Contacts of the helix formed by residues 425 - 433 (chain A) in PDB entry 2JIP
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 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A PRO* 1.3 75.9 - - - +
426A LEU* 1.3 64.2 + - - +
427A ASN* 3.4 4.1 + - - +
428A LYS* 3.2 34.4 + - + +
429A VAL* 3.3 9.7 + - - +
667A ARG* 3.7 35.8 - - - +
697A ASN 2.9 4.7 + - - -
698A LYS* 4.7 2.9 - - - +
700A PHE 2.9 22.4 + - - +
701A LEU* 4.2 4.8 - - - +
702A ASP* 3.6 35.4 + - + +
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Residues in contact with LEU 426 (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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419A PRO 3.9 7.0 - - - +
420A ALA 3.0 35.4 - - - +
421A HIS 3.7 12.3 - - - +
423A LEU 3.3 24.7 - - - +
424A PRO 3.5 0.2 - - - -
425A ASN* 1.3 67.5 - - - +
427A ASN* 1.3 59.1 + - - +
429A VAL* 2.9 7.2 + - + +
430A HIS* 2.7 56.9 + - + +
695A LEU* 3.6 31.6 - - + +
697A ASN* 2.7 23.2 + - + +
698A LYS* 3.6 13.4 - - + +
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Residues in contact with ASN 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ASN* 3.4 3.7 + - - +
426A LEU* 1.3 76.6 - - - +
428A LYS* 1.3 64.5 + - - +
430A HIS* 4.0 7.4 + - - +
431A LYS* 3.2 37.5 + - - +
667A ARG* 3.1 20.8 + - - +
668A ASP* 2.7 30.9 + - - +
698A LYS* 3.7 29.2 + - - +
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Residues in contact with LYS 428 (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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398A VAL* 4.8 2.6 - - - +
402A GLU* 2.8 43.1 + - - -
425A ASN* 3.2 27.6 + - - +
427A ASN* 1.3 79.0 - - - +
429A VAL* 1.3 65.2 + - + +
431A LYS* 3.6 10.4 + - - +
432A ALA* 3.2 20.4 + - + +
702A ASP* 2.8 28.4 + - - +
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Residues in contact with VAL 429 (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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401A PHE* 4.1 14.4 - - + -
419A PRO 4.6 1.6 - - - +
423A LEU* 3.5 37.5 - - + -
424A PRO 3.4 16.8 - - - +
425A ASN* 3.3 15.2 + - + +
426A LEU* 2.9 12.2 + - + +
428A LYS* 1.3 81.3 - - + +
430A HIS* 1.3 55.7 + - - +
432A ALA* 3.1 7.8 + - - +
433A MET* 2.8 59.7 + - + +
702A ASP* 5.7 0.7 - - - +
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Residues in contact with HIS 430 (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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420A ALA* 2.7 28.7 + - + +
426A LEU* 2.7 44.8 + - + +
427A ASN* 4.0 7.3 + - - +
429A VAL* 1.3 68.5 - - - +
431A LYS* 1.3 63.0 + - - +
433A MET* 3.3 26.6 + - + -
434A SER* 2.9 29.1 + - - -
450A VAL* 5.4 1.0 - - + +
454A TYR* 3.2 26.9 + + + +
695A LEU* 4.2 13.9 - - + +
698A LYS* 4.7 12.1 - - - -
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Residues in contact with LYS 431 (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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427A ASN* 3.2 29.0 + - - +
428A LYS* 3.6 7.6 - - - +
430A HIS* 1.3 76.0 - - - +
432A ALA* 1.3 65.8 + - - +
434A SER* 3.1 17.4 + - - -
435A HIS* 3.5 7.8 + - - +
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Residues in contact with ALA 432 (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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401A PHE* 3.2 29.8 - - + +
402A GLU* 5.2 1.3 - - - -
404A LEU* 3.4 18.6 - - + +
405A GLY* 3.7 17.4 - - - -
428A LYS* 3.2 11.7 + - + +
429A VAL* 3.1 13.2 + - - +
431A LYS* 1.3 79.9 - - - +
433A MET* 1.3 61.0 + - + +
434A SER 3.2 0.9 + - - -
435A HIS* 3.5 13.7 + - - +
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Residues in contact with MET 433 (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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72A LYS* 4.5 4.5 + - - -
401A PHE* 4.0 29.4 - - + -
404A LEU* 3.8 10.8 - - + -
414A ILE* 5.4 5.2 - - - -
419A PRO* 4.7 5.2 - - - -
420A ALA* 3.5 31.9 - - + -
429A VAL* 2.8 33.3 + - + +
430A HIS* 3.3 35.0 + - + +
431A LYS 3.2 0.6 - - - -
432A ALA* 1.3 72.7 - - - +
434A SER* 1.3 58.7 + - - +
435A HIS 3.4 1.0 + - - -
438A SER* 4.2 4.0 + - - -
440A ILE* 3.5 21.7 - - + +
451A THR* 5.4 1.8 - - - -
454A TYR* 3.9 31.3 - - + +
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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