 4.0 19.3 - - - +
487C ARG* 3.8 18.9 + - - -
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Residues in contact with ALA 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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301C LEU* 3.4 28.2 - - + +
302C GLY 3.6 2.0 + - - -
304C THR* 1.3 76.8 - - - +
306C MET* 1.3 66.7 + - - +
308C LYS* 4.4 2.9 - - - -
309C TYR* 3.0 43.3 + - + +
486C LYS* 3.9 14.1 - - - +
496C ALA* 3.8 24.9 - - + -
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Residues in contact with MET 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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293C TYR* 3.4 28.5 - - + +
297C LEU* 4.0 2.5 - - + -
298C PRO* 3.7 37.0 - - + -
301C LEU* 4.0 13.3 - - + +
302C GLY 2.9 21.4 + - - +
303C PRO* 3.5 9.0 - - + +
304C THR 3.3 0.2 - - - -
305C ALA* 1.3 76.6 - - - +
307C ARG* 1.3 58.3 + - + +
310C LEU* 2.8 73.9 + - + +
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Residues in contact with ARG 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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16C ACY 3.4 40.8 + - - +
303C PRO* 3.0 32.6 + - - +
304C THR* 3.9 18.0 + - - +
305C ALA 3.3 0.2 - - - -
306C MET* 1.3 76.4 - - + +
308C LYS* 1.3 62.3 + - - +
310C LEU 4.7 3.6 - - - -
311C PRO* 3.7 20.8 - - - +
487C ARG* 4.9 0.6 - - - +
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Residues in contact with LYS 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 THR* 3.2 19.1 + - + +
305C ALA* 3.9 5.2 - - - +
306C MET 3.3 0.2 - - - -
307C ARG* 1.3 81.1 - - - +
309C TYR* 1.3 99.5 + - + +
311C PRO* 3.8 7.6 - - - +
440C CYS 5.7 2.7 - - - -
504C ARG* 4.8 4.2 + - - -
3F BMA 5.1 0.2 - - - -
4F MAN 3.0 61.1 + - - +
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Residues in contact with TYR 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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301C LEU* 5.0 1.3 - - + -
305C ALA* 3.0 35.7 + - + +
308C LYS* 1.3 110.2 - - + +
310C LEU* 1.3 61.4 + - + +
311C PRO* 3.3 5.8 - - - -
440C CYS 4.9 4.0 + - - -
442C LEU* 5.9 2.8 - - - +
486C LYS* 5.9 1.6 - - - -
493C PRO 4.7 1.7 + - - -
496C ALA* 3.7 21.8 - - + -
497C CYS* 3.4 30.4 + - - +
500C GLY* 3.6 23.3 - - - -
501C THR* 3.8 22.2 - - - -
504C ARG* 3.2 34.2 - - - +
3F BMA 3.9 16.3 + - - -
4F MAN 5.1 2.7 - - - -
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Residues in contact with LEU 310 (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 TYR* 4.0 13.7 - - + -
297C LEU* 3.9 23.8 - - + -
301C LEU* 4.1 11.9 - - + -
306C MET* 2.8 58.0 + - + +
307C ARG* 4.7 1.2 - - - -
309C TYR* 1.3 80.8 - - + +
311C PRO* 1.4 66.5 - - - +
312C THR 3.8 0.3 + - - -
500C GLY 4.4 4.7 - - - +
503C PHE* 4.0 7.6 - - + -
504C ARG* 3.5 35.7 - - + +
507C ARG* 4.1 16.7 + - - +
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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