Contacts of the strand formed by residues 268 - 274 (chain A) in PDB entry 1JEQ
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 VAL 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LYS* 3.7 35.2 - - + -
261A LEU 3.9 6.3 - - - +
262A LYS* 3.5 24.2 - - + -
265A LYS 3.8 9.2 - - - +
266A ASP 2.6 21.0 + - - +
267A ILE* 1.3 77.8 - - - +
269A ILE* 1.3 72.5 + - - +
375A VAL* 3.8 19.1 - - + +
539B LEU* 3.5 19.3 - - - +
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Residues in contact with ILE 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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260A LYS* 3.7 0.7 - - - -
261A LEU* 2.8 63.7 + - + +
263A LEU* 5.2 3.6 - - + -
268A VAL* 1.3 85.8 - - - +
270A SER* 1.3 58.9 + - - +
271A VAL* 4.0 9.6 - - + -
375A VAL* 4.5 1.3 - - - -
378A SER* 3.6 17.7 - - - +
381A LEU* 3.5 35.2 - - + -
382A PHE* 4.1 33.0 - - + +
385A LEU* 5.1 7.4 - - + -
539B LEU* 4.4 5.6 - - + -
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Residues in contact with SER 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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259A LEU 3.4 9.4 - - - -
260A LYS* 4.8 2.5 - - - +
269A ILE* 1.3 73.3 - - - +
271A VAL* 1.3 65.7 + - - +
370A PRO* 3.8 0.3 - - - +
371A GLU* 2.6 46.1 + - - -
374A LEU* 3.8 25.8 - - - -
375A VAL* 3.4 20.6 + - - +
378A SER* 3.3 15.5 + - - -
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Residues in contact with VAL 271 (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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258A ARG* 3.2 5.4 - - - +
259A LEU* 2.9 38.9 + - + +
261A LEU* 4.0 13.9 - - + -
269A ILE* 4.0 18.2 - - + -
270A SER* 1.3 79.8 - - - +
272A GLY* 1.3 59.4 + - - +
273A ILE* 4.1 7.6 + - + -
345A LEU* 4.0 20.6 - - + -
368A VAL* 3.6 27.1 - - + -
369A TYR 3.3 13.2 - - - +
371A GLU* 3.8 6.5 - - - +
382A PHE* 4.1 12.6 - - + -
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Residues in contact with GLY 272 (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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255A ALA* 4.6 1.1 - - - -
257A SER 3.4 9.4 - - - -
258A ARG* 4.3 6.3 - - - -
271A VAL* 1.3 74.1 - - - +
273A ILE* 1.3 63.2 + - - +
274A TYR* 3.2 31.6 - - - -
367A PHE 3.4 1.6 - - - +
368A VAL* 3.7 2.8 - - - -
369A TYR 2.7 27.8 + - - -
371A GLU* 3.9 7.7 - - - +
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Residues in contact with ILE 273 (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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255A ALA 3.4 0.5 - - - -
256A LEU* 2.4 47.6 + - + +
257A SER* 2.9 28.4 + - - +
259A LEU* 3.9 20.2 - - + -
271A VAL* 4.2 7.2 - - + +
272A GLY* 1.3 75.3 - - - +
274A TYR* 1.3 56.7 + - - +
345A LEU* 4.2 15.7 - - + -
366A LEU* 3.7 36.3 - - + -
367A PHE 3.5 1.3 - - - +
368A VAL* 3.7 27.1 - - + -
400A TYR* 4.4 5.8 - - + +
434A LEU* 4.1 10.8 - - + -
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Residues in contact with TYR 274 (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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253A LYS* 4.0 24.3 + - + +
254A ARG 3.6 11.9 - - - +
255A ALA* 3.5 38.1 - - + +
256A LEU 4.2 2.5 - - - +
272A GLY* 3.2 28.7 - - - -
273A ILE* 1.3 73.9 - - - +
275A ASN* 1.3 61.2 + - - +
276A LEU* 3.7 12.8 - - + -
366A LEU* 3.4 8.2 - - - +
367A PHE* 2.6 58.5 + + + +
369A TYR* 3.6 14.3 - - + +
370A PRO 5.0 0.5 + - - -
371A GLU* 4.4 13.3 + - - -
433B TYR* 4.5 4.5 - + + -
435B PHE* 3.6 36.8 - + + -
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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