Contacts of the strand formed by residues 204 - 209 (chain A) in PDB entry 3AF5
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 ALA 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLY* 3.7 1.2 - - - -
194A LEU* 2.7 41.8 + - + -
195A GLY 2.8 14.1 + - - +
197A PHE* 4.8 0.2 - - - -
202A ARG 3.9 1.3 - - - +
203A SER* 1.3 77.3 - - - +
205A LEU* 1.3 56.5 + - - +
215A LEU* 4.6 2.5 - - + -
216A VAL 3.9 1.1 + - - -
217A ASP 3.5 8.1 - - - +
218A PHE* 3.9 15.7 - - + -
233A PRO* 3.7 33.4 - - + -
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Residues in contact with LEU 205 (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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191A ILE* 4.1 17.5 - - + -
192A THR 3.4 8.5 - - - +
197A PHE* 4.1 26.9 - - + -
204A ALA* 1.3 75.5 - - - +
206A LEU* 1.3 65.1 + - - +
207A VAL* 3.4 29.5 + - + -
215A LEU* 3.5 7.3 - - - +
216A VAL* 2.9 45.1 + - + +
364A ILE* 4.1 22.7 - - + -
390A VAL* 4.2 27.6 - - + -
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Residues in contact with LEU 206 (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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190A ARG 3.6 1.4 - - - +
191A ILE* 3.3 4.3 - - - -
192A THR* 2.8 44.3 + - - +
194A LEU* 4.1 12.5 - - + +
204A ALA 4.3 0.2 - - - -
205A LEU* 1.3 72.0 - - - +
207A VAL* 1.3 64.5 + - - +
208A GLN* 4.1 19.5 - - + +
213A PHE* 4.8 6.5 - - + -
214A VAL 3.9 17.5 - - - +
215A LEU* 4.3 10.1 - - + +
239A GLU* 4.3 24.0 - - + -
240A PHE* 4.1 29.2 - - + -
243A VAL* 4.4 12.6 - - + -
249A LEU* 4.4 13.2 - - + -
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Residues in contact with VAL 207 (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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189A ILE* 4.8 2.0 - - + -
190A ARG 3.6 5.8 - - - +
191A ILE* 4.3 5.4 - - + -
205A LEU* 3.4 24.0 - - + -
206A LEU* 1.3 73.5 - - - +
208A GLN* 1.3 66.9 + - - +
209A THR* 5.1 0.9 - - + -
212A SER 4.1 0.4 - - - +
213A PHE* 3.3 7.6 - - - +
214A VAL* 2.8 55.3 + - + +
216A VAL* 4.1 5.8 - - + -
335A ILE* 5.0 7.2 - - + -
353A LEU* 3.9 21.3 - - + -
355A ILE* 4.2 18.6 - - + -
362A ILE* 4.5 7.6 - - + -
364A ILE* 4.6 2.9 - - + -
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Residues in contact with GLN 208 (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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188A TRP* 3.8 11.5 - - + -
189A ILE* 3.1 6.8 - - - +
190A ARG* 2.8 81.8 + - - +
192A THR* 2.9 31.3 + - - -
206A LEU* 4.1 13.4 + - + +
207A VAL* 1.3 78.4 - - - +
209A THR* 1.3 66.2 + - - +
212A SER 3.7 4.5 - - - -
213A PHE* 3.5 29.4 - - + -
239A GLU* 4.4 16.6 + - - +
647A THR* 4.3 1.6 - - - +
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Residues in contact with THR 209 (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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186A SER* 4.0 3.4 - - - +
188A TRP* 3.1 30.2 - - - +
189A ILE* 4.4 4.7 - - + -
207A VAL* 5.1 2.5 - - + -
208A GLN* 1.3 80.5 - - - +
210A ASP* 1.3 60.7 + - - +
211A GLU 2.9 6.1 + - - -
212A SER* 2.7 36.1 + - - +
213A PHE* 4.4 6.6 - - - -
334A ASP* 2.9 25.9 + - - +
335A ILE* 4.3 15.0 - - + -
355A ILE* 3.9 23.3 - - + -
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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