Contacts of the helix formed by residues 221 - 229 (chain C) in PDB entry 3SAJ
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 ASP 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192C ASN* 3.0 35.3 + - - +
219C ASP 5.2 0.5 - - - +
220C ILE* 1.3 74.6 - - - +
222C LEU* 1.3 63.5 + - - +
223C ASN* 3.1 18.6 + - - +
224C LYS* 3.5 11.6 + - + +
225C PHE* 2.9 27.6 - - + -
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Residues in contact with LEU 222 (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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217C PHE* 4.0 20.0 - - + +
218C MET* 4.2 33.4 - - + +
220C ILE* 3.0 33.8 + - + +
221C ASP* 1.3 72.7 - - - +
223C ASN* 1.3 53.6 + - - +
225C PHE* 3.4 3.2 + - - -
226C LYS* 2.7 41.2 + - + +
353C MET* 3.6 27.7 - - + +
358C ILE* 4.8 13.2 - - + -
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Residues in contact with ASN 223 (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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221C ASP* 3.3 24.9 - - - +
222C LEU* 1.3 79.1 - - - +
224C LYS* 1.3 73.4 + - - +
226C LYS* 4.5 5.2 - - - -
227C GLU* 2.5 54.7 + - + +
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Residues in contact with LYS 224 (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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192C ASN* 5.6 1.6 - - - -
196C GLY* 4.4 10.5 - - - -
199C VAL* 3.5 21.3 - - + +
221C ASP* 3.5 11.0 + - + +
222C LEU 3.4 0.6 - - - -
223C ASN* 1.3 89.4 + - - +
225C PHE* 1.3 99.5 + - - +
227C GLU* 3.6 11.4 - - - +
228C SER* 2.3 44.0 + - - +
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Residues in contact with PHE 225 (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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192C ASN* 4.3 11.7 - - - -
195C LEU* 3.3 37.0 - - + -
196C GLY 4.2 0.9 - - - -
199C VAL* 3.7 20.0 - - + -
220C ILE* 4.1 21.1 - - + -
221C ASP* 2.9 29.4 - - + -
222C LEU* 3.4 1.3 + - - +
223C ASN 3.3 0.2 - - - -
224C LYS* 1.3 111.0 - - - +
226C LYS* 1.3 64.3 + - - +
227C GLU 3.2 0.2 - - - -
228C SER* 3.2 5.3 + - - -
229C GLY* 3.1 4.0 + - - -
230C ALA* 3.1 41.8 + - + +
232C VAL* 4.5 10.8 - - + -
353C MET* 3.6 19.3 - - - +
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Residues in contact with LYS 226 (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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222C LEU* 2.7 27.3 + - + +
223C ASN* 4.2 4.3 - - - +
225C PHE* 1.3 71.8 - - - +
227C GLU* 1.3 62.3 + - + +
229C GLY* 3.4 6.1 + - - -
353C MET* 3.5 16.2 - - + -
355C HIS 3.0 25.3 - - - +
356C ASP* 2.3 79.0 + - - +
357C GLY 4.0 0.2 - - - +
358C ILE* 4.1 23.9 - - + +
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Residues in contact with GLU 227 (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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223C ASN* 2.5 47.1 + - + +
224C LYS* 3.6 10.8 - - - +
226C LYS* 1.3 79.9 - - + +
228C SER* 1.3 63.0 - - - +
229C GLY* 3.2 1.0 + - - -
356C ASP* 4.3 8.3 - - - +
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Residues in contact with SER 228 (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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199C VAL* 6.5 0.9 - - - -
224C LYS* 2.3 36.1 + - - +
225C PHE* 3.2 10.9 + - - -
227C GLU* 1.3 76.4 - - - +
229C GLY* 1.3 60.0 + - - +
230C ALA* 3.6 9.1 + - - -
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Residues in contact with GLY 229 (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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225C PHE 3.1 4.7 + - - -
226C LYS 3.4 7.0 + - - -
227C GLU 3.1 5.2 + - - -
228C SER* 1.3 78.9 - - - +
230C ALA* 1.3 67.4 + - - +
231C ASN* 3.6 11.1 + - - +
355C HIS* 4.4 19.9 + - - -
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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