Contacts of the strand formed by residues 210 - 214 (chain C) in PDB entry 3CMM
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 PHE 210 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A PHE* 3.7 27.8 - + - -
226A THR* 6.0 0.7 - - + -
227A LEU* 3.6 36.6 - - + -
229A LYS 5.5 1.1 - - - -
208C GLY 3.6 14.1 - - - -
209C ASN* 1.3 73.7 - - - +
211C VAL* 1.3 63.1 + - - +
227C LEU* 4.3 13.0 - - + -
228C PHE 3.5 3.6 - - - -
229C LYS* 3.6 41.3 - - + -
257C GLU* 3.2 11.1 + - - +
258C VAL* 2.9 39.3 + - - +
260C VAL* 3.7 40.8 - - + -
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Residues in contact with VAL 211 (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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205C LEU* 4.8 8.3 - - + -
210C PHE* 1.3 75.4 - - - +
212C ARG* 1.3 59.0 + - - +
213C PHE* 3.7 31.4 - - + -
227C LEU* 3.4 7.2 - - - -
228C PHE* 2.8 43.0 + - + +
230C VAL* 4.1 15.0 - - + -
238C PHE* 4.3 4.5 - - + -
240C ILE* 4.5 0.2 - - + -
255C PHE* 3.1 39.3 - - + -
256C THR 3.3 15.7 - - - +
257C GLU* 3.7 6.3 - - + +
258C VAL 4.5 0.4 - - - +
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Residues in contact with ARG 212 (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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263A LYS* 3.4 56.5 + - - +
211C VAL* 1.3 75.6 - - - +
213C PHE* 1.3 68.5 + - - +
214C SER* 4.6 15.4 + - - -
225C GLY* 4.3 16.2 - - - +
226C THR 3.6 16.4 - - - +
227C LEU* 3.9 10.0 - - + +
255C PHE* 3.5 5.7 - - - +
256C THR* 2.7 74.1 + - - +
258C VAL* 3.8 16.6 - - + +
848C GLU* 4.7 5.9 + - - -
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Residues in contact with PHE 213 (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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186C VAL* 4.4 8.7 - - + -
189C ILE* 4.0 13.9 - - + -
195C VAL* 4.2 15.0 - - + -
211C VAL* 3.7 25.1 - - + -
212C ARG* 1.3 82.6 + - - +
214C SER* 1.3 63.0 + - - +
216C VAL* 4.0 17.0 - - + -
222C LEU* 3.4 26.9 + - + +
223C ASN* 3.3 32.8 - - - +
225C GLY* 4.9 1.4 + - - +
226C THR 4.6 0.4 + - - -
228C PHE* 3.8 19.3 - + - -
238C PHE* 4.3 3.8 - + - -
240C ILE* 3.6 31.2 - - + -
254C ILE 3.4 12.8 - - - -
255C PHE* 3.8 18.2 - - + -
256C THR* 5.0 0.4 - - - +
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Residues in contact with SER 214 (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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263A LYS* 5.7 1.7 + - - -
212C ARG* 4.6 15.6 + - - -
213C PHE* 1.3 75.5 + - - +
215C GLU* 1.3 66.7 + - - +
216C VAL* 3.1 6.8 + - - +
223C ASN* 3.2 10.7 + - - +
253C GLY* 3.3 1.0 - - - -
254C ILE* 2.8 45.9 + - - +
256C THR* 5.8 1.8 - - - -
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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