Contacts of the helix formed by residues 343 - 351 (chain A) in PDB entry 1JB0
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 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A GLU* 4.7 3.0 + - - -
341A HIS 3.4 0.6 + - - -
342A LYS* 1.3 77.7 - - - +
344A LEU* 1.3 63.9 + - - +
345A TYR* 3.2 3.7 - - - +
346A GLU* 3.3 25.6 + - - +
347A VAL* 3.0 28.0 + - - +
424A MET* 3.6 19.3 - - - +
428A ASN* 4.6 1.1 - - - -
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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
----------------------------------------------------------
329A LEU* 4.5 9.9 - - + -
341A HIS* 3.2 35.6 + - + +
342A LYS 3.2 2.2 - - - +
343A GLY* 1.3 74.2 - - - +
345A TYR* 1.3 59.9 + - - +
347A VAL* 3.5 10.3 - - + +
348A LEU* 2.8 36.9 + - + +
425A ASN* 4.3 7.2 - - - +
428A ASN* 4.2 15.3 - - - +
429A VAL* 3.9 11.0 - - + -
430A LEU* 4.4 8.3 - - + -
1122A CLA 3.6 57.0 - - + -
4007A BCR 4.7 7.2 - - + -
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Residues in contact with TYR 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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191A GLN 4.5 4.9 + - - -
193A VAL* 3.3 21.6 - - + +
194A GLU* 3.2 24.2 + - - -
325A LEU* 3.7 24.7 - - + -
326A LYS* 3.6 51.4 - - + -
329A LEU* 3.9 17.8 - - + +
341A HIS 4.6 0.2 + - - -
343A GLY 3.2 1.4 - - - +
344A LEU* 1.3 78.7 - - - +
346A GLU* 1.3 62.2 + - + +
348A LEU* 3.5 2.3 + - - +
349A THR* 2.8 54.7 + - + -
1123A CLA 4.3 11.3 - - + +
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Residues in contact with GLU 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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326A LYS* 3.5 27.0 - - - -
330A GLU* 4.4 4.9 - - - +
342A LYS* 5.4 3.5 + - - +
343A GLY* 3.3 30.9 + - - +
344A LEU 3.3 0.2 - - - -
345A TYR* 1.3 82.6 - - + +
347A VAL* 1.3 61.9 + - - +
349A THR* 4.0 9.6 - - + -
350A THR* 2.8 37.1 + - + +
424A MET* 3.8 20.0 - - + -
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLY 3.0 17.0 + - - +
344A LEU* 3.5 16.8 - - + +
345A TYR 3.2 0.2 - - - -
346A GLU* 1.3 77.1 - - - +
348A LEU* 1.3 59.7 + - + +
349A THR 3.1 0.3 + - - -
350A THR* 4.2 1.6 - - - -
351A SER* 3.1 33.0 + - - -
354A ALA* 4.1 10.1 - - + -
415A PHE* 3.6 33.9 - - + -
424A MET* 3.9 17.7 - - - -
425A ASN* 3.6 26.7 - - - +
430A LEU* 5.0 0.4 - - + -
4007A BCR 4.7 10.3 - - + -
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Residues in contact with LEU 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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193A VAL* 4.8 1.0 - - - +
344A LEU* 2.8 21.5 + - + +
345A TYR 3.7 0.7 - - - -
347A VAL* 1.3 77.4 - - + +
349A THR* 1.3 58.0 + - - +
350A THR 3.6 0.4 - - - -
351A SER 4.7 1.1 - - - -
354A ALA* 3.9 26.7 - - + -
355A GLN* 3.1 34.2 + - - +
358A ILE* 3.6 25.4 - - + -
1122A CLA 4.0 16.4 - - + -
1123A CLA 3.5 66.6 - - + +
4007A BCR 4.0 8.3 - - + -
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Residues in contact with THR 349 (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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191A GLN* 3.2 34.8 + - + +
193A VAL* 4.1 17.7 - - - +
345A TYR* 2.8 39.9 + - + +
346A GLU* 3.7 9.9 - - + +
347A VAL 3.0 1.0 - - - -
348A LEU* 1.3 77.5 - - - +
350A THR* 1.3 72.6 + - + +
1123A CLA 3.5 19.2 - - - +
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Residues in contact with THR 350 (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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65A LEU* 3.9 24.4 - - + +
191A GLN* 4.4 8.3 - - - +
346A GLU* 2.8 25.7 + - + +
347A VAL* 3.8 4.0 + - - -
349A THR* 1.3 95.0 - - + +
351A SER* 1.3 59.8 + - - +
352A TRP 4.1 0.5 + - - -
419A ASP* 5.1 2.6 - - - +
424A MET* 4.4 13.4 - - + +
1123A CLA 3.6 11.4 - - - +
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Residues in contact with SER 351 (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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347A VAL* 3.1 16.2 + - - +
348A LEU 4.9 0.3 - - - +
350A THR* 1.3 80.4 - - - +
352A TRP* 1.3 63.2 + - - +
354A ALA* 3.0 29.3 + - - +
355A GLN* 3.5 15.9 + - - +
415A PHE* 3.2 12.1 - - - -
419A ASP* 2.5 37.6 + - - -
1123A CLA 3.7 3.5 - - - +
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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