Contacts of the helix formed by residues 221 - 225 (chain W) in PDB entry 5O9G
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 221 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216W LYS* 4.4 3.6 - - - +
217W TRP 4.9 0.9 + - - +
220W GLU* 1.3 89.1 - - - +
222W HIS* 1.3 74.2 + - - +
223W LEU* 3.1 18.3 + - - +
224W HIS* 3.6 15.7 + - - +
225W ASN* 4.5 2.4 - - - +
311W TRP* 3.1 26.4 - - - +
318W GLU 5.9 0.2 - - - -
320W THR* 3.4 19.3 + - - +
322W GLU* 3.3 24.7 - - - -
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Residues in contact with HIS 222 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181W ILE* 4.2 12.8 - - + +
183W ILE* 4.5 7.9 - - + -
216W LYS* 3.6 37.1 + - + -
220W GLU 5.2 0.2 - - - -
221W SER* 1.3 78.8 + - - +
223W LEU* 1.3 56.9 + - - -
224W HIS 3.3 1.8 - - - -
225W ASN* 2.7 36.1 + - - +
281W PHE 5.5 0.4 - - - -
284W PHE* 3.4 60.9 + + + +
285W HIS* 3.2 18.4 - - + +
311W TRP* 5.3 5.8 - + - -
314W LEU* 4.5 17.5 - - + +
318W GLU* 5.4 7.2 - - + -
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Residues in contact with LEU 223 (chain W).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221W SER* 3.1 18.2 - - - +
222W HIS* 1.3 77.9 - - - +
224W HIS* 1.3 70.7 + - + +
225W ASN 3.4 4.8 + - - +
284W PHE 4.4 0.9 - - - +
285W HIS* 3.4 48.0 - - + +
311W TRP* 3.7 20.6 - - + -
322W GLU* 5.9 2.0 - - - +
330W LEU* 5.4 9.4 - - + -
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Residues in contact with HIS 224 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177W HIS* 6.5 0.2 - - + -
217W TRP* 3.6 19.8 - - + -
220W GLU* 3.2 45.3 + - + +
221W SER* 3.6 7.3 + - - +
222W HIS 3.3 1.2 - - - -
223W LEU* 1.3 92.1 + - + +
225W ASN* 1.3 65.0 + - - +
226W THR* 3.5 11.3 + - - +
322W GLU* 4.1 24.9 - - - -
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Residues in contact with ASN 225 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183W ILE* 3.5 31.6 - - - +
214W LEU* 3.6 28.1 - - + +
215W ILE 3.7 6.5 - - - +
216W LYS* 3.3 29.8 - - - +
217W TRP 4.7 0.2 + - - -
221W SER 4.5 0.5 - - - +
222W HIS* 2.7 26.7 + - - +
223W LEU 3.4 4.1 + - - +
224W HIS* 1.3 78.0 - - - +
226W THR* 1.3 61.5 + - - +
227W TRP* 5.1 1.6 + - - -
285W HIS* 3.8 14.5 - - - -
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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