Contacts of the strand formed by residues 343 - 348 (chain A) in PDB entry 5JEL
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 ALA 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A ALA 3.6 0.5 - - - +
295A VAL* 3.4 2.2 - - - -
296A SER 2.8 41.6 + - - +
297A GLU 3.8 18.4 - - - +
298A GLU* 4.1 4.5 - - - +
341A ARG 3.9 0.2 - - - -
342A TYR* 1.3 80.7 - - + +
344A LEU* 1.3 62.1 + - - +
345A TRP* 3.6 10.6 + - - +
366A LYS* 4.0 6.7 - - + -
367A VAL 3.9 4.5 - - - -
368A VAL* 3.9 20.2 - - + -
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 4.1 17.5 - - + -
281A LEU* 3.8 28.0 - - + -
293A TRP* 4.1 11.9 - - + -
294A ALA 3.6 1.3 - - - +
295A VAL* 3.5 28.7 - - + -
319A VAL* 3.8 32.5 - - + +
320A PHE* 4.6 4.9 - - + -
342A TYR 3.4 6.0 + - - +
343A ALA* 1.3 70.8 - - - +
345A TRP* 1.3 61.0 + - - +
346A PHE* 3.8 17.4 - - + -
365A VAL 3.6 1.0 - - - +
366A LYS* 3.3 3.1 - - - -
367A VAL* 2.8 45.6 + - + +
369A PRO* 5.3 2.5 - - + -
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Residues in contact with TRP 345 (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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209A PHE* 3.5 42.0 - + - -
293A TRP* 3.1 6.8 - - - +
294A ALA 2.9 35.1 + - - +
296A SER* 3.7 17.5 - - - -
297A GLU 3.0 18.8 + - - -
298A GLU 3.4 21.5 - - - -
299A LEU* 4.6 1.8 - - - -
300A LEU 4.4 2.0 - - - -
301A PRO* 3.4 47.6 - - + +
343A ALA* 3.6 16.5 - - + +
344A LEU* 1.3 75.0 - - - +
346A PHE* 1.3 61.6 + - - +
352A TRP* 3.7 10.4 - - + -
358A TRP* 4.4 9.9 - + - -
364A MET* 4.1 16.2 - - + -
365A VAL 3.4 9.6 - - - -
366A LYS* 3.5 25.9 - - + +
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Residues in contact with PHE 346 (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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228A LEU* 5.4 0.7 - - + -
272A LEU* 3.7 33.4 - - + -
274A LEU* 4.3 25.4 - - + -
283A ALA* 4.4 10.3 - - + -
291A THR* 3.9 12.8 - - + -
292A TYR 3.3 4.0 - - - -
293A TRP* 3.7 25.8 - + + -
311A VAL* 4.1 11.9 - - + -
319A VAL* 5.0 1.8 - - + -
344A LEU* 3.8 32.3 - - + -
345A TRP* 1.3 74.0 - - - +
347A CYS* 1.3 60.3 + - - +
348A VAL* 3.8 5.7 + - + +
363A VAL 3.8 0.2 - - - +
364A MET* 3.3 9.3 - - - +
365A VAL* 2.8 48.2 + - + +
367A VAL* 3.9 20.6 - - + -
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Residues in contact with CYS 347 (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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290A HIS 3.9 0.5 - - - +
291A THR* 3.3 5.3 - - - -
292A TYR* 2.8 31.7 + - + +
346A PHE* 1.3 69.5 - - - +
348A VAL* 1.3 62.2 + - - +
349A GLY 3.8 0.7 + - - -
350A GLU* 3.6 15.7 - - - +
351A SER 3.4 25.1 - - - -
352A TRP* 3.7 23.4 - - + -
353A PRO* 4.1 2.5 - - - -
361A ARG* 3.8 19.1 - - - -
363A VAL 4.7 0.9 - - - -
364A MET* 3.5 25.4 - - - -
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Residues in contact with VAL 348 (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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228A LEU* 5.4 1.6 - - + -
264A VAL* 3.7 21.6 - - + +
268A LEU* 3.8 32.1 - - + -
272A LEU* 4.5 9.0 - - + -
289A CYS* 4.1 6.1 - - + -
291A THR* 3.9 22.4 - - + +
346A PHE* 4.2 13.7 - - + +
347A CYS* 1.3 72.7 - - - +
349A GLY* 1.3 65.4 + - - +
350A GLU* 3.3 6.6 + - - +
362A LEU* 5.4 0.2 - - - +
363A VAL* 3.0 41.3 + - + +
365A VAL* 4.5 8.1 - - + -
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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