Contacts of the strand formed by residues 209 - 214 (chain C) in PDB entry 2CMH
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 GLY 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170C VAL* 3.9 0.3 - - - -
171C ALA* 2.7 28.1 + - - +
172C LYS 3.2 17.4 + - - -
174C PRO* 4.3 6.1 - - - -
181C MET* 5.5 0.2 - - - -
198C PHE 3.8 9.2 - - - -
199C VAL* 5.0 0.4 - - - -
208C LYS* 1.3 77.4 - - - +
210C TYR* 1.3 79.0 + - - -
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Residues in contact with TYR 210 (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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58C GLU* 2.7 45.9 + - + +
61C LEU* 4.5 3.1 - - + -
62C LEU* 3.9 16.6 - - + -
168C ILE* 5.0 0.9 - - + -
169C SER 3.3 10.8 - - - +
170C VAL* 4.0 15.3 - - + -
171C ALA* 4.4 4.3 - - - +
181C MET* 4.6 2.2 - - - +
197C PRO* 3.2 6.6 - - - +
198C PHE* 2.8 72.9 + + + -
199C VAL* 4.1 2.0 - - - -
200C ALA* 4.1 24.1 - - + +
203C ARG* 3.7 13.5 + - - -
208C LYS* 3.5 23.8 - - + +
209C GLY* 1.3 82.7 - - - -
211C ILE* 1.3 66.6 + - - +
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Residues in contact with ILE 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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167C PHE 3.7 1.2 - - - +
168C ILE* 3.4 7.8 - - - +
169C SER* 3.0 37.8 + - - +
170C VAL 5.8 0.4 - - - +
171C ALA* 4.6 6.1 - - + -
181C MET* 3.3 36.3 - - + -
184C ALA* 3.5 33.4 - - + +
185C LEU* 3.7 11.9 - - + -
188C MET* 4.0 27.6 - - + -
195C ALA* 4.5 0.7 - - - -
196C MET 3.4 16.6 - - - +
197C PRO* 4.7 0.2 - - + -
198C PHE* 4.0 3.1 - - - -
210C TYR* 1.3 76.5 - - - +
212C TYR* 1.3 70.7 + - - +
213C ALA 4.2 0.2 - - - +
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Residues in contact with TYR 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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65C MET* 3.5 33.9 - - + -
69C THR* 2.7 33.9 + - - -
166C VAL* 3.5 34.7 - - + +
167C PHE 3.9 1.8 - - - -
168C ILE* 3.9 13.7 - - + -
194C VAL* 3.4 6.3 - - + +
196C MET* 2.8 34.9 + - - +
198C PHE* 3.9 12.5 - - + -
211C ILE* 1.3 74.3 - - - +
213C ALA* 1.3 64.8 + - - +
214C SER* 4.5 0.9 - - - -
217C THR* 3.4 28.7 - - - +
219C PRO* 3.6 30.5 - - + -
246C PHE* 4.1 7.2 - - + -
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Residues in contact with ALA 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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166C VAL* 3.6 4.9 - - - +
167C PHE* 2.7 43.8 + - + +
188C MET* 3.3 37.9 - - + -
192C PHE* 3.6 17.0 - - + -
194C VAL 2.9 7.4 - - - +
195C ALA* 4.5 0.2 - - - +
211C ILE* 3.8 1.8 - - + -
212C TYR* 1.3 75.0 - - - +
214C SER* 1.3 66.4 + - - +
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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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165C GLY 3.5 17.3 - - - -
166C VAL* 4.3 3.6 - - - -
192C PHE* 3.3 15.5 - - - +
193C SER 3.0 7.4 + - - -
194C VAL* 2.9 37.6 + - - +
212C TYR* 4.5 1.6 - - - -
213C ALA* 1.3 78.8 - - - +
215C PHE* 1.3 59.9 + - - +
217C THR* 2.7 44.9 + - - -
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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