Contacts of the helix formed by residues 305 - 310 (chain C) in PDB entry 2J2M
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 305 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ARG* 5.2 4.9 - - - +
369A ASP* 5.0 1.6 + - - -
376A GLN* 3.2 29.3 + - + +
377A GLN 4.6 6.3 + - - -
378A THR* 4.4 22.2 + - + -
379A SER 5.5 0.4 + - - -
303C VAL* 3.3 2.6 - - - -
304C ASP* 1.3 81.6 + - - +
306C TYR* 1.3 64.7 + - - +
307C PHE* 3.4 5.9 + - - +
308C ALA* 2.9 32.3 + - + +
309C GLU* 2.8 34.4 + - - +
153D PRO* 3.8 29.0 + - - +
154D ARG* 4.9 0.2 - - - +
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Residues in contact with TYR 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA 5.0 1.9 + - - -
58C ARG* 5.8 0.9 - - - -
59C GLY* 2.8 31.8 + - - -
60C PHE* 4.6 9.4 - + - -
61C GLY 5.3 0.7 - - - -
93C ARG* 4.9 2.8 + - - -
243C SER* 6.4 0.9 - - - -
303C VAL* 3.9 12.3 - - + +
305C ASN* 1.3 71.0 - - - +
307C PHE* 1.3 65.2 + - + +
310C THR* 2.7 54.9 + - + +
311C GLU* 3.0 31.2 + - + -
153D PRO* 2.9 21.9 + - + +
154D ARG 4.2 13.2 - - - +
155D THR 5.1 0.7 - - - -
156D ASN* 3.7 46.9 + - + +
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Residues in contact with PHE 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASP* 3.5 33.0 - - - +
370A GLY 3.6 15.0 - - - -
371A ALA* 5.3 0.2 - - - -
373A PRO* 3.6 27.1 - - + -
376A GLN* 3.7 16.2 - - - -
48C GLU 3.9 20.6 - - - -
49C ARG* 5.4 1.6 - - - -
50C VAL* 3.9 33.2 - - + -
305C ASN* 3.4 7.4 + - - +
306C TYR* 1.3 81.3 - - + +
308C ALA* 1.3 56.5 + - - +
311C GLU* 3.3 22.2 - - + +
312C SER* 2.8 37.9 + - - -
153D PRO 4.5 0.6 + - - -
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Residues in contact with ALA 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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373A PRO* 4.3 12.6 - - + +
376A GLN* 4.0 24.0 - - + -
378A THR* 6.2 0.9 - - + -
305C ASN* 2.9 19.9 + - + +
307C PHE* 1.3 79.0 - - - +
309C GLU* 1.3 64.6 + - + +
312C SER* 3.5 20.0 - - - -
354C LEU* 5.5 1.2 - - - +
356C ILE* 3.7 14.9 + - - +
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Residues in contact with GLU 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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378A THR* 5.4 1.6 - - - +
63C HIS* 2.6 30.8 + - - -
91C PHE* 4.0 9.2 - - + -
303C VAL* 3.3 20.2 - - + -
304C ASP* 2.9 20.3 + - - +
305C ASN* 2.8 38.1 + - - +
308C ALA* 1.3 85.5 - - + +
310C THR* 1.3 61.0 + - - +
311C GLU 3.5 0.4 - - - -
313C VAL* 3.1 34.3 + - - +
356C ILE* 3.5 16.5 - - + +
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Residues in contact with THR 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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53C ARG* 2.9 23.2 + - - -
60C PHE* 3.8 3.4 - - - -
61C GLY* 3.3 39.3 + - - +
91C PHE* 3.6 6.9 - - - -
93C ARG* 3.4 24.5 + - - +
303C VAL* 3.5 14.9 - - - +
306C TYR* 2.7 45.8 + - + +
309C GLU* 1.3 73.1 - - - +
311C GLU* 1.3 55.0 + - - -
313C VAL* 3.6 1.9 - - - +
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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