Contacts of the strand formed by residues 263 - 270 (chain A) in PDB entry 5I4E
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 GLY 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A PHE* 1.3 84.1 - - - +
264A LYS* 1.3 61.4 + - - -
283A THR* 3.2 1.4 - - - -
284A TYR* 2.8 44.8 + - - -
478A ASP 3.8 7.0 - - - -
479A ILE* 4.0 15.0 - - - -
480A ALA* 4.2 2.6 - - - +
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A THR* 5.5 3.3 - - - +
208A THR* 3.6 12.7 - - - +
209A LYS* 5.9 0.8 - - - +
242A ASN* 3.4 29.5 - - - +
245A LEU* 4.5 10.1 - - + -
246A GLU* 5.8 5.6 - - - -
262A PHE* 3.9 28.9 - - + +
263A GLY* 1.3 75.3 - - - +
265A PHE* 1.3 60.9 + - - +
266A ILE* 3.6 26.5 - - + +
281A ILE* 4.9 2.5 - - + -
282A GLU 3.2 12.1 - - - +
283A THR* 4.1 3.6 - - + -
284A TYR* 4.2 4.6 - - - -
476A ILE 3.7 1.2 - - - +
477A LEU* 3.7 4.1 - - - +
478A ASP* 2.8 67.7 + - + +
479A ILE* 4.4 1.4 - - - +
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Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A SER* 5.4 0.7 - - - -
264A LYS* 1.3 74.3 - - - +
266A ILE* 1.3 62.3 + - - +
267A ARG* 3.3 38.1 - - + -
280A ASN 3.9 1.4 - - - +
282A GLU* 3.0 40.0 + - + +
284A TYR* 3.9 19.9 - - + +
473A PHE* 4.2 11.4 - + - -
475A GLY* 3.7 28.0 - - - -
476A ILE 3.7 2.0 - - - -
477A LEU* 4.4 16.2 - - + -
681A LEU* 3.5 22.0 - - + -
684A THR* 4.5 13.7 - - + -
685A LEU* 3.6 27.6 - - + -
688A THR* 5.7 0.9 - - + -
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Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A THR* 4.5 6.7 - - + -
212A ILE* 3.7 28.3 - - + -
238A LEU* 6.0 2.0 - - + -
242A ASN* 4.0 6.7 - - - +
264A LYS* 3.6 40.4 - - + +
265A PHE* 1.3 79.0 - - - +
267A ARG* 1.3 71.6 + - - +
268A ILE* 4.3 13.0 - - + -
279A ALA* 4.9 6.1 - - + -
280A ASN 3.5 9.4 - - - +
281A ILE* 4.5 16.8 - - + -
474A LEU 3.5 2.3 - - - +
475A GLY* 3.3 4.2 - - - -
476A ILE* 2.9 37.3 + - + +
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Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A PHE* 3.3 28.0 - - + -
266A ILE* 1.3 74.4 - - - +
268A ILE* 1.3 61.5 + - - +
269A ASN* 3.9 11.6 + - - +
279A ALA* 3.1 7.8 - - - +
280A ASN* 2.9 52.2 + - + +
282A GLU* 5.7 4.0 + - + +
469A GLN* 5.6 5.5 + - - +
473A PHE* 3.8 37.5 - - + -
474A LEU 3.8 4.0 - - - -
475A GLY* 4.5 0.2 - - - -
684A THR* 3.3 32.1 + - - +
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ILE* 4.4 14.6 - - + -
215A LEU* 3.8 19.7 - - + -
238A LEU* 5.1 10.1 - - + -
266A ILE* 4.3 11.7 - - + -
267A ARG* 1.3 78.1 - - - +
269A ASN* 1.3 62.2 + - - +
270A PHE* 3.5 27.7 - - + -
276A ILE* 3.8 28.7 - - + -
278A GLY 3.7 3.4 - - - +
279A ALA* 4.6 5.6 - - + -
473A PHE* 3.1 5.7 - - - -
474A LEU* 3.0 37.5 + - + +
476A ILE* 3.8 25.4 - - + -
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ARG* 4.5 12.2 + - - +
268A ILE* 1.3 71.7 - - - +
270A PHE* 1.3 54.4 + - - +
276A ILE* 3.5 4.3 - - - +
277A VAL* 2.7 39.5 + - + -
278A GLY* 2.8 24.9 + - - +
279A ALA* 4.9 5.3 - - - +
280A ASN* 5.2 6.5 - - - +
464A ASP* 5.0 9.7 + - - -
465A ARG 5.5 2.8 + - - +
467A PRO* 6.2 2.0 - - - +
469A GLN* 3.0 39.5 + - + +
472A SER 4.2 2.5 - - - -
473A PHE* 3.5 17.5 - - - +
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 4.0 6.5 - + - -
185A MET* 3.3 31.6 - - + -
215A LEU* 4.3 16.6 - - + -
219A ALA* 4.0 13.2 - - + -
268A ILE* 3.5 32.5 - - + -
269A ASN* 1.3 73.7 - - - +
271A ASP* 1.3 57.8 + - - +
274A GLY 3.9 8.3 - - - -
275A TYR 3.2 22.7 - - - +
276A ILE* 3.4 21.8 - - + -
277A VAL* 4.0 4.0 - - - -
469A GLN* 3.2 1.7 - - - +
470A GLY* 2.4 33.5 + - - -
472A SER* 3.8 17.3 + - - +
473A PHE* 4.3 2.5 - - - -
474A LEU* 3.6 24.5 - - + -
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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