Contacts of the helix formed by residues 322 - 327 (chain C) in PDB entry 2ONL
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 HIS 322 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298C VAL* 4.7 25.9 + - + +
302C ILE* 4.3 18.3 - - + +
314C MET* 5.2 8.9 - - + +
318C GLU* 4.0 11.4 - - + +
319C PHE* 3.3 8.5 - - - +
320C MET 3.1 2.6 - - - -
321C ASN* 1.3 79.7 - - - +
323C PRO* 1.3 76.1 - - + +
324C TRP* 3.3 25.9 + - + +
325C ILE* 2.9 22.9 + - + +
326C MET* 2.2 42.2 + - - +
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Residues in contact with PRO 323 (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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321C ASN 4.2 4.3 - - - +
322C HIS* 1.3 102.6 - - + +
324C TRP* 1.3 58.7 + - - +
326C MET* 4.0 10.0 - - + -
327C GLN* 2.6 56.3 + - + +
330C LYS* 4.7 8.4 + - - +
331C VAL* 4.8 0.8 - - - +
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Residues in contact with TRP 324 (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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160C GLU* 2.9 42.0 + - + -
163C ALA* 4.7 5.2 - - + -
164C SER* 2.9 65.8 + - - -
167C MET* 5.2 4.7 - - + -
253C MET* 4.4 12.8 - - + -
296C GLU* 3.8 16.7 + - - -
298C VAL* 4.2 15.9 - - + -
299C LYS* 2.9 45.5 - - + +
302C ILE* 5.1 3.6 - - + -
322C HIS* 3.2 21.5 + - + +
323C PRO* 1.3 79.0 - - - +
325C ILE* 1.3 73.3 + - + +
328C SER* 3.4 10.2 - - - -
331C VAL* 3.7 22.1 - - + +
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Residues in contact with ILE 325 (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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164C SER* 4.4 2.7 - - - +
167C MET* 5.2 2.9 - - + -
168C LYS* 3.5 20.0 - - + +
302C ILE* 3.9 16.6 - - + -
319C PHE* 3.5 33.9 - - + +
320C MET* 3.3 39.0 - - + -
322C HIS* 2.9 30.5 + - + +
324C TRP* 1.3 99.3 - - + +
326C MET* 1.3 62.4 + - - +
328C SER* 2.6 26.5 + - - -
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Residues in contact with MET 326 (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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168C LYS* 3.8 12.3 + - - +
320C MET 2.7 20.1 + - - +
321C ASN* 3.4 42.0 - - - +
322C HIS 2.2 33.5 + - - +
323C PRO* 4.0 9.2 - - + -
325C ILE* 1.3 72.1 - - - +
327C GLN* 1.3 63.8 + - + +
328C SER 3.3 2.3 + - - +
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Residues in contact with GLN 327 (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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323C PRO* 2.6 33.5 + - + +
326C MET* 1.3 82.1 - - + +
328C SER* 1.3 67.7 + - - +
330C LYS* 3.3 49.9 + - + +
331C VAL* 4.2 2.4 + - - +
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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