Contacts of the helix formed by residues 299 - 306 (chain C) in PDB entry 2PT9
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 299 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B LEU 4.0 3.4 + - - -
312B ALA* 4.1 12.7 - - + +
315B LEU* 3.4 30.3 - - - +
297C TYR 3.5 1.6 + - - -
298C TYR* 1.3 85.7 - - - +
300C TYR* 1.3 68.5 + - - +
301C GLU* 3.2 7.8 + - - +
302C ASN* 2.7 48.5 + - - +
303C HIS* 3.1 21.8 + - - +
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Residues in contact with TYR 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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283C PRO* 3.8 47.8 + - + +
285C LYS 4.4 2.7 - - - -
286C LYS* 3.7 53.8 - - + +
298C TYR* 4.3 6.9 - - - -
299C ASN* 1.3 74.3 - - - +
301C GLU* 1.3 81.6 + - + +
303C HIS* 3.2 20.0 - - - +
304C SER* 4.1 5.2 + - - -
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Residues in contact with GLU 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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309B LYS* 3.0 42.7 + - + +
299C ASN* 3.2 8.1 + - - +
300C TYR* 1.3 94.5 - - + +
302C ASN* 1.3 64.4 + - - +
303C HIS 3.2 1.7 + - - -
304C SER* 3.7 5.4 + - - -
305C ALA* 3.3 21.5 + - - +
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Residues in contact with ASN 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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309B LYS* 3.4 16.9 - - - +
310B LEU 3.0 23.1 + - - +
311B PRO* 3.7 6.1 - - - +
104C MET* 4.2 10.4 - - + +
297C TYR* 2.6 44.5 + - + -
299C ASN* 2.7 33.0 + - - +
301C GLU* 1.3 73.8 - - - +
303C HIS* 1.3 66.9 + - - +
305C ALA* 3.6 7.8 - - - +
306C ALA* 3.0 25.8 + - - +
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Residues in contact with HIS 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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104C MET* 4.6 5.2 - - - +
108C VAL* 3.3 27.0 - - + +
111C THR* 3.2 19.0 + - - -
112C VAL* 3.7 9.6 - - + +
280C LEU 2.7 29.1 + - - -
281C THR 3.9 10.2 - - - -
283C PRO* 3.3 14.9 - - + +
298C TYR* 2.7 37.2 + + + +
299C ASN 3.1 4.2 + - - +
300C TYR 3.2 15.0 - - - +
301C GLU 3.2 0.4 - - - -
302C ASN* 1.3 82.4 - - - +
304C SER* 1.3 62.0 + - - +
306C ALA* 3.5 7.1 - - - +
307C PHE* 3.3 20.4 - + - -
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Residues in contact with SER 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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281C THR* 2.9 26.7 + - - +
282C LYS* 4.6 3.7 - - - +
283C PRO* 4.3 9.7 - - - +
300C TYR 4.1 3.7 + - - -
301C GLU* 3.7 6.5 + - - -
302C ASN 3.3 0.2 - - - -
303C HIS* 1.3 72.3 - - - +
305C ALA* 1.3 66.0 + - - +
306C ALA 3.1 2.0 - - - -
307C PHE* 3.0 22.4 + - - +
308C LYS* 3.8 20.8 + - - +
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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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306B ALA* 3.9 22.1 - - + +
309B LYS* 3.6 31.0 - - + +
301C GLU 3.3 16.5 + - - +
302C ASN* 3.2 6.7 + - - +
304C SER* 1.3 77.9 - - - +
306C ALA* 1.3 56.6 + - - +
308C LYS* 2.9 31.6 + - - +
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Residues in contact with ALA 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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104C MET* 3.6 22.2 - - + -
256C ALA* 3.4 12.3 - - + -
257C ASN* 3.1 40.8 + - - +
258C ILE* 6.0 0.2 - - + -
302C ASN 3.0 11.2 + - - +
303C HIS 3.5 13.7 - - - +
305C ALA* 1.3 77.3 - - - +
307C PHE* 1.3 58.1 + - + +
308C LYS 3.2 2.8 + - - +
309C LEU* 3.9 5.4 - - - +
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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