Contacts of the helix formed by residues 418 - 423 (chain A) in PDB entry 2JIR
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 ASN 418 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A THR* 1.3 74.3 - - - +
419A PRO* 1.4 58.2 - - - +
420A ALA 3.2 0.2 - - - -
421A HIS* 3.0 32.0 + - - +
422A THR* 3.1 10.4 + - - -
449A ALA* 3.8 28.3 - - + +
450A VAL* 3.7 4.3 + - - +
451A THR* 2.5 37.6 + - - -
624A THR* 3.2 29.2 + - + +
626A THR* 4.3 2.0 - - - +
811A MGD 2.8 33.0 + - - +
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Residues in contact with PRO 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 3.6 27.4 - - + -
401A PHE* 4.1 5.8 - - + -
414A ILE* 3.7 31.0 - - + -
417A THR* 3.5 11.9 - - - +
418A ASN* 1.4 82.6 - - - +
420A ALA* 1.3 58.4 + - - +
421A HIS 3.0 5.4 - - - -
422A THR* 3.7 9.9 - - - +
423A LEU* 3.0 50.2 + - + +
426A LEU* 3.8 2.3 - - - +
433A MET* 4.3 4.7 - - - +
451A THR* 3.4 9.4 - - + +
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Residues in contact with ALA 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A PRO* 1.3 78.4 - - - +
421A HIS* 1.3 57.1 + - - +
426A LEU* 3.3 9.1 - - - +
430A HIS* 2.6 26.5 + - - +
433A MET* 3.4 26.0 - - + -
450A VAL* 3.8 11.4 - - + +
451A THR* 2.9 26.1 + - - +
454A TYR* 3.7 23.6 - - + -
695A LEU* 4.1 1.2 - - - +
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Residues in contact with HIS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ASN* 3.0 20.8 + - - +
420A ALA* 1.3 81.5 - - - +
422A THR* 1.3 61.1 + - + +
423A LEU 3.8 1.1 - - - -
426A LEU* 3.6 13.9 - - - +
450A VAL* 3.8 10.0 - - + +
624A THR* 3.5 38.2 + - + +
689A PHE* 2.6 32.0 + + + +
690A PHE 3.9 6.5 - - - -
691A ASP 3.8 5.1 + - - -
692A PRO* 3.7 35.7 - - + +
695A LEU* 3.7 15.4 - - + +
696A VAL 5.8 0.6 + - - -
697A ASN* 3.4 14.2 + - - +
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Residues in contact with THR 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.0 5.6 - - - +
417A THR* 5.0 1.6 - - - +
418A ASN 3.1 7.1 + - - +
419A PRO* 3.7 3.5 - - - +
421A HIS* 1.3 82.2 - - + +
423A LEU* 1.3 63.5 + - - +
624A THR* 3.2 28.5 - - + -
689A PHE* 4.5 8.3 - - + -
697A ASN* 3.4 8.3 + - - +
713A TYR* 2.9 18.0 + - - -
811A MGD 2.6 67.4 + - - +
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Residues in contact with LEU 423 (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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107A TYR* 3.6 21.3 - - - +
139A LEU* 3.9 14.1 - - + -
397A THR* 3.6 20.2 - - + +
398A VAL* 5.9 2.5 - - + -
401A PHE* 3.6 30.3 - - + -
419A PRO* 3.0 31.8 + - + +
421A HIS 3.8 0.2 - - - -
422A THR* 1.3 77.4 + - - +
424A PRO* 1.3 71.2 - - + +
426A LEU* 3.4 8.0 - - + +
429A VAL* 3.5 37.0 - - + -
697A ASN* 3.1 20.3 - - - +
713A TYR* 4.1 0.4 - - - -
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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