Contacts of the strand formed by residues 266 - 270 (chain G) in PDB entry 2I3T
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 LEU 266 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ALA* 4.4 4.5 - - + -
218G VAL* 4.0 26.5 - - + -
238G PHE* 4.6 4.0 - - + -
257G ILE* 4.2 13.7 - - + -
258G GLU* 3.6 20.9 - - - +
259G PHE* 3.5 38.8 - - + -
265G PHE* 1.3 71.7 - - - +
267G TYR* 1.3 59.4 + - - +
268G THR* 4.1 15.9 - - + -
278G TRP* 2.7 52.8 + - + +
280G LEU* 4.0 27.5 - - + +
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Residues in contact with TYR 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257G ILE* 3.2 5.9 - - - +
258G GLU 2.7 40.7 + - - +
260G SER* 3.6 25.8 - - - -
265G PHE* 3.7 19.2 - - + -
266G LEU* 1.3 72.6 - - - +
268G THR* 1.3 60.2 + - - +
275G ILE* 4.3 3.1 - - + -
276G SER 3.3 13.2 - - - +
277G CYS* 3.7 24.8 - - + -
287G LYS* 5.9 0.4 - - + +
289G PHE* 3.9 24.7 - + - -
300G ILE* 3.3 18.2 - - + +
302G CYS* 4.1 11.0 - - - -
307G LEU* 3.6 18.4 - - + -
339G TYR* 3.5 24.1 + + - -
340G GLU* 3.0 23.6 + - - +
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Residues in contact with THR 268 (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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218G VAL* 4.0 18.4 - - + -
240G CYS* 5.0 0.4 - - - +
241G HIS* 3.0 22.2 + - - -
254G VAL* 3.9 8.1 - - - -
256G SER 3.5 3.8 - - - -
257G ILE* 3.6 18.4 - - + -
266G LEU* 4.1 10.3 - - + -
267G TYR* 1.3 76.0 - - - +
269G ALA* 1.3 58.8 + - - +
275G ILE* 3.2 5.6 - - - +
276G SER* 2.9 32.7 + - - +
278G TRP* 2.9 33.3 + - + +
300G ILE* 4.5 1.8 - - - -
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Residues in contact with ALA 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G HIS* 4.0 2.2 - - - -
254G VAL* 3.5 3.1 - - - +
255G ASN* 2.9 25.5 + - - +
256G SER* 2.8 22.5 + - - +
268G THR* 1.3 74.5 - - - +
270G GLY* 1.3 59.9 + - - +
274G ILE 3.8 4.5 - - - -
275G ILE* 4.2 1.6 - - + -
297G VAL* 3.3 35.2 - - + +
299G LYS 5.1 0.2 - - - +
300G ILE* 3.6 19.1 - - + -
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Residues in contact with GLY 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G HIS* 3.3 21.9 - - - -
253G PRO 3.2 11.4 - - - -
254G VAL* 4.2 0.4 - - - -
255G ASN* 3.6 5.4 - - - -
269G ALA* 1.3 75.4 - - - +
271G SER* 1.3 58.2 + - - -
272G ASP* 3.0 10.4 + - - +
273G GLY* 3.2 6.6 + - - -
274G ILE 3.2 10.9 + - - -
297G VAL* 3.2 22.0 + - - +
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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