Contacts of the strand formed by residues 209 - 214 (chain B) in PDB entry 2CMG
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL* 3.6 1.2 - - - +
171B ALA* 2.7 35.8 + - - +
172B LYS 3.3 16.8 + - - -
181B MET* 4.1 2.5 - - - -
198B PHE 3.8 8.7 - - - -
199B VAL* 4.4 5.8 - - - -
208B LYS* 1.3 73.1 - - - +
210B TYR* 1.3 72.6 + - - -
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Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU* 3.0 31.0 + - + +
61B LEU* 4.4 6.7 - - + -
62B LEU* 4.0 15.9 - - + -
168B ILE* 4.9 0.7 - - + -
169B SER 3.2 15.5 - - - +
170B VAL* 4.2 10.3 - - + -
181B MET* 3.8 2.3 - - - +
197B PRO* 3.2 8.0 - - - +
198B PHE* 2.9 74.2 + + + -
199B VAL* 4.2 1.8 - - - -
200B ALA* 4.0 28.6 - - + +
203B ARG* 5.1 5.9 + - - -
208B LYS* 3.5 37.6 - - + +
209B GLY* 1.3 84.7 - - - -
211B ILE* 1.3 69.7 + - - +
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B PHE 3.6 1.9 - - - +
168B ILE* 3.4 11.1 - - - +
169B SER* 3.0 36.5 + - - +
170B VAL 4.2 1.1 - - - +
171B ALA* 3.1 36.8 - - + +
181B MET* 4.0 6.3 - - + -
184B ALA* 4.4 8.3 - - + -
185B LEU* 4.1 22.7 - - + -
188B MET* 3.5 39.5 - - + -
195B ALA* 4.5 0.7 - - - -
196B MET 3.4 16.8 - - - +
197B PRO* 4.7 0.4 - - + -
198B PHE* 3.9 3.6 - - - -
210B TYR* 1.3 80.4 - - - +
212B TYR* 1.3 67.2 + - - +
213B ALA* 4.2 2.5 - - + +
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Residues in contact with TYR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B MET* 3.7 40.8 - - + -
69B THR* 3.1 26.2 + - + +
166B VAL* 3.6 27.4 - - + +
167B PHE 4.2 1.8 - - - -
168B ILE* 4.6 5.4 - - + -
194B VAL* 3.9 6.0 - - + +
195B ALA* 3.6 1.9 - - - -
196B MET* 2.9 33.7 + - - +
198B PHE* 3.9 5.6 - - + -
211B ILE* 1.3 72.0 - - - +
213B ALA* 1.3 61.4 + - - +
214B SER* 4.5 2.7 - - - -
217B THR* 3.3 35.9 + - - -
218B HIS 3.8 2.6 + - - -
219B PRO* 3.4 37.5 - - + -
246B PHE* 3.9 14.1 - - + -
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 3.6 2.8 - - - +
167B PHE* 2.9 36.0 + - - +
188B MET* 3.1 32.8 - - + -
192B PHE* 3.7 21.9 - - + -
194B VAL 3.1 10.8 - - - +
195B ALA* 4.6 1.8 - - + -
211B ILE* 4.3 3.1 - - + -
212B TYR* 1.3 75.5 - - - +
214B SER* 1.3 64.3 + - - +
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLY 3.6 7.4 - - - -
166B VAL* 4.6 0.4 - - - -
192B PHE* 3.0 33.5 - - - +
193B SER 3.1 7.3 + - - -
194B VAL* 2.9 22.5 + - - +
212B TYR* 4.5 2.9 - - - -
213B ALA* 1.3 76.7 - - - +
215B PHE* 1.3 63.1 + - - +
216B LYS 3.0 10.4 + - - -
217B THR* 2.8 46.1 + - - -
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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