Contacts of the strand formed by residues 205 - 209 (chain A) in PDB entry 2W27
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ASP 3.0 10.2 + - - +
171A LEU* 3.0 23.3 - - + +
172A LEU 3.0 23.9 + - - -
203A GLY 4.2 0.8 + - - -
204A ALA* 1.3 72.9 - - - +
206A LEU* 1.3 61.2 + - - +
226A ARG* 3.7 37.7 - - + +
227A TYR* 4.0 3.8 - - + -
372B LEU* 4.6 8.6 - - + +
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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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171A LEU* 4.4 1.1 - - - -
172A LEU* 3.7 24.0 - - + -
174A ILE* 4.1 14.1 - - + -
195A ILE* 5.1 1.3 - - + -
196A SER* 3.7 24.0 - - - +
199A ALA* 3.6 27.8 - - + -
204A ALA 4.6 0.7 - - - +
205A ALA* 1.3 73.0 - - - +
207A LEU* 1.3 59.8 + - - +
208A TYR* 3.7 20.6 - - + +
223A ASN 3.5 24.5 - - - +
224A GLY* 3.7 19.9 + - - +
226A ARG* 2.9 27.7 + - - +
227A TYR* 3.2 7.8 + - - +
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.9 29.4 - - + -
86A PHE* 4.2 14.1 - - + -
171A LEU* 4.3 12.6 - - + -
172A LEU 2.8 13.9 + - - +
173A LYS* 3.2 37.3 - - + +
174A ILE* 2.9 25.3 + - - -
205A ALA 3.7 0.6 + - - -
206A LEU* 1.3 73.6 - - - +
208A TYR* 1.3 81.3 + - - +
209A GLU 3.9 0.5 + - - -
227A TYR* 3.2 28.9 - - + +
228A PHE* 3.5 8.5 - - - +
229A GLN* 4.2 3.8 - - + +
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Residues in contact with TYR 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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174A ILE* 3.2 39.6 - - + +
176A LEU* 3.4 34.5 - - + -
192A LEU* 5.2 6.2 - - + +
196A SER* 5.7 0.7 - - - -
206A LEU* 3.7 13.8 - - + +
207A LEU* 1.3 80.8 - - - +
209A GLU* 1.3 59.6 + - - +
211A ILE* 3.9 5.1 - - + +
219A TYR* 4.9 6.7 - + - -
220A ALA* 3.3 49.1 - - + -
223A ASN* 2.6 31.2 + - + +
225A GLY* 3.4 22.4 - - - -
227A TYR 3.2 8.5 + - - +
228A PHE* 3.5 1.0 - - - -
229A GLN 3.0 24.4 + - - +
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Residues in contact with GLU 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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33A GLU* 5.8 0.2 - - - -
122A GLU* 4.9 0.5 - - - +
152A ASP* 3.6 12.0 - - - +
153A ASN* 5.6 2.0 + - - +
173A LYS* 3.2 36.9 + - + +
174A ILE 2.8 16.5 + - - +
175A ASP* 3.4 17.1 - - + +
176A LEU* 3.2 21.3 + - - +
208A TYR* 1.3 74.5 - - - +
210A ASP* 1.3 98.1 + - - +
211A ILE* 3.1 5.0 + - - +
229A GLN* 3.3 27.4 - - + +
501A 5GP 4.2 20.0 + - - +
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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