Contacts of the strand formed by residues 206 - 213 (chain A) in PDB entry 2WUB
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 VAL 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A CYS* 3.6 29.8 - - - -
202A GLU* 3.3 6.1 - - - -
203A LYS 3.0 34.8 + - - +
204A ASN* 3.9 11.4 - - + +
205A GLY* 1.3 82.6 - - - +
207A ALA* 1.3 62.9 - - - +
208A TYR* 3.6 24.5 - - + +
393B CYS 3.8 8.1 - - - +
394B GLY 4.1 2.7 - - - -
395B ARG* 4.1 21.1 - - - +
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TRP* 3.6 27.4 - - + -
121A ILE* 4.0 5.6 - - + -
122A CYS* 3.2 28.1 + - - +
200A ALA* 4.7 5.6 - - + -
201A CYS 3.9 5.2 - - - +
202A GLU* 4.5 4.5 - - + -
206A VAL* 1.3 74.4 - - - +
208A TYR* 1.3 61.2 + - - +
394B GLY* 3.0 27.5 + - - +
396B ARG* 4.2 10.1 - - - +
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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
----------------------------------------------------------
121A ILE* 3.7 4.5 - - - -
122A CYS* 3.3 26.5 - - + +
123A LEU 3.9 17.9 - - - -
124A PRO* 4.0 17.5 - - + -
125A GLU* 5.8 3.6 - - + -
130A PHE* 4.3 20.0 - + + -
200A ALA* 3.1 23.2 - - - -
201A CYS 3.1 18.7 + - - +
203A LYS* 3.9 27.5 + - + +
204A ASN* 5.2 3.5 + - - -
206A VAL* 3.6 38.9 - - + +
207A ALA* 1.3 73.0 - - - +
209A LEU* 1.3 60.8 + - - +
210A TYR* 3.2 4.5 + - - +
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Residues in contact with LEU 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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45A SER* 3.9 21.5 - - - +
47A VAL* 4.2 10.8 - - + -
53A VAL* 4.0 28.5 - - + -
121A ILE* 3.7 19.2 - - + +
122A CYS 2.8 12.7 + - - +
123A LEU* 5.0 2.7 - - + -
124A PRO* 3.1 22.2 - - + +
198A PRO* 3.5 27.4 - - + -
199A LEU 3.9 2.9 - - - +
208A TYR* 1.3 69.0 - - - +
210A TYR* 1.3 61.0 + - - +
211A GLY 2.9 29.2 - - - +
212A ILE* 4.6 2.2 - - + -
231A VAL* 3.2 18.3 - - + +
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Residues in contact with TYR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 4.7 11.7 - - + -
128A SER* 4.1 7.9 - - - -
129A THR* 3.1 24.6 - - - +
130A PHE* 3.0 55.5 + + + -
162A LEU* 3.6 22.7 - - + -
181A LEU* 3.4 36.6 - - + +
199A LEU* 3.1 15.9 + - + +
201A CYS* 3.7 18.8 - - + -
208A TYR 3.2 4.2 + - - +
209A LEU* 1.3 73.9 - - - +
211A GLY* 1.3 58.5 + - - +
229A THR 3.8 0.3 - - - +
230A ARG* 3.6 18.2 + - + +
231A VAL* 3.2 19.9 + - - +
232A ALA* 4.1 7.5 + - + -
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Residues in contact with GLY 211 (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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181A LEU* 4.7 1.6 - - - -
199A LEU* 3.0 36.5 + - - +
209A LEU* 2.9 22.8 - - - +
210A TYR* 1.3 80.5 - - - +
212A ILE* 1.3 58.1 + - - -
228A TYR* 4.3 2.0 - - - -
229A THR 3.1 11.9 - - - -
231A VAL* 3.4 7.4 - - - -
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Residues in contact with ILE 212 (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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45A SER* 6.0 0.4 - - - +
53A VAL* 3.3 34.1 - - + +
54A SER* 3.8 10.8 - - - +
55A ALA* 4.1 14.4 - - + +
102A ASP 4.4 6.3 - - - +
103A LEU* 3.9 13.2 - - + -
196A GLY* 3.7 24.2 - - - +
197A GLY 3.7 2.9 - - - +
198A PRO* 5.8 0.2 - - + -
209A LEU* 4.6 4.0 - - + -
211A GLY* 1.3 74.4 - - - +
213A ILE* 1.3 70.4 + - - +
214A SER* 2.8 11.1 + - - -
228A TYR* 3.3 6.4 - - - +
229A THR* 3.0 38.5 + - + +
231A VAL* 3.5 21.1 - - + -
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Residues in contact with ILE 213 (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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16A ILE* 4.9 1.6 - - + -
55A ALA* 4.2 1.0 - - - +
138A ILE* 4.2 20.6 - - + -
139A ALA 4.6 5.8 - - - +
190A ALA* 4.8 11.4 - - + -
191A CYS 5.5 1.6 - - - +
194A ASP* 3.4 42.4 - - + +
195A SER* 4.0 0.7 - - - +
196A GLY* 2.7 29.3 + - - -
197A GLY* 2.8 29.8 + - - +
198A PRO 3.9 10.5 - - - +
211A GLY 4.3 0.2 - - - -
212A ILE* 1.3 70.8 - - - +
214A SER* 1.3 72.9 + - - +
215A TRP 5.0 2.5 - - - +
216A GLY* 5.5 1.3 - - - -
227A VAL 4.8 1.1 - - - +
228A TYR* 3.5 28.3 - - + -
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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