Contacts of the strand formed by residues 204 - 209 (chain B) in PDB entry 2CXN
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 SER 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B ILE* 4.4 0.9 - - - -
151B ASP* 3.4 7.0 + - - +
153B ILE* 3.6 17.5 - - - -
199B LEU* 3.5 27.3 - - - +
200B SER 2.8 21.5 + - - -
201B PRO* 4.0 2.4 + - - +
202B GLU 3.7 0.4 - - - -
203B THR* 1.3 80.1 + - - +
205B LEU* 1.3 59.6 + - - +
206B PHE* 4.3 16.5 - - - -
228B TRP* 4.7 2.5 - - - -
229B PHE* 5.6 0.2 - - - -
242B HIS* 2.8 30.4 + - - +
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Residues in contact with LEU 205 (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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132B PHE* 3.9 24.5 - - + -
136B VAL* 4.8 3.4 - - + -
141B TRP* 3.5 43.1 - - + +
149B ILE* 4.0 12.1 - - + -
151B ASP 2.9 7.9 + - - -
152B ILE* 3.3 26.7 - - + +
153B ILE* 2.9 25.8 + - - -
203B THR 4.2 0.2 + - - -
204B SER* 1.3 73.3 - - - +
206B PHE* 1.3 73.5 + - - +
207B ILE* 4.0 7.1 + - + -
241B LYS 3.7 8.7 - - - +
242B HIS* 3.5 12.3 - - - +
243B PHE 4.6 0.2 - - - +
244B VAL* 4.1 11.4 - - + -
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Residues in contact with PHE 206 (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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153B ILE* 3.4 39.0 - - + +
155B ILE* 3.8 17.3 - - + -
192B ILE* 4.9 0.9 - - + -
196B LEU* 3.7 17.7 - - + -
199B LEU* 4.9 0.4 - - + -
204B SER* 4.3 14.6 - - - -
205B LEU* 1.3 74.7 - - - +
207B ILE* 1.3 62.1 + - - +
208B ILE* 4.0 6.3 - - + -
225B ALA* 3.7 14.1 - - + -
228B TRP* 3.6 35.2 - + - -
229B PHE* 5.1 4.5 - + + -
242B HIS* 2.7 20.2 + - + +
243B PHE* 3.4 38.2 - + + -
244B VAL* 2.9 28.8 + - - +
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Residues in contact with ILE 207 (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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152B ILE* 3.5 30.7 - - + -
153B ILE 2.8 11.0 + - - +
154B ASN* 3.5 11.2 - - - +
155B ILE* 2.8 29.6 + - - +
205B LEU* 4.1 4.9 - - + -
206B PHE* 1.3 74.6 - - - +
208B ILE* 1.3 62.3 + - - +
209B ALA 3.6 0.5 + - - -
244B VAL* 3.7 18.8 - - + -
246B LEU* 3.5 43.1 - - + -
282B LEU* 4.2 5.4 - - + -
283B SER* 4.1 19.3 - - - +
286B LEU* 3.6 20.6 - - + -
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Residues in contact with ILE 208 (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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155B ILE* 3.7 25.8 - - + -
206B PHE* 4.2 3.6 - - + +
207B ILE* 1.3 74.8 - - - +
209B ALA* 1.3 62.4 + - - +
210B SER* 3.6 2.0 + - - -
213B PHE* 3.5 35.6 - - + -
218B THR* 4.1 16.2 - - + -
219B ILE* 4.1 5.2 - - + -
222B ALA* 3.6 35.7 - - + -
243B PHE* 4.1 25.6 - - + -
244B VAL 2.9 18.5 + - - +
245B ALA* 3.4 2.6 - - - -
246B LEU 2.9 24.7 + - - +
256B PHE* 4.8 1.1 - - + -
258B ILE* 4.6 2.7 - - + -
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Residues in contact with ALA 209 (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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154B ASN* 4.3 7.4 - - - +
155B ILE 2.9 16.8 + - - +
156B GLY* 3.9 0.9 - - - -
160B SER* 3.6 41.8 + - - +
207B ILE 3.6 0.2 + - - -
208B ILE* 1.3 71.0 - - - +
210B SER* 1.3 62.3 + - - +
218B THR* 3.6 13.4 + - - +
246B LEU* 3.9 27.1 - - + -
280B ILE* 3.9 6.7 - - + -
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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