Contacts of the strand formed by residues 366 - 370 (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 LEU 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A LEU* 4.0 16.4 - - + -
273A ILE* 3.7 16.6 - - + -
274A TYR 3.4 7.4 - - - +
275A ASN* 3.6 30.7 - - + -
276A LEU* 5.6 0.7 - - - -
363A ARG* 4.3 12.1 - - - +
365A SER* 1.3 80.5 - - - +
367A PHE* 1.3 61.6 + - - +
400A TYR* 3.5 24.5 - - - +
433A GLN* 3.6 8.7 - - - +
434A LEU* 2.9 44.0 + - + -
436A PHE* 4.1 24.2 - - + -
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Residues in contact with PHE 367 (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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272A GLY 3.4 3.3 - - - +
273A ILE* 3.5 2.6 - - - +
274A TYR* 2.6 49.2 + + + +
276A LEU* 3.7 26.2 - - + -
366A LEU* 1.3 76.5 - - - +
368A VAL* 1.3 61.8 + - - +
369A TYR* 3.9 8.3 - + + -
416A GLN* 3.3 32.8 - - - -
429A PRO* 3.6 10.8 - - + -
430A PRO 2.7 33.2 - - - -
431A GLY* 3.9 10.5 - - - -
432A PHE 3.6 12.1 - - - -
433A GLN* 4.9 1.3 - - + -
435B PHE* 3.8 46.9 - + - -
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Residues in contact with VAL 368 (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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261A LEU* 5.0 1.8 - - + -
271A VAL* 3.6 37.0 - - + -
272A GLY 3.7 2.0 - - - +
273A ILE* 3.7 18.2 - - + -
345A LEU* 4.8 4.9 - - + -
367A PHE* 1.3 78.9 - - - +
369A TYR* 1.3 61.8 + - - +
382A PHE* 3.2 13.6 - - + -
413A LEU* 4.5 18.2 - - + -
431A GLY* 3.7 2.9 - - - -
432A PHE* 2.7 44.2 + - + +
434A LEU* 3.8 25.6 - - + -
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Residues in contact with TYR 369 (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* 3.8 18.6 - - - -
271A VAL* 3.3 3.6 - - - -
272A GLY 2.7 34.7 + - - -
274A TYR* 3.6 22.7 - - + -
367A PHE* 3.9 3.3 + + + -
368A VAL* 1.3 75.1 - - - +
370A PRO* 1.3 92.7 - - + +
382A PHE* 3.8 4.0 - - - -
430A PRO* 3.5 24.9 - - + -
431A GLY* 5.0 0.4 - - - -
435B PHE* 3.3 34.3 - + + -
436B SER* 2.5 44.7 + - - -
438B LEU* 3.6 21.6 - - + +
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Residues in contact with PRO 370 (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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270A SER 3.8 6.7 - - - +
271A VAL* 4.2 0.7 - - - -
272A GLY 4.7 0.2 + - - -
274A TYR* 5.0 1.4 + - - -
369A TYR* 1.3 121.5 - - + +
371A GLU* 1.3 63.9 + - - +
372A GLU 3.7 2.7 + - - -
378A SER* 4.4 1.6 - - - -
379A SER* 3.8 38.3 + - - +
382A PHE* 3.6 37.0 - - + -
438B LEU* 4.0 15.3 - - + -
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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