Contacts of the strand formed by residues 307 - 314 (chain A) in PDB entry 3URF
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 TYR 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A HIS* 3.4 29.8 - + + -
168A LEU 3.1 15.7 - - - +
169A THR* 4.0 12.1 - - + -
187A TRP* 3.6 8.6 - - - -
217A TYR* 3.8 22.7 - + - -
218A ALA* 3.4 1.0 - - - +
219A ASN* 2.8 66.9 + - + +
220A ILE* 4.6 1.4 - - - +
276A ASN* 4.8 3.0 + - - -
303A GLN 3.5 17.3 - - - +
304A ASP* 3.7 19.7 - - - -
305A ALA 4.1 0.7 - - - -
306A THR* 1.3 81.6 - - - +
308A PHE* 1.3 64.1 + - - +
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Residues in contact with PHE 308 (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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167A HIS* 3.5 2.4 + - - -
168A LEU* 2.8 62.1 + - + +
187A TRP* 3.4 49.6 - + + -
201A PHE* 4.7 4.9 - + - -
204A GLY 5.4 1.3 - - - -
206A LEU* 4.3 19.5 - - + -
217A TYR* 3.2 21.1 - - - +
218A ALA* 3.7 12.3 - - + +
220A ILE* 5.8 0.2 - - + -
242A VAL* 5.6 0.9 - - + -
289A ILE* 4.4 23.1 - - + -
290A SER* 5.3 0.4 - - - -
291A ILE* 3.6 27.4 - - + -
307A TYR* 1.3 78.8 - - - +
309A GLY* 1.3 63.7 + - - +
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Residues in contact with GLY 309 (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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166A ALA* 3.1 16.2 - - - -
168A LEU* 5.6 0.2 - - - -
206A LEU* 5.2 2.5 - - - -
216A LEU* 3.4 4.0 - - - +
217A TYR* 3.0 49.6 + - - +
308A PHE* 1.3 83.5 - - - +
310A ALA* 1.3 64.1 + - - +
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Residues in contact with ALA 310 (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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165A PHE* 3.1 3.9 - - - +
166A ALA 2.8 32.7 + - - +
199A MET* 4.4 6.5 - - + -
206A LEU* 4.3 20.0 - - + -
214A TYR* 4.4 10.8 - - + -
215A TYR 3.1 7.4 - - - -
216A LEU* 3.4 22.9 - - + -
217A TYR* 3.8 2.5 - - - -
283A LEU* 5.8 0.4 - - + -
289A ILE* 5.9 0.7 - - + -
309A GLY* 1.3 76.3 - - - +
311A PHE* 1.3 65.7 + - - +
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Residues in contact with PHE 311 (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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164A PRO 3.5 5.4 - - - +
165A PHE* 4.0 14.6 - - + -
214A TYR* 3.1 6.4 - - - -
215A TYR* 2.9 68.3 + + + -
217A TYR* 4.1 17.9 - + - -
310A ALA* 1.3 78.6 - - - +
312A LYS* 1.3 68.2 + - - +
313A VAL* 3.5 15.6 + - + -
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Residues in contact with LYS 312 (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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162A ALA 4.3 5.6 - - - -
163A GLN* 4.4 14.7 - - + +
164A PRO* 2.9 32.3 + - + +
210A GLN* 3.3 25.2 + - - +
211A ASP 2.8 27.5 + - - -
212A GLY* 4.0 0.2 - - - -
213A PHE 3.4 4.3 - - - +
214A TYR* 3.4 31.8 - - + +
311A PHE* 1.3 77.6 - - - +
313A VAL* 1.3 62.9 + - - +
314A ARG 3.1 26.0 + - - +
315A ASP* 3.0 27.2 + - - -
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Residues in contact with VAL 313 (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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213A PHE 2.6 14.0 + - - +
215A TYR* 4.2 7.4 - - + +
280A PHE* 3.9 28.3 - - + -
311A PHE* 3.8 29.8 - - + +
312A LYS* 1.3 81.3 - - - +
314A ARG* 1.3 68.4 + - + +
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Residues in contact with ARG 314 (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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212A GLY* 3.1 1.2 - - - -
213A PHE* 2.9 54.3 + - + -
280A PHE* 4.9 8.1 - - + -
312A LYS* 3.1 17.2 - - - +
313A VAL* 1.3 93.4 - - + +
315A ASP* 1.3 77.3 + - - +
317A ASP* 3.3 26.6 - - - +
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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