Contacts of the strand formed by residues 183 - 189 (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 THR 183 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C PRO 4.5 6.5 - - - +
182C ARG* 1.3 78.6 - - - +
184C GLY* 1.3 59.4 + - - +
202C ARG 5.2 4.9 - - - +
203C HIS 5.0 1.4 - - - +
254C ILE* 3.7 10.7 - - - +
255C PHE* 2.9 27.6 + - - -
256C THR* 3.6 14.8 + - - -
608C LYS* 3.3 39.0 + - - +
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Residues in contact with GLY 184 (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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183C THR* 1.3 77.4 + - - +
185C MET* 1.3 64.3 + - - -
197C MET* 4.8 3.6 - - - -
201C ASN* 6.2 2.0 - - - -
202C ARG 6.1 0.4 - - - -
254C ILE* 3.2 7.3 - - - +
255C PHE* 2.7 56.9 + - - -
608C LYS* 6.0 0.4 - - - -
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Residues in contact with MET 185 (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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184C GLY* 1.3 75.5 - - - -
186C VAL* 1.3 62.0 + - - +
197C MET* 3.7 12.1 - - - +
198C LEU* 3.3 44.7 + - + +
201C ASN* 4.2 16.7 + - - +
253C GLY 3.4 5.8 - - - +
254C ILE* 4.4 16.8 - - + -
607C ASN* 4.0 31.2 - - - +
608C LYS* 6.1 2.2 - - + -
710C GLY* 3.9 8.1 - - - +
711C ALA* 3.8 32.1 - - + -
713C ARG* 6.2 1.3 - - - +
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Residues in contact with VAL 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C MET* 1.3 76.1 - - - +
187C SER* 1.3 61.1 + - - +
188C ASP 3.6 15.0 - - - +
189C ILE* 3.7 25.1 - - + -
195C VAL* 3.9 19.1 - - + -
196C THR 3.8 2.9 - - - +
197C MET* 4.4 5.4 - - + -
198C LEU* 4.4 8.7 - - - +
213C PHE* 4.4 17.5 - - + -
249C TYR* 3.6 6.5 + - + +
252C GLY* 3.6 24.8 + - - +
253C GLY* 2.7 28.8 + - - +
255C PHE* 4.5 8.3 - - + +
710C GLY* 5.7 1.7 - - - -
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Residues in contact with SER 187 (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* 1.3 74.6 - - - +
188C ASP* 1.3 61.1 + - - +
196C THR* 2.7 23.8 + - - +
197C MET 3.4 20.4 - - - -
198C LEU* 3.8 15.5 - - - +
199C ASP 4.9 2.1 + - - -
249C TYR* 3.5 15.4 + - - -
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Residues in contact with ASP 188 (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* 3.6 2.4 - - - +
187C SER* 1.3 84.6 - - - +
189C ILE* 1.3 82.3 + - - +
190C GLU* 4.3 15.6 - - + +
194C THR 3.7 0.9 - - - +
195C VAL* 3.3 2.8 - - - -
196C THR* 2.7 46.5 + - - +
249C TYR* 3.6 20.2 - - - +
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Residues in contact with ILE 189 (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* 3.7 14.6 - - + -
188C ASP* 1.3 84.8 + - - +
190C GLU* 1.3 72.0 + - - +
191C PRO* 4.0 1.0 - - - +
193C GLY* 4.5 7.6 - - - -
194C THR 3.6 2.9 - - - +
195C VAL* 4.1 20.0 - - + -
213C PHE* 4.0 16.2 - - + -
216C VAL* 3.8 25.6 - - + -
219C LEU* 3.9 12.6 - - + +
222C LEU* 3.7 26.0 - - + -
240C ILE* 4.7 2.7 - - + -
243C VAL* 4.5 11.3 - - + +
249C TYR* 3.2 34.1 + - + +
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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