Contacts of the strand formed by residues 213 - 217 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G ILE* 4.0 1.0 - - - +
103G CYS* 3.1 14.9 - - + +
105G VAL* 5.4 0.4 - - + -
203G LEU* 3.9 19.1 - - + -
206G LEU* 3.8 26.7 - - + -
208G ARG* 3.6 16.6 + - - +
209G ASP 3.1 14.4 + - - -
210G LEU* 3.7 14.5 + - + +
211G ARG 3.8 0.6 - - - -
212G LYS* 1.3 80.1 + - - +
214G LEU* 1.3 70.3 + - - +
229G ASN* 2.8 25.9 + - - -
261G VAL* 3.4 12.6 - - - +
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Residues in contact with LEU 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G ILE* 4.1 16.4 - - + -
103G CYS 2.7 8.6 + - - +
104G VAL* 3.4 12.7 - - + -
105G VAL* 2.8 28.5 + - - +
157G PHE* 5.0 1.8 - - + -
203G LEU* 4.8 0.4 - - - -
213G THR* 1.3 84.8 - - - +
215G ILE* 1.3 61.6 + - - +
229G ASN* 3.3 16.8 - - - +
231G VAL* 4.0 13.9 - - + -
252G PHE* 4.1 21.1 - - + -
255G LEU* 4.1 24.0 - - + -
261G VAL* 3.9 18.8 - - + -
265G LEU* 3.8 28.7 - - + -
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Residues in contact with ILE 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G VAL* 3.5 27.1 - - + +
201G LYS* 4.1 26.5 - - + +
203G LEU* 4.0 26.9 - - + -
214G LEU* 1.3 74.7 - - - +
216G LEU* 1.3 60.2 + - - +
217G ASP* 4.0 19.5 + - + +
222G SER 4.6 0.9 - - - +
223G TYR* 4.0 26.6 - - + -
229G ASN* 2.8 24.2 + - + +
230G ALA* 3.4 18.4 - - + +
231G VAL* 2.7 34.7 + - - +
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Residues in contact with LEU 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G VAL* 4.6 4.9 - - + +
105G VAL 2.9 13.6 + - - +
106G ILE* 3.6 23.9 - - + +
107G ASP* 3.2 24.3 + - - +
111G THR* 4.3 10.8 - - + +
112G LEU* 5.1 1.3 - - + -
149G PHE* 4.0 28.9 - - + -
214G LEU 4.2 0.4 - - - -
215G ILE* 1.3 73.2 - - - +
217G ASP* 1.3 61.4 + - - +
231G VAL* 3.2 18.6 - - + +
232G PRO 4.6 0.2 - - - -
233G VAL* 3.7 26.0 - - + -
245G LEU* 4.9 6.1 - - + -
248G LEU* 4.0 14.6 - - + -
252G PHE* 4.0 21.8 - - + -
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Residues in contact with ASP 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MG 3.3 12.3 - - - -
107G ASP* 3.2 11.2 - - - +
111G THR* 4.0 5.8 - - - -
201G LYS* 2.6 32.9 + - - +
215G ILE* 4.0 7.8 + - + +
216G LEU* 1.3 76.3 - - - +
218G ASN* 1.3 63.9 + - - +
219G SER* 2.8 27.4 + - - -
222G SER* 3.3 15.2 + - - -
223G TYR* 4.1 26.4 + - + -
231G VAL 3.9 2.4 + - - -
232G PRO* 3.8 7.3 - - - +
233G VAL* 3.3 21.9 + - - -
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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
------------------------------------------------------------
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