Contacts of the strand formed by residues 224 - 228 (chain C) in PDB entry 1C2O
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 ARG 224 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C MET 5.6 0.4 + - - -
196C SER* 3.5 29.7 - - - +
197C VAL 3.2 4.2 + - - -
198C THR* 2.9 22.5 + - - +
199C LEU 3.1 19.8 + - - -
222C PHE* 3.5 11.6 - - - -
223C HIS* 1.3 93.1 - - - +
225C ALA* 1.3 60.5 + - - +
324C LEU* 5.0 0.7 - - - -
325C GLN* 3.1 45.6 + - + +
483C PHE* 3.1 25.2 + - + -
484C ALA 2.6 30.5 + - - -
485C ARG 3.5 15.1 + - - -
486C THR 4.8 2.3 + - - -
487C GLY* 3.4 7.5 - - - +
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Residues in contact with ALA 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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199C LEU 3.4 7.0 - - - +
209C VAL* 3.7 22.4 - - + -
213C ILE* 3.9 20.6 - - + -
222C PHE* 4.4 8.7 - - + -
224C ARG* 1.3 77.6 - - - +
226C VAL* 1.3 63.3 + - - +
227C LEU* 4.3 3.6 - - + -
324C LEU* 4.5 2.2 - - + -
325C GLN 3.4 9.6 + - - +
326C VAL* 3.2 5.7 - - + +
327C LEU 2.9 22.7 + - - +
483C PHE* 3.4 3.2 - - - -
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Residues in contact with VAL 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C THR* 4.3 7.0 - - + -
199C LEU 2.9 7.0 + - - +
200C PHE* 3.5 22.7 - - + -
201C GLY 3.7 5.6 + - - -
209C VAL* 3.6 19.6 - - - +
225C ALA* 1.3 77.1 - - - +
227C LEU* 1.3 71.1 + - - +
228C GLN* 3.9 17.5 - - + +
327C LEU* 3.3 19.7 - - + +
480C TRP* 3.2 39.3 - - + +
483C PHE* 4.0 21.5 - - + -
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Residues in contact with LEU 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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201C GLY 3.8 4.5 - - - -
206C ALA* 3.8 22.4 - - + +
209C VAL* 4.1 11.0 - - + -
210C GLY* 4.0 17.0 - - - -
213C ILE* 4.6 7.0 - - + -
225C ALA* 4.3 3.6 - - + -
226C VAL* 1.3 86.0 - - - +
228C GLN* 1.3 61.2 + - - +
229C SER 3.9 0.7 + - - -
230C GLY 3.8 17.8 + - - +
231C THR* 5.8 0.2 - - + -
232C PRO* 4.3 3.4 - - + -
326C VAL* 3.5 30.3 - - + -
327C LEU 3.0 8.4 + - - +
328C VAL* 3.6 10.9 - - + +
329C GLY 3.4 21.1 + - - +
411C VAL* 6.0 0.2 - - - +
414C LEU* 3.7 26.7 - - + -
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Residues in contact with GLN 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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117C TRP* 4.0 10.8 - - - -
200C PHE* 3.6 20.3 - - - -
201C GLY 2.9 17.0 + - - +
202C GLU* 3.1 26.3 - - + +
203C SER 3.1 0.7 + - - -
206C ALA* 3.4 0.7 - - - +
226C VAL* 3.9 12.6 - - + -
227C LEU* 1.3 73.3 - - - +
229C SER* 1.3 72.4 + - - +
230C GLY 3.0 2.8 + - - -
428C TYR* 3.4 18.7 + - - +
450C GLU* 2.7 41.8 + - - +
451C ILE* 5.0 3.2 - - - +
454C ILE* 4.0 10.5 - - - +
480C TRP* 3.5 24.1 + - + -
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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