Contacts of the helix formed by residues 461 - 468 (chain A) in PDB entry 2JI8
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 GLU 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.4 12.9 - - + -
54A ARG* 3.0 20.0 + - - +
55A HIS* 3.1 25.8 + - - +
58A HIS* 3.4 39.3 - - + +
432A MET* 3.5 16.2 - - + +
436A VAL* 5.6 0.4 - - + -
458A SER 3.3 15.5 - - - +
459A GLY 2.9 1.2 + - - -
460A MET* 1.3 75.3 - - + +
462A LEU* 1.3 63.6 + - - +
463A GLU 3.1 1.3 - - - +
464A THR* 2.8 32.0 + - - +
465A ILE* 3.0 28.3 + - - +
456B GLY 5.0 0.2 - - - +
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Residues in contact with LEU 462 (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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432A MET* 4.1 10.6 - - - +
455A PHE* 3.5 18.4 - - + -
459A GLY 3.0 16.7 + - - +
460A MET 4.7 0.2 - - - +
461A GLU* 1.3 75.6 - - - +
463A GLU* 1.3 57.1 + - - +
465A ILE* 3.1 9.5 + - + +
466A CYS* 2.9 33.3 + - - -
474A VAL* 3.9 28.0 - - + -
505A TYR* 4.7 0.4 - - + +
508A MET* 4.2 24.2 - - + -
509A MET* 3.9 30.7 - - + +
512A PHE* 4.9 5.8 - - + -
540A LEU* 3.4 26.9 - - + -
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Residues in contact with GLU 463 (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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54A ARG* 3.2 29.7 + - + +
460A MET* 3.4 16.1 + - + +
461A GLU 3.1 0.6 - - - -
462A LEU* 1.3 78.4 - - - +
464A THR* 1.3 54.1 + - - +
466A CYS* 3.4 1.9 + - - +
467A ARG* 2.8 62.2 + - - +
512A PHE* 3.6 42.2 - - + -
500B LEU* 4.2 1.1 - - - +
501B THR* 2.5 43.7 + - - +
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Residues in contact with THR 464 (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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52A SER 3.4 20.6 - - - +
53A PHE* 3.8 18.0 - - + -
54A ARG* 3.6 7.8 - - - +
436A VAL* 4.3 13.0 - - + -
461A GLU* 2.8 35.4 + - - +
463A GLU* 1.3 77.7 - - - +
465A ILE* 1.3 65.9 + - - +
467A ARG* 3.2 18.7 + - - +
468A TYR* 3.1 41.4 + - + -
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Residues in contact with ILE 465 (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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432A MET* 3.6 36.1 - - + -
435A CYS* 4.3 16.2 - - + -
436A VAL* 3.9 18.4 - - + -
461A GLU 3.0 16.8 + - - +
462A LEU* 3.1 15.2 + - + +
464A THR* 1.3 77.5 - - - +
466A CYS* 1.3 59.4 + - - +
468A TYR 3.7 0.5 + - - -
469A ASN 3.3 2.6 + - - -
470A LEU* 3.2 33.3 + - + +
472A VAL* 3.9 31.2 - - + -
474A VAL* 4.6 0.9 - - + -
509A MET* 4.7 6.5 - - + -
538A PRO* 3.9 19.4 - - + +
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Residues in contact with CYS 466 (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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462A LEU 2.9 16.8 + - - +
463A GLU 3.6 7.6 - - - +
465A ILE* 1.3 74.7 - - - +
467A ARG* 1.3 61.0 + - - +
468A TYR 3.2 0.4 - - - -
469A ASN* 2.9 23.4 + - - +
509A MET* 3.5 27.4 - - - -
512A PHE* 3.4 28.7 - - + +
513A GLY 4.8 1.1 - - - -
514A GLY* 3.6 24.5 - - - +
538A PRO* 3.9 13.9 - - + +
501B THR* 5.1 0.9 - - - +
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Residues in contact with ARG 467 (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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52A SER* 3.2 30.3 + - - -
53A PHE 4.5 0.8 + - - -
54A ARG* 3.8 10.1 - - - +
463A GLU* 2.8 53.7 + - - +
464A THR* 3.2 23.6 + - - +
466A CYS* 1.3 72.4 - - - +
468A TYR* 1.3 85.8 + - + +
469A ASN* 3.5 1.2 - - - +
495B ILE* 3.8 32.3 - - + +
496B SER 5.6 0.8 + - - -
499B ARG 3.4 27.1 + - - -
500B LEU* 3.9 13.0 - - - +
501B THR* 3.9 10.7 + - - +
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Residues in contact with TYR 468 (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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50A PHE 3.6 11.3 + - - -
51A TYR* 3.8 32.1 - + + -
52A SER* 2.9 37.6 + - - -
436A VAL* 5.5 0.2 - - + -
464A THR* 3.1 31.3 + - + +
466A CYS 3.2 0.6 - - - -
467A ARG* 1.3 105.3 + - + +
469A ASN* 1.3 71.2 + - - +
470A LEU* 3.2 30.6 + - + +
495B ILE* 3.6 30.7 + - + +
496B SER 5.1 2.4 + - - -
497B CYS* 5.2 1.0 - - - -
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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