Contacts of the strand formed by residues 213 - 216 (chain D) in PDB entry 2Q5E
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 THR 213 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D CYS* 3.1 9.3 - - - +
105D VAL* 5.5 0.2 - - + -
203D LEU* 3.7 29.2 - - + +
206D LEU* 3.8 21.9 - - + +
208D ARG* 3.4 18.5 + - - +
209D ASP 3.0 19.3 + - - -
210D LEU* 3.9 9.6 + - + -
211D ARG 3.7 2.0 - - - -
212D LYS* 1.3 75.3 + - - +
214D LEU* 1.3 75.9 + - - +
229D ASN* 2.8 28.1 + - - -
261D VAL* 3.9 4.2 - - - +
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Residues in contact with LEU 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ILE* 3.8 21.5 - - + -
103D CYS 2.9 8.1 + - - +
104D VAL* 3.7 16.2 - - + -
105D VAL* 3.2 26.1 + - - +
157D PHE* 4.2 3.6 - - + -
203D LEU* 5.0 0.4 - - - -
213D THR* 1.3 84.4 - - - +
215D ILE* 1.3 65.7 + - - +
229D ASN 3.5 13.9 - - - +
231D VAL* 4.4 5.8 - - + -
252D PHE* 3.3 32.3 - - + -
255D LEU* 3.6 22.2 - - + -
261D VAL* 3.9 14.8 - - + -
265D LEU* 3.8 23.3 - - + -
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Residues in contact with ILE 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D VAL* 3.4 24.0 - - + +
106D ILE* 5.6 0.2 - - - -
107D ASP 5.9 0.2 - - - +
201D LYS* 3.7 39.5 - - + +
203D LEU* 4.0 22.0 - - + -
214D LEU* 1.3 81.0 - - - +
216D LEU* 1.3 63.5 + - - +
217D ASP* 4.0 20.2 + - + +
222D SER* 4.7 0.7 - - - -
223D TYR* 4.1 25.7 - - + -
226D HIS 4.9 0.2 - - - +
229D ASN* 3.1 15.5 + - + +
230D ALA* 3.5 11.2 - - + +
231D VAL* 2.8 27.2 + - - +
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Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D VAL* 4.7 2.2 - - + +
105D VAL 2.9 10.7 + - - +
106D ILE* 3.5 27.1 - - + -
107D ASP* 3.1 24.3 + - - +
111D THR* 4.1 12.7 - - + +
112D LEU* 4.9 1.1 - - + -
149D PHE* 3.6 32.3 - - + -
215D ILE* 1.3 72.2 - - - +
217D ASP* 1.3 61.1 + - - +
231D VAL* 3.3 25.1 - - + +
233D VAL* 4.2 9.2 - - + -
245D LEU* 5.2 2.0 - - + -
248D LEU* 3.5 27.8 - - + -
252D PHE* 4.4 15.5 - - + -
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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