Contacts of the strand formed by residues 222 - 225 (chain C) in PDB entry 3CB4
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 LYS 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C GLY 3.6 0.6 + - - -
221C ASP* 1.3 72.3 - - - +
223C VAL* 1.3 62.7 + - - +
231C THR* 5.2 8.3 - - - +
232C TYR 3.2 13.0 - - - +
233C ASN* 3.5 27.5 + - - +
276C LEU* 4.0 3.8 - - - +
277C ALA* 3.1 42.5 + - + -
278C ARG* 4.5 10.7 + - - +
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Residues in contact with VAL 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C LEU* 4.7 4.5 - - + -
217C LEU* 3.6 31.6 - - + -
221C ASP* 3.8 1.1 + - + +
222C LYS* 1.3 78.6 - - - +
224C LYS* 1.3 63.0 + - - +
225C VAL* 5.6 0.2 - - + -
231C THR* 3.3 25.8 - - - +
232C TYR* 2.7 32.1 + - + +
234C ALA* 4.2 12.3 - - + +
258C LEU* 4.7 10.1 - - + -
260C CYS* 4.1 21.8 - - - -
274C LEU* 4.7 16.2 - - + -
275C THR 3.4 11.9 - - - +
276C LEU* 4.5 1.1 - - + +
277C ALA* 4.4 0.6 - - - +
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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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223C VAL* 1.3 77.6 - - - +
225C VAL* 1.3 69.2 + - - +
226C MET* 3.6 6.3 + - + +
229C GLY* 3.9 25.3 + - - +
230C GLN 3.6 7.9 - - - +
231C THR* 3.8 18.0 - - + +
274C LEU* 3.5 4.5 - - - -
275C THR* 2.7 52.7 + - + +
276C LEU 4.4 9.6 - - - +
277C ALA* 4.5 4.5 - - - +
280C PRO* 5.2 8.8 - - + +
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Residues in contact with VAL 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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195C ILE* 5.1 0.2 - - + -
223C VAL* 5.6 1.1 - - + -
224C LYS* 1.3 70.5 - - - +
226C MET* 1.3 54.3 + - - +
227C SER 4.3 0.2 - - - +
228C THR* 3.5 16.6 - - + +
229C GLY* 2.7 36.4 + - - -
230C GLN 3.0 5.3 + - - -
232C TYR* 4.0 24.2 - - + -
262C ILE* 4.4 8.1 - - + -
267C GLY 3.3 27.1 - - - +
268C ALA* 4.7 3.1 - - - -
269C PRO* 4.1 3.8 - - + -
272C ASP* 3.3 26.9 - - + +
274C LEU* 3.3 25.4 - - + -
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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