Contacts of the helix formed by residues 304 - 312 (chain C) in PDB entry 2JC6
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 SER 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C GLU* 2.6 38.1 + - - -
303C LYS* 1.3 74.6 - - - +
305C LYS* 1.3 59.9 + - - +
306C TRP* 3.3 10.2 + - - -
307C ARG* 3.6 29.4 + - - +
308C GLN* 3.0 32.6 + - - +
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Residues in contact with LYS 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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148C GLU* 6.4 1.1 - - + +
303C LYS 4.3 0.2 - - - -
304C SER* 1.3 70.0 + - - +
306C TRP* 1.3 66.5 + - + +
308C GLN* 3.8 16.6 + - - +
309C ALA* 3.0 27.5 + - - +
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Residues in contact with TRP 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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105C GLU* 3.6 33.4 - - + +
148C GLU* 2.9 26.3 + - + +
149C ASN* 3.9 16.3 + - - -
151C LEU* 3.8 27.5 - - + +
164C SER* 3.5 31.0 - - - -
304C SER* 3.3 3.1 - - - -
305C LYS* 1.3 79.4 - - + +
307C ARG* 1.3 60.9 + - - +
309C ALA* 3.4 0.6 + - - -
310C PHE* 2.9 26.2 + - - +
1314C QPP 3.1 76.1 - + + -
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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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105C GLU* 4.5 3.0 + - - +
302C ALA 3.3 24.4 + - - -
303C LYS* 4.6 0.6 - - - +
304C SER* 3.5 34.2 + - - +
306C TRP* 1.3 79.8 - - - +
308C GLN* 1.3 59.3 + - - +
310C PHE* 3.3 10.2 + - + +
311C ASN* 2.9 50.3 + - - +
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Residues in contact with GLN 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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31C THR 4.9 0.3 - - - +
303C LYS* 4.7 16.3 - - + +
304C SER 3.0 27.0 + - - +
305C LYS* 3.8 13.0 + - - +
306C TRP 3.3 0.2 - - - -
307C ARG* 1.3 79.6 - - - +
309C ALA* 1.3 61.4 + - - +
311C ASN* 3.3 9.2 + - - +
312C ALA* 3.2 18.4 + - - -
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Residues in contact with ALA 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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30C GLY* 3.4 1.2 - - - -
31C THR 2.9 44.5 + - - +
32C GLY* 5.4 1.6 - - - -
305C LYS 3.0 18.8 + - - +
306C TRP 3.7 0.2 - - - +
308C GLN* 1.3 73.1 - - - +
310C PHE* 1.3 66.9 + - - +
311C ASN 3.4 0.2 + - - -
312C ALA* 3.5 8.7 + - - +
1314C QPP 3.5 25.8 - - + -
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Residues in contact with PHE 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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28C THR 4.9 8.3 - - - -
29C LEU* 3.6 26.0 - - - +
30C GLY* 4.0 2.0 - - - -
306C TRP 2.9 17.4 + - - +
307C ARG* 3.5 11.0 - - + +
309C ALA* 1.3 76.1 - - - +
311C ASN* 1.3 76.3 + - - +
312C ALA* 3.2 10.4 - - - +
1314C QPP 4.6 2.2 - - + -
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Residues in contact with ASN 311 (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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307C ARG* 2.9 41.0 + - - +
308C GLN* 3.3 8.7 + - - +
310C PHE* 1.3 89.8 - - - +
312C ALA* 1.3 68.7 + - - +
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Residues in contact with ALA 312 (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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28C THR* 6.2 0.9 - - + -
30C GLY* 5.8 0.4 - - - -
31C THR* 4.0 21.1 - - - +
308C GLN 3.2 11.7 + - - -
309C ALA 3.6 11.7 - - - +
310C PHE 3.2 13.0 - - - +
311C ASN* 1.3 81.9 - - - +
313C THR* 1.3 71.4 + - - +
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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