Contacts of the helix formed by residues 265 - 270 (chain C) in PDB entry 6C3P
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 265 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238C ILE* 3.4 13.3 - - - +
239C PRO* 6.1 1.8 - - - -
259C HIS* 3.1 34.9 + - - -
261C ILE* 4.2 4.0 - - - -
262C ASP* 2.7 28.3 + - - +
263C ALA 4.2 1.4 - - - +
264C ASN* 1.3 74.7 - - - +
266C PRO* 1.3 69.9 - - - +
267C LEU* 3.3 13.4 + - - +
268C TYR* 3.0 20.4 + - - +
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Residues in contact with PRO 266 (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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219C VAL* 4.2 14.1 - - + -
221C ARG* 4.2 18.3 + - - +
236C VAL* 3.7 38.8 - - + -
238C ILE* 4.9 6.3 - - + -
264C ASN 3.7 5.4 - - - +
265C SER* 1.3 90.2 - - - +
267C LEU* 1.3 61.2 + - + +
268C TYR* 3.0 5.3 + - - +
269C ASP* 3.7 14.0 + - - +
270C LEU 4.8 0.5 + - - -
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C PHE* 4.6 18.8 - - + -
219C VAL* 3.9 31.4 - - + -
221C ARG* 4.8 6.7 - - - +
238C ILE* 3.6 27.6 - - + -
261C ILE* 3.3 24.7 - - + +
265C SER* 3.1 8.6 - - - +
266C PRO* 1.3 75.8 - - + +
268C TYR* 1.3 58.7 + - - +
269C ASP 3.1 2.9 - - - -
270C LEU* 3.1 49.1 + - + +
281C LEU* 5.6 1.3 - - + -
283C ILE* 3.7 23.6 - - + -
309C ILE* 6.0 0.2 - - + -
346C ALA* 5.0 1.2 - - - +
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Residues in contact with TYR 268 (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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195C ARG* 5.0 1.8 - - - -
261C ILE* 3.6 12.0 - - - +
262C ASP* 3.1 22.0 - - - +
263C ALA* 3.4 33.5 - - + +
265C SER 3.0 16.5 + - - +
266C PRO 3.0 2.2 - - - -
267C LEU* 1.3 77.6 - - - +
269C ASP* 1.3 60.0 + - - +
270C LEU 3.4 0.7 - - - -
346C ALA* 3.2 33.2 + - + +
347C ARG* 3.2 60.7 + - + +
350C ASP* 2.2 47.2 + - - +
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Residues in contact with ASP 269 (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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266C PRO 3.7 8.7 + - - +
267C LEU 3.1 0.8 - - - -
268C TYR* 1.3 75.3 - - - +
270C LEU* 1.3 64.5 + - - +
271C ALA* 3.7 0.9 + - - +
274C ASP* 4.7 5.7 - - - +
345C THR* 3.3 16.6 - - - +
347C ARG* 2.6 46.0 + - - -
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Residues in contact with LEU 270 (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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189C ILE* 5.7 2.2 - - + -
221C ARG* 5.7 2.9 - - - +
261C ILE* 6.0 4.3 - - + -
266C PRO 4.8 0.2 + - - -
267C LEU* 3.1 45.2 + - + +
269C ASP* 1.3 79.1 - - - +
271C ALA* 1.3 83.5 + - - +
274C ASP* 4.8 10.1 - - + +
275C LEU* 4.8 11.7 - - + +
281C LEU* 3.8 29.4 - - + -
309C ILE* 5.7 7.6 - - + -
311C TRP* 3.5 31.4 - - + -
344C CYS 4.5 0.2 - - - +
345C THR* 3.1 21.0 - - - -
346C ALA* 3.8 4.5 + - - +
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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