Contacts of the strand formed by residues 213 - 219 (chain A) in PDB entry 1O7F
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 THR 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A ASP* 4.5 12.3 + - - +
207A ARG 3.5 7.7 + - - -
208A LYS* 4.7 13.5 - - - +
212A LYS* 1.3 85.0 - - - +
214A TYR* 1.3 68.9 + - - +
215A ARG* 3.8 4.0 + - - +
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Residues in contact with TYR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ASP* 3.1 1.7 - - - -
207A ARG 2.6 48.4 + - - +
209A TYR* 3.3 42.0 - + + -
212A LYS* 3.1 45.3 - - + +
213A THR* 1.3 74.2 - - - +
215A ARG* 1.3 61.6 + - - +
217A CYS* 3.8 21.3 - - - -
256A VAL* 3.2 43.3 - - + -
257A ASP* 4.4 12.8 + - - -
268A PHE* 3.7 15.9 - + + -
270A ARG* 5.2 0.2 - - - +
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Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ASP* 3.3 18.8 - - - +
213A THR* 3.8 4.8 + - - +
214A TYR* 1.3 74.4 - - - +
216A GLN* 1.3 81.6 + - + +
217A CYS* 3.1 3.2 + - - +
270A ARG* 2.4 49.4 + - - +
274A ASP* 2.7 30.7 + - - +
275A GLU 4.2 6.4 + - - -
276A ARG 2.6 35.3 + - - -
277A GLU* 3.2 29.5 + - - +
279A ALA* 5.5 0.8 - - - +
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Residues in contact with GLN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 5.9 1.4 - - - +
204A ILE* 3.7 29.2 + - + +
205A ARG* 3.6 23.6 + - - +
206A ASP* 2.8 34.0 + - - +
215A ARG* 1.3 93.7 - - + +
217A CYS* 1.3 58.2 + - - +
218A CYS* 5.7 0.2 - - - -
270A ARG* 3.7 16.6 - - - +
271A PHE 5.2 0.2 + - - -
274A ASP* 3.9 27.7 - - + +
277A GLU 5.7 1.8 - - - +
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Residues in contact with CYS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A MET 3.3 1.6 - - - +
204A ILE* 4.4 0.2 - - - -
205A ARG 3.1 16.9 + - - +
207A ARG* 2.6 50.3 + - - -
214A TYR* 3.8 24.0 - - - -
215A ARG 3.1 6.7 + - - +
216A GLN* 1.3 76.8 - - - +
218A CYS* 1.3 58.8 + - - +
256A VAL* 5.1 2.2 - - + -
268A PHE* 3.5 25.8 - - + -
269A TYR 3.0 19.3 - - - +
270A ARG* 4.4 7.9 - - + +
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Residues in contact with CYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ILE* 5.4 1.1 - - - -
203A MET* 3.6 15.9 - - + +
204A ILE* 3.5 33.2 - - - -
207A ARG* 3.6 0.7 - - - +
217A CYS* 1.3 74.1 - - - +
219A VAL* 1.3 65.0 + - - +
223A LEU* 3.8 28.5 - - + -
253A LEU* 5.9 0.2 - - + -
268A PHE* 3.1 8.8 - - - +
269A TYR 2.7 33.6 + - - +
270A ARG* 5.7 0.2 - - - -
271A PHE* 3.8 25.6 - - - -
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A MET 4.7 0.6 + - - -
207A ARG* 3.4 39.7 - - - +
218A CYS* 1.3 76.1 - - - +
220A GLY* 1.3 71.5 + - - +
221A THR* 3.6 20.2 - - - +
222A GLU* 2.8 28.7 + - + +
223A LEU* 2.9 14.5 + - - +
265A LYS 3.9 5.4 - - - +
266A TYR* 3.8 31.9 - - + -
267A LEU 3.4 4.0 - - - +
268A PHE* 4.1 9.6 - - + -
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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