Contacts of the strand formed by residues 205 - 209 (chain L) in PDB entry 6C23
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 LEU 205 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198L PHE* 3.5 7.7 - - - -
199L HIS* 3.1 66.0 + - + +
202L ASP* 3.6 13.6 + - + +
203L PRO 3.3 1.4 - - - -
204L ASN* 1.3 75.2 - - - +
206L LEU* 1.3 62.0 + - - +
207L LEU 3.5 1.6 + - - -
217L LEU* 4.2 26.0 - - + -
218L TRP 3.4 9.6 - - - +
219L ASN* 5.1 3.6 - - + -
226L VAL* 4.9 8.1 - - + -
244L TYR* 3.9 1.0 + - - +
265L ILE* 5.5 0.4 - - + -
274L ILE* 4.2 35.9 - - + -
278L TYR* 4.3 10.8 - - + +
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Residues in contact with LEU 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164L ALA* 5.1 0.4 - - + -
172L ILE* 3.8 37.7 - - + -
174L ILE* 4.8 7.2 - - + -
186L TYR* 5.0 1.1 - - + -
196L LEU* 3.9 17.5 - - + -
197L LYS 3.0 27.4 - - - +
198L PHE* 3.6 25.6 - - + -
204L ASN 3.5 1.2 + - - -
205L LEU* 1.3 70.5 - - - +
207L LEU* 1.3 76.9 + - - +
217L LEU* 3.6 3.0 - - - -
218L TRP* 2.9 42.7 + - + +
220L ILE* 4.2 24.0 - - + -
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Residues in contact with LEU 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196L LEU* 3.8 1.3 - - - +
197L LYS* 3.7 34.8 + - + -
205L LEU 3.5 1.2 + - - -
206L LEU* 1.3 94.8 - - - +
208L SER* 1.3 71.0 + - - +
209L VAL* 4.3 4.9 - - + -
215L LEU* 3.8 15.9 - - + -
216L ARG 3.4 18.6 - - - +
217L LEU* 3.7 8.5 - - + -
229L PHE* 5.0 4.5 - - + -
242L ALA* 3.6 29.4 - - + -
244L TYR* 3.4 28.8 + - + +
251L ILE* 3.4 31.2 - - + -
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Residues in contact with SER 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L ILE* 3.7 25.8 - - - -
189L HIS* 3.1 22.1 + - - -
193L ILE* 4.4 2.2 - - - -
195L GLU 4.0 7.2 - - - -
196L LEU* 3.9 5.6 - - - +
207L LEU* 1.3 81.7 - - - +
209L VAL* 1.3 65.8 + - - +
215L LEU* 3.6 2.1 - - - +
216L ARG* 2.9 31.6 + - - +
218L TRP* 3.4 13.8 + - - -
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Residues in contact with VAL 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189L HIS* 4.6 0.2 - - - -
193L ILE* 3.3 10.7 - - - +
194L ASN* 3.0 19.4 + - + -
195L GLU* 3.6 24.6 + - + +
196L LEU 5.5 0.2 - - - +
207L LEU* 4.3 5.4 - - + -
208L SER* 1.3 82.8 - - - +
210L SER* 1.3 67.6 + - - +
214L ALA 4.0 6.1 - - - +
215L LEU* 3.9 11.2 - - + -
239L VAL* 3.1 43.5 - - + +
240L LEU 4.9 1.8 - - - -
241L SER 4.5 6.3 - - - +
242L ALA* 3.6 29.6 - - + -
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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