Contacts of the strand formed by residues 161 - 165 (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 HIS 161 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101O GLY* 3.7 15.7 - - - -
102O HIS 3.4 22.9 - - - -
103O GLN* 3.9 3.3 + - - -
106O TRP* 3.6 18.2 - - + -
156O SER* 3.8 3.1 - - - -
158O ASP* 3.0 22.4 + - - -
159O VAL* 3.4 29.2 - - + +
160O LEU* 1.3 72.5 - - - +
162O SER* 1.3 60.2 + - - +
173O ASP* 3.5 4.0 - - - +
174O ALA* 2.6 35.4 + - + +
196O CYS* 3.9 2.9 - - - -
198O GLU* 3.6 11.8 - - - +
200O CYS* 3.2 19.0 - - + -
207O MET* 3.2 8.8 - - + +
301O CUA 2.0 32.6 - - - -
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Residues in contact with SER 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O TRP* 3.5 4.5 - - - -
161O HIS* 1.3 77.1 - - - +
163O TRP* 1.3 61.9 + - - +
164O ALA 3.6 1.3 + - - -
171O LYS* 3.4 21.7 - - - +
172O THR 3.6 6.9 + - - -
173O ASP* 2.7 26.8 + - - -
174O ALA 3.9 0.2 - - - +
196O CYS* 3.5 12.6 - - - -
197O SER* 2.8 47.3 + - - -
198O GLU* 3.8 3.8 - - - +
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Residues in contact with TRP 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O THR* 3.7 10.5 - - + -
106O TRP* 3.5 34.4 - + + -
108O TYR* 3.1 28.5 + + - -
142O VAL* 5.3 0.4 - - + -
152O MET* 3.7 34.8 - - + -
154O VAL* 4.0 17.0 - - + -
162O SER* 1.3 70.0 - - - +
164O ALA* 1.3 60.4 + - - +
165O VAL* 3.9 10.8 - - + -
170O LEU* 3.8 26.5 - - + -
171O LYS* 3.2 2.8 + - - -
172O THR* 2.8 39.8 + - - +
174O ALA 4.8 0.4 - - - +
182O THR* 5.3 3.4 - - + -
184O LEU* 4.0 11.7 - - + -
209O ILE* 3.5 20.7 - - + +
211O LEU* 3.6 32.3 - - + -
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Residues in contact with ALA 164 (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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162O SER 3.6 1.2 + - - -
163O TRP* 1.3 75.7 - - - +
165O VAL* 1.3 69.4 + - - +
166O PRO* 3.9 9.2 - - + -
170O LEU 3.3 11.4 - - - +
171O LYS* 3.9 15.9 - - + +
194O GLY* 3.1 21.7 - - - -
195O GLN 3.8 5.4 - - - +
197O SER* 3.3 26.0 - - - +
209O ILE* 3.4 14.5 - - - +
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Residues in contact with VAL 165 (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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163O TRP* 3.9 29.6 - - + -
164O ALA* 1.3 79.5 - - - +
166O PRO* 1.3 66.6 - - - +
167O SER* 4.3 4.3 - - - +
168O LEU* 3.2 33.7 + - + -
170O LEU* 3.0 34.3 + - + +
192O TYR* 4.2 18.2 - - + +
193O TYR 3.8 15.0 - - - +
194O GLY* 4.9 0.9 - - - -
209O ILE* 4.0 15.0 - - + -
211O LEU* 4.2 8.3 - - + -
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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