Contacts of the strand formed by residues 205 - 214 (chain F) in PDB entry 3CB4
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 205 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200F PHE* 4.0 16.2 - - - -
201F ASP 2.8 36.8 + - - -
203F TYR 3.5 1.6 - - - -
204F LEU* 1.3 78.3 - - - +
206F VAL* 1.3 64.6 + - - -
207F VAL* 3.3 7.4 + - - +
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Residues in contact with VAL 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F SER* 4.7 2.9 - - - -
199F TRP 3.5 8.1 - - - +
200F PHE* 4.0 13.8 - - + -
204F LEU 4.2 0.2 + - - -
205F GLY* 1.3 70.5 - - - -
207F VAL* 1.3 69.1 + - - +
208F SER* 4.5 8.9 + - - +
258F LEU 4.2 5.2 - - - +
259F VAL* 4.3 7.3 - - - +
260F CYS 3.9 14.4 + - - +
261F ALA* 6.1 1.0 - - - +
262F ILE* 3.4 48.4 + - + +
263F LYS 3.8 3.6 - - - +
264F ASP* 3.5 27.6 - - - -
265F ILE* 3.7 17.3 - - + +
268F ALA* 4.8 1.6 - - + -
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Residues in contact with VAL 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F SER* 3.2 3.7 - - - -
199F TRP* 2.9 65.4 + - + +
201F ASP* 3.9 17.9 - - + +
204F LEU* 4.2 8.5 - - + -
205F GLY 3.4 15.0 - - - +
206F VAL* 1.3 75.3 - - - +
208F SER* 1.3 65.8 + - - +
240F PHE* 5.4 0.7 - - + -
244F GLN* 5.9 2.7 - - - +
257F TRP* 4.0 20.2 - - + -
258F LEU 3.7 5.4 - - - +
259F VAL* 3.7 28.0 - - + -
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Residues in contact with SER 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F ILE* 4.6 13.0 - - - -
197F ASP 3.1 5.4 - - - -
198F SER* 2.8 22.1 + - - -
199F TRP* 4.4 2.7 - - - -
206F VAL* 4.5 3.3 - - - +
207F VAL* 1.3 74.7 - - - +
209F LEU* 1.3 64.0 + - - +
210F ILE* 3.8 6.8 + - - +
257F TRP* 3.2 3.5 - - - -
258F LEU* 2.8 47.4 + - - +
262F ILE* 4.9 3.5 - - - +
268F ALA* 3.6 15.6 - - - +
274F LEU* 5.9 1.6 - - - -
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Residues in contact with LEU 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F GLN* 5.2 12.1 - - + +
58F SER* 3.4 36.1 - - - +
76F ILE* 4.5 5.6 - - + -
194F LEU 3.8 0.3 - - - +
195F ILE* 3.9 3.3 - - - -
196F ILE* 2.9 56.4 + - + +
197F ASP* 2.8 17.6 + - + +
199F TRP* 3.8 16.1 - - + -
208F SER* 1.3 72.1 - - - +
210F ILE* 1.3 61.4 + - - +
240F PHE* 3.8 27.4 - - + -
255F VAL* 4.3 8.7 - - + -
256F GLY* 3.4 16.4 - - - +
257F TRP* 4.4 0.9 - - - +
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Residues in contact with ILE 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F ALA* 3.4 26.2 - - + -
194F LEU 3.6 5.8 - - - +
195F ILE* 5.2 4.3 - - + -
196F ILE* 3.7 4.3 - - - -
208F SER* 4.1 13.0 - - - +
209F LEU* 1.3 77.4 - - - +
211F ARG* 1.3 64.2 + - - +
212F ILE* 3.5 17.9 - - + -
217F LEU* 4.2 13.0 - - + -
250F LEU* 4.8 6.7 - - + +
254F GLU 3.9 0.3 - - - +
255F VAL* 3.3 9.9 - - - +
256F GLY 2.6 37.3 + - - +
258F LEU* 3.5 30.3 - - + +
274F LEU* 3.7 26.9 - - + -
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Residues in contact with ARG 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 5.5 0.6 - - - +
6F ASN* 3.2 13.9 - - - +
94F ALA* 3.1 46.2 + - + +
96F GLU* 2.6 43.6 + - - -
183F PRO* 3.4 9.5 - - - +
184F GLU 4.8 4.2 + - - +
193F ALA* 3.3 2.9 - - - -
194F LEU* 2.8 39.7 + - + +
196F ILE* 3.7 4.9 - - + +
210F ILE* 1.3 77.8 - - - +
212F ILE* 1.3 93.5 + - - +
213F LYS* 3.5 28.5 + - - +
253F GLY* 3.6 12.3 - - - -
254F GLU 3.6 5.6 - - - -
255F VAL* 3.8 16.2 - - + -
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Residues in contact with ILE 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F LEU* 4.1 8.1 - - + -
192F GLN 3.9 1.6 - - - -
193F ALA* 4.1 7.2 - - + +
210F ILE* 3.5 24.7 - - + -
211F ARG* 1.3 96.2 + - - +
213F LYS* 1.3 52.5 + - - +
214F ASN 3.5 14.1 - - - +
215F GLY 3.4 26.0 - - - +
216F THR* 4.8 0.4 - - - +
217F LEU* 4.5 13.0 - - + -
250F LEU* 4.0 31.0 - - + +
251F LYS 3.5 20.2 - - - +
252F CYS* 4.0 5.2 - - - -
253F GLY 2.9 17.4 + - - +
254F GLU 3.0 17.7 + - - +
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Residues in contact with LYS 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ALA* 2.9 29.4 + - - -
94F ALA* 4.8 1.0 - - - +
95F CYS 5.4 1.4 + - - -
96F GLU* 5.1 3.4 + - - -
184F GLU 3.3 20.7 - - - +
192F GLN* 2.8 13.8 + - + +
194F LEU* 4.5 13.2 - - + -
211F ARG* 3.8 34.0 - - - +
212F ILE* 1.3 75.9 - - - +
214F ASN* 1.3 71.5 + - + +
252F CYS* 3.5 9.0 - - - -
285F LEU* 3.7 39.0 - - + -
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Residues in contact with ASN 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F GLY* 3.3 5.7 - - - -
186F ASP* 3.1 24.2 + - - +
189F GLY* 4.0 16.8 - - - -
190F PRO* 3.2 23.9 + - - +
191F LEU* 3.3 6.9 - - - +
192F GLN* 2.8 46.4 + - + +
212F ILE* 3.5 3.6 - - - +
213F LYS* 1.3 86.9 - - - +
215F GLY* 1.3 64.1 + - - +
252F CYS* 4.0 4.0 - - - -
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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