Contacts of the helix formed by residues 246 - 250 (chain C) in PDB entry 2R2N
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 PHE 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C THR* 4.0 16.2 - - + -
198C PRO* 4.4 2.9 - - + -
208C LEU* 3.7 25.1 - - + -
213C LYS* 3.4 51.2 - - + +
216C ILE* 3.9 25.6 - - + -
217C TYR* 4.4 7.0 - + + -
227C ILE* 3.8 31.6 - - + -
229C GLU* 2.8 36.2 + - + +
245C THR* 1.3 70.2 - - - +
247C LEU* 1.3 62.8 + - - +
249C MET* 3.0 22.8 + - - +
250C ASP* 3.3 9.5 + - - +
255C VAL* 3.8 19.6 - - + +
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Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLN* 4.4 3.6 - - - +
95C HIS* 4.1 14.1 - - + +
97C PRO* 3.9 29.6 - - + +
98C PRO* 3.6 8.7 - - - +
99C THR* 5.2 4.9 - - + -
109C MET* 5.3 0.7 - - + -
229C GLU* 3.2 16.3 + - - +
245C THR* 3.2 6.1 - - - +
246C PHE* 1.3 76.0 - - - +
248C SER* 1.3 59.1 + - - +
250C ASP* 3.0 38.1 + - + +
255C VAL* 4.0 18.5 - - + +
257C ARG* 3.9 23.6 - - + -
275C THR* 3.9 32.3 - - + +
276C GLY* 5.4 1.6 - - - +
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Residues in contact with SER 248 (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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94C LEU 5.4 0.7 - - - -
95C HIS* 3.1 35.4 - - - +
96C ASN 4.5 1.6 - - - +
98C PRO* 3.8 14.0 - - - +
244C PRO* 3.8 12.4 - - - +
245C THR* 2.7 39.7 + - - -
247C LEU* 1.3 77.5 - - - +
249C MET* 1.3 58.6 + - - +
250C ASP 3.4 0.2 - - - -
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Residues in contact with MET 249 (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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98C PRO* 4.3 3.1 - - - -
210C SER* 4.6 3.6 - - - +
213C LYS* 3.7 45.3 - - + +
214C LYS* 3.9 24.5 - - + +
217C TYR* 3.6 30.6 - - + -
244C PRO* 4.4 17.5 - - + +
245C THR 3.4 15.0 + - - +
246C PHE* 3.0 15.1 + - - +
248C SER* 1.3 80.3 + - - +
250C ASP* 1.3 55.8 + - - +
251C VAL* 2.9 14.6 + - - +
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Residues in contact with ASP 250 (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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98C PRO* 3.7 14.3 - - + +
99C THR* 4.2 12.3 - - + +
217C TYR* 2.5 31.9 + - - -
246C PHE 3.7 7.9 - - - +
247C LEU* 3.0 26.2 + - + +
248C SER 3.4 1.0 - - - -
249C MET* 1.3 72.9 - - - +
251C VAL* 1.3 61.1 + - - +
252C ASP 3.3 0.2 + - - -
253C GLY* 3.0 19.0 + - - -
254C ARG 2.8 18.9 + - - -
255C VAL* 2.9 35.9 + - + +
277C PRO* 5.3 0.5 - - - +
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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