Contacts of the helix formed by residues 270 - 274 (chain C) in PDB entry 6O81
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 PRO 270 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C THR* 3.6 24.0 - - + +
151C ILE* 4.5 6.7 - - + -
173C THR* 4.7 11.7 - - - +
239C ILE* 4.6 5.2 - - - +
268C CYS 4.5 2.5 - - - +
269C ALA* 1.3 92.4 - - + +
271C MET* 1.3 67.1 + - - +
272C PHE* 3.4 41.7 + - + -
273C LYS* 3.7 33.7 + - + +
274C LEU* 4.6 2.4 + - - +
326C SER* 4.8 4.0 - - - -
327C ASN* 5.3 0.2 - - - +
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Residues in contact with MET 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C MET* 4.7 3.3 - - - +
84C ARG* 5.5 6.5 + - - +
147C THR* 4.9 1.0 + - - -
270C PRO* 1.3 75.1 - - - +
272C PHE* 1.3 62.3 + - + +
273C LYS 3.2 3.0 + - - -
274C LEU* 3.6 28.8 + - - +
326C SER* 3.4 28.0 - - - +
327C ASN* 3.5 23.5 + - - +
328C ILE* 3.8 25.8 - - + -
339C LEU* 3.9 25.4 - - + -
343C LEU* 3.8 32.6 - - + +
344C TYR* 3.9 7.4 + - - -
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Residues in contact with PHE 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C SER* 3.6 31.4 - - - -
32C GLU* 4.0 20.6 - - + -
35C ALA* 4.2 6.1 - - + -
77C THR* 3.7 22.0 - - + +
80C ASN* 3.0 23.1 + - - +
81C MET* 3.7 33.4 - - + -
144C LEU* 4.1 31.9 - - + -
147C THR* 4.2 12.8 - - + -
270C PRO* 3.6 32.1 - - + -
271C MET* 1.3 76.8 - - - +
273C LYS* 1.3 62.7 + - + +
274C LEU 3.3 4.5 - - - -
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Residues in contact with LYS 273 (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 SER* 4.0 26.5 + - - -
77C THR* 5.0 5.6 - - - +
80C ASN* 4.6 3.4 - - - +
171C SER* 5.0 13.3 - - - -
173C THR* 5.1 5.7 + - - -
236C THR 2.9 31.1 + - - +
237C LYS* 3.6 24.0 - - - +
238C THR* 3.3 6.7 - - - +
239C ILE* 2.7 37.5 + - + +
268C CYS 5.7 1.4 + - - -
269C ALA* 4.7 8.5 - - + +
270C PRO* 3.7 41.0 + - + +
271C MET 3.2 1.4 - - - -
272C PHE* 1.3 84.6 - - + +
274C LEU* 1.3 54.0 + - - +
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Residues in contact with LEU 274 (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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80C ASN* 3.3 8.7 - - - +
239C ILE* 3.6 25.1 - - + +
240C LEU 3.9 1.1 - - - +
270C PRO 5.1 1.6 - - - +
271C MET* 3.6 20.6 - - - +
272C PHE 3.3 1.8 - - - -
273C LYS* 1.3 78.8 - - - +
275C SER* 1.3 66.1 + - - +
336C ILE* 3.7 23.3 - - + -
339C LEU* 3.7 37.7 - - + -
340C MET* 3.8 19.7 - - + -
343C LEU* 4.0 16.2 - - + -
344C TYR* 2.5 33.3 + - + +
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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