Contacts of the strand formed by residues 263 - 271 (chain E) in PDB entry 3IT8
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 TYR 263 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E ASP* 2.5 38.6 + - + +
206E SER* 2.8 21.5 + - - -
207E PHE* 2.8 34.4 + - + -
208E TYR* 3.8 9.0 - + - -
210E PRO* 3.8 26.7 - - + -
254E ILE* 3.9 17.0 - - + -
255E LYS* 3.7 3.4 - - - -
256E LYS* 3.6 45.7 + - + +
257E ASP* 3.4 4.9 - - - -
261E ASN 3.3 15.3 - - - -
262E THR* 1.3 81.8 + - - +
264E SER* 1.3 61.7 + - - +
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Residues in contact with SER 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E VAL 3.5 8.3 - - - -
205E ASN* 3.8 11.5 + - - +
206E SER* 3.0 13.2 + - - -
207E PHE* 3.7 2.9 - - - -
253E ASN 3.7 0.5 - - - +
254E ILE* 3.2 5.7 - - - +
255E LYS* 3.0 36.7 + - - +
257E ASP* 2.8 27.9 + - - +
258E LYS* 5.3 0.9 + - - -
263E TYR* 1.3 71.6 - - - +
265E LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E CYS 5.1 0.2 - - - +
203E THR* 3.3 2.8 - - - -
204E VAL* 2.8 50.1 + - + +
205E ASN* 5.2 0.5 - - - +
207E PHE* 3.7 15.2 - - + -
212E VAL* 3.5 32.8 - - + +
214E THR* 5.1 6.5 - - - -
252E TRP* 4.3 20.0 - - + -
253E ASN 3.3 29.2 - - - +
254E ILE* 4.0 10.5 - - + -
264E SER* 1.3 75.8 - - - +
266E THR* 1.3 88.6 + - - +
267E ASP* 4.2 9.2 - - + +
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Residues in contact with THR 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E GLU* 3.9 32.1 + - + +
202E CYS 3.6 4.3 - - - +
203E THR* 4.2 8.1 - - + +
253E ASN* 3.1 37.0 + - + +
265E LEU* 1.3 83.2 + - - +
267E ASP* 1.3 62.6 + - - +
268E LEU* 4.1 4.5 + - + +
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Residues in contact with ASP 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E GLU* 3.4 1.9 - - - -
202E CYS* 2.7 49.0 + - + +
214E THR* 2.9 27.4 - - + +
216E TRP* 2.7 32.6 + - - -
239E ARG* 3.4 31.2 + - - -
252E TRP* 3.7 8.1 - - - -
253E ASN 5.9 0.7 + - - -
265E LEU* 4.2 12.2 - - + +
266E THR* 1.3 74.8 - - - +
268E LEU* 1.3 64.2 + - - +
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Residues in contact with LEU 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E ASN* 5.2 0.2 - - - +
193E LEU* 4.1 22.2 - - + -
199E THR* 3.8 24.5 - - + +
200E LEU 3.3 14.4 - - - +
201E GLU* 3.4 32.1 - - + +
239E ARG* 4.8 7.3 + - - -
266E THR* 4.1 5.0 + - + -
267E ASP* 1.3 79.8 + - - +
269E VAL* 1.3 73.5 + - - +
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Residues in contact with VAL 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E THR* 3.3 7.5 + - - -
200E LEU* 2.7 40.3 + - + +
216E TRP* 3.0 55.9 - - + +
237E TRP* 5.3 8.5 - - + -
239E ARG* 5.3 5.4 - - - -
267E ASP* 4.4 0.2 - - - +
268E LEU* 1.3 81.2 - - - +
270E ARG* 1.3 70.6 + - - +
271E THR* 3.2 6.9 + - - +
275E MET* 5.3 0.7 - - + -
279E PRO* 4.7 13.7 - - + -
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Residues in contact with ARG 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E LEU* 6.1 6.1 - - + +
195E ASP* 3.2 22.6 + - - -
196E GLY* 2.9 38.0 - - - +
197E ASN* 3.5 17.2 + - - +
198E MET 4.3 6.0 + - - -
199E THR* 4.6 4.7 - - - +
269E VAL* 1.3 77.3 - - - +
271E THR* 1.3 53.5 + - - +
272E THR* 2.7 42.6 + - - +
275E MET* 4.4 4.0 - - - +
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Residues in contact with THR 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E ASN* 2.5 32.0 + - - +
198E MET* 2.9 44.5 + - + +
200E LEU* 3.6 34.2 + - + +
269E VAL* 3.2 3.1 + - - +
270E ARG* 1.3 67.9 - - - +
272E THR* 1.3 53.8 + - - +
275E MET* 3.8 28.9 - - - -
278E GLN* 5.2 4.7 - - + -
279E PRO* 4.8 4.0 - - + +
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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
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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