Contacts of the strand formed by residues 211 - 217 (chain B) in PDB entry 3OF6
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 PHE 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B VAL* 5.7 1.2 - - - +
146B LEU* 3.5 30.5 - - + -
162B TRP* 5.2 0.9 - - + -
163B TRP 3.8 3.1 - - - -
164B VAL* 4.1 15.5 - - + -
197B LEU* 4.1 9.9 - - + -
199B VAL* 4.5 11.2 - - + -
203B PHE* 3.3 41.3 - + - -
204B TRP* 3.6 33.0 - + - -
209B ASN* 3.7 26.9 - - + -
210B HIS* 1.3 82.1 - - - +
212B ARG* 1.3 60.7 + - - +
241B GLU* 3.1 6.8 - - - +
242B ALA 3.0 46.0 + - - +
244B GLY* 4.0 6.1 - - - -
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Residues in contact with ARG 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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162B TRP* 3.5 9.8 - - - -
163B TRP* 2.9 81.0 + - - +
166B GLY* 5.9 1.6 - - - -
210B HIS* 3.7 15.8 - - + -
211B PHE* 1.3 77.3 - - - +
213B CYS* 1.3 62.1 + - - +
214B GLN* 3.4 26.2 + - - +
237B ILE* 5.2 0.2 - - - +
239B SER* 2.9 38.2 + - - -
240B ALA 3.3 14.4 - - - +
241B GLU* 4.0 13.9 - - + -
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Residues in contact with CYS 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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128B VAL* 3.8 3.3 - - + +
130B VAL* 3.5 14.4 - - + +
148B CYS* 2.0 56.5 - - + -
160B LEU* 3.5 28.3 - - - -
161B SER 3.8 2.5 - - - -
162B TRP* 3.8 10.3 - - + -
212B ARG* 1.3 73.2 - - - +
214B GLN* 1.3 60.0 + - - +
215B VAL* 4.2 2.0 - - - -
239B SER* 3.2 6.4 - - - -
240B ALA 2.9 28.5 + - - -
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Residues in contact with GLN 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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159B GLU 3.6 1.6 - - - +
160B LEU* 3.3 2.9 - - - +
161B SER* 2.8 44.9 + - - +
163B TRP* 2.8 48.9 - - + +
212B ARG* 3.4 29.6 + - - +
213B CYS* 1.3 72.5 - - - +
215B VAL* 1.3 67.0 + - - +
216B GLN* 4.0 4.4 - - - +
237B ILE* 3.5 32.7 - - + +
239B SER* 3.5 4.0 - - - +
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Residues in contact with VAL 215 (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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126B PRO* 4.0 17.5 - - + -
128B VAL* 3.5 21.3 - - + -
148B CYS* 4.3 0.4 - - - -
150B ALA* 4.1 12.6 - - + -
158B VAL* 3.9 27.1 - - + -
159B GLU 3.4 5.6 - - - +
160B LEU* 3.7 28.3 - - + -
193B LEU* 6.0 0.4 - - + -
213B CYS* 4.2 6.3 - - - -
214B GLN* 1.3 80.9 - - - +
216B GLN* 1.3 61.6 + - - +
217B PHE* 3.3 4.3 + - - +
237B ILE* 4.7 0.2 - - - -
238B VAL* 3.0 35.7 + - - +
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Residues in contact with GLN 216 (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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158B VAL* 3.1 7.3 - - - -
159B GLU* 2.8 50.1 + - + +
214B GLN* 4.0 6.1 - - + +
215B VAL* 1.3 69.5 - - - +
217B PHE* 1.3 79.3 + - - +
218B TYR* 3.4 32.0 - - + +
235B THR* 3.6 18.0 - - - +
236B GLN 3.5 3.8 + - - -
237B ILE* 3.1 40.2 - - + +
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Residues in contact with PHE 217 (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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123B VAL* 3.8 10.5 - - + -
124B PHE 3.3 28.7 - - - -
125B PRO* 4.3 4.5 - - + -
126B PRO* 3.4 33.4 - - + -
153B PHE* 4.3 1.3 - - + -
154B TYR 3.3 21.8 - - - -
155B PRO* 4.1 13.7 - - + -
157B HIS 3.7 2.7 - - - -
158B VAL* 3.5 14.8 - - + -
215B VAL 3.3 1.9 + - - +
216B GLN* 1.3 81.3 + - - +
218B TYR* 1.3 75.3 + - - +
219B GLY* 3.7 17.7 - - - -
233B PRO* 4.8 1.1 - - + -
234B VAL 3.4 21.1 - - - -
235B THR* 3.2 3.3 - - - -
236B GLN* 2.9 42.7 + - + +
238B VAL* 5.5 0.7 - - + -
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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