Contacts of the strand formed by residues 209 - 214 (chain A) in PDB entry 5BOU
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 ILE 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A THR 3.8 1.3 - - - +
48A GLU* 4.3 9.0 - - + -
49A LYS* 4.0 7.1 - - - -
193A LEU* 4.7 13.9 - - + -
196A LEU* 3.8 28.3 - - + -
200A VAL* 4.3 7.6 - - + -
204A PHE* 3.5 40.2 - - + -
205A ASN 3.1 20.0 + - - +
206A GLY 3.2 16.5 - - - +
207A ASP 3.6 0.2 - - - -
208A THR* 1.3 92.9 - - - +
210A GLU* 1.3 69.3 + - - +
211A LEU* 4.6 10.1 - - + -
243A ILE* 3.6 18.0 - - + +
247A LEU* 6.0 0.4 - - + -
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Residues in contact with GLU 210 (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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46A ALA* 3.4 2.9 - - - +
47A THR* 2.9 47.0 + - + +
49A LYS* 3.2 35.1 - - + +
61A LEU 3.8 3.1 - - - +
62A SER* 3.4 5.4 + - - -
63A LYS* 3.0 26.0 + - - +
64A VAL* 2.9 31.1 + - + +
208A THR 4.4 0.4 + - - -
209A ILE* 1.3 72.7 - - - +
211A LEU* 1.3 62.1 + - - +
237A LYS* 3.1 39.3 + - - +
243A ILE* 5.0 0.2 - - - -
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Residues in contact with LEU 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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44A VAL* 3.6 24.7 - - + -
45A ILE 3.6 9.6 - - - +
46A ALA* 3.9 16.4 - - + -
64A VAL* 5.0 1.1 - - - -
189A ILE* 4.5 10.8 - - + -
192A ALA* 4.7 4.9 - - + -
193A LEU* 3.9 31.6 - - + +
196A LEU* 6.0 0.2 - - + -
209A ILE* 4.1 5.2 + - + -
210A GLU* 1.3 76.9 - - - +
212A ALA* 1.3 68.4 + - - +
213A ILE* 4.3 3.8 - - + -
237A LYS* 3.9 5.0 - - - +
238A LEU* 3.0 54.5 + - + +
243A ILE* 4.3 18.9 - - + +
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Residues in contact with ALA 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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44A VAL* 3.6 4.0 - - - +
45A ILE* 3.0 36.3 + - + +
64A VAL* 3.5 28.2 - - + +
211A LEU* 1.3 76.5 - - - +
213A ILE* 1.3 65.8 + - - +
235A PHE* 3.9 16.8 - - + -
236A ARG 3.4 12.6 - - - +
237A LYS* 3.9 8.3 - - + -
238A LEU 4.3 0.7 - - - +
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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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43A VAL 3.3 10.8 - - - +
44A VAL* 4.2 4.9 - - + -
45A ILE* 5.6 1.3 - - - -
185A LEU* 3.9 27.4 - - + -
189A ILE* 4.0 29.8 - - + -
211A LEU* 4.3 5.4 - - + -
212A ALA* 1.3 79.0 - - - +
214A ILE* 1.3 66.1 + - - +
215A GLY* 4.7 7.6 - - - +
216A ASP 5.8 0.7 - - - +
218A ASN* 6.2 0.9 - - - +
234A ARG 3.4 1.2 - - - +
235A PHE* 3.4 5.2 - - - -
236A ARG* 2.8 67.1 + - + +
238A LEU* 4.3 13.0 - - + -
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Residues in contact with ILE 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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42A GLY* 3.1 5.4 - - - -
43A VAL* 2.7 45.7 + - + +
45A ILE* 5.9 2.2 - - + -
70A ASP 3.7 20.2 - - - +
72A GLY* 3.8 6.1 - - - +
137A ALA* 3.8 41.3 - - + +
138A GLY* 3.8 2.0 - - - -
139A HIS* 3.8 27.6 - - + +
145A PHE* 3.5 5.2 - - + -
185A LEU* 4.7 0.2 - - - +
213A ILE* 1.3 80.3 - - - +
215A GLY* 1.3 59.9 + - - +
234A ARG* 3.5 9.9 - - + -
235A PHE* 3.7 30.7 - - + -
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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