Contacts of the strand formed by residues 194 - 198 (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 VAL 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B PHE* 3.2 6.6 - - - +
193B SER* 1.3 92.7 - - - +
195B ALA* 1.3 65.7 + - - +
196B MET* 4.5 4.9 - - - -
212B TYR* 3.9 17.9 - - + +
213B ALA* 3.1 4.5 - - - -
214B SER* 2.9 50.2 + - - +
216B LYS* 4.0 16.6 - - - +
217B THR 4.0 9.2 - - - +
218B HIS* 5.1 1.6 - - - +
219B PRO* 4.5 9.4 - - + -
261B LYS 3.2 10.3 - - - +
262B SER 3.9 16.6 - - - +
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Residues in contact with ALA 195 (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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185B LEU* 4.0 10.7 - - + +
188B MET* 4.1 28.5 - - + +
189B GLY* 4.4 11.4 - - - +
192B PHE* 5.2 0.2 - - + -
194B VAL* 1.3 75.0 - - - +
196B MET* 1.3 60.0 - - - +
211B ILE* 4.5 2.7 - - + -
212B TYR 3.6 4.7 - - - -
213B ALA* 4.4 2.0 - - + +
259B ASN 3.9 9.8 - - - +
260B ILE* 3.5 9.0 - - - -
261B LYS* 2.8 33.7 + - + +
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Residues in contact with MET 196 (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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194B VAL* 4.5 3.1 - - + -
195B ALA* 1.3 78.1 - - - +
197B PRO* 1.3 68.6 - - + +
198B PHE 3.9 0.3 + - - -
211B ILE* 3.4 4.3 - - - +
212B TYR* 2.9 40.1 + - - +
218B HIS* 3.8 27.1 - - + +
219B PRO* 3.8 26.7 - - + -
220B LEU* 4.6 10.8 - - + -
246B PHE* 3.9 25.5 - - + -
260B ILE* 3.9 6.3 - - + -
261B LYS 3.5 6.3 - - - +
262B SER* 3.3 32.1 - - - +
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Residues in contact with PRO 197 (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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174B PRO* 5.2 4.9 - - + -
181B MET* 3.8 35.0 - - + -
185B LEU* 3.9 19.9 - - + -
196B MET* 1.3 85.7 - - + +
198B PHE* 1.3 63.3 + - - +
210B TYR 3.2 7.9 - - - +
211B ILE* 4.4 1.3 - - + -
246B PHE* 3.7 18.2 - - - +
248B LEU* 4.2 30.2 - - + +
256B PHE* 4.9 2.7 - - + -
260B ILE* 4.0 17.7 - - + -
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Residues in contact with PHE 198 (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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61B LEU* 3.6 19.1 - - + -
62B LEU* 3.8 13.0 - - + -
65B MET* 4.0 27.8 - - + -
168B ILE* 4.2 5.4 - - + -
174B PRO* 5.8 0.9 - - - -
181B MET* 5.1 0.9 - - - +
197B PRO* 1.3 75.4 - - - +
199B VAL* 1.3 77.2 + - - +
209B GLY* 3.8 0.3 - - - -
210B TYR* 2.9 71.2 + + + -
211B ILE 3.9 16.8 - - - -
212B TYR* 3.9 13.9 - + + -
245B ALA* 3.1 24.0 - - + +
246B PHE* 3.7 26.2 - + + -
248B LEU* 6.4 0.2 - - - -
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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