Contacts of the strand formed by residues 209 - 214 (chain O) in PDB entry 2DYS
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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O TRP* 3.6 22.4 - - + +
108O TYR* 3.9 7.6 - - + +
120O SER* 5.8 0.9 - - - -
138O VAL* 5.0 0.2 - - - -
163O TRP* 3.5 49.8 - - + +
164O ALA 3.4 35.2 - - - +
165O VAL* 4.0 13.2 - - + -
193O TYR* 3.5 4.7 - - - +
194O GLY 2.8 32.2 + - - +
195O GLN 4.1 16.2 - - - +
208O PRO* 1.3 78.9 - - - +
210O VAL* 1.3 65.4 + - - +
211O LEU* 4.0 7.4 - - + -
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Residues in contact with VAL 210 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120O SER* 5.6 0.6 + - - -
136O LEU 3.1 28.0 - - - +
137O GLU* 4.4 0.7 - - - -
138O VAL* 3.6 32.9 - - + +
141O ARG* 3.7 28.6 - - + +
142O VAL* 2.9 29.3 + - - +
191O LEU* 4.6 3.4 - - + -
192O TYR 3.5 3.6 - - - +
193O TYR* 3.5 31.2 - - + -
209O ILE* 1.3 78.9 - - - +
211O LEU* 1.3 69.9 + - - +
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Residues in contact with LEU 211 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142O VAL* 3.5 22.9 - - + +
144O LEU* 3.9 10.3 - - + -
163O TRP* 3.6 29.4 - - + -
165O VAL* 4.2 13.2 - - + -
168O LEU* 3.5 31.9 - - + -
184O LEU* 3.6 17.9 - - + -
190O GLY 3.5 0.9 - - - +
191O LEU* 3.2 8.3 - - - +
192O TYR* 2.8 41.3 + - + +
209O ILE* 4.0 6.1 - - + -
210O VAL* 1.3 76.5 - - - +
212O GLU* 1.3 61.3 + - - +
213O LEU* 3.5 15.2 - - + +
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Residues in contact with GLU 212 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141O ARG* 3.1 32.8 + - + -
142O VAL 2.8 12.5 + - - +
143O VAL* 3.4 14.0 - - + +
144O LEU 2.8 28.6 + - - +
190O GLY 3.4 2.9 - - - -
191O LEU* 3.7 5.7 - - + +
210O VAL 4.1 0.2 + - - -
211O LEU* 1.3 72.3 - - - +
213O LEU* 1.3 61.0 + - - +
214O VAL* 3.7 6.8 + - + -
69V PHE* 3.5 25.6 - - + -
70V GLN* 2.9 31.1 + - - +
71V SER* 2.9 36.2 + - - -
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Residues in contact with LEU 213 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144O LEU* 3.4 25.6 - - + +
145O PRO 3.8 18.4 - - - +
146O MET* 4.1 3.8 - - + -
150O ILE* 4.8 0.2 - - + -
168O LEU* 5.5 0.4 - - + -
184O LEU* 4.6 6.7 - - + -
186O SER* 3.5 31.2 - - - +
188O ARG 3.6 16.2 - - - +
189O PRO* 3.1 9.6 - - + +
190O GLY 2.7 37.5 + - - +
192O TYR* 3.8 15.0 - - + -
211O LEU* 3.5 33.0 - - + -
212O GLU* 1.3 74.6 - - - +
214O VAL* 1.3 65.9 + - - +
69V PHE* 3.9 2.8 - - - -
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Residues in contact with VAL 214 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143O VAL* 4.1 15.3 - - + -
144O LEU 3.0 10.1 + - - +
145O PRO* 3.2 5.7 - - - +
146O MET* 2.7 28.8 + - - -
212O GLU* 4.0 17.0 - - + +
213O LEU* 1.3 81.2 - - - +
215O PRO* 1.4 80.4 - - + +
218O TYR* 4.0 8.7 - - + -
219O PHE* 3.8 16.6 - - - +
60V PHE* 3.8 15.9 - - + -
69V PHE* 4.2 7.0 - - + -
71V SER* 3.7 17.0 - - - +
72V ALA* 4.9 1.3 - - + -
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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