Contacts of the helix formed by residues 455 - 469 (chain A) in PDB entry 1JEQ
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 THR 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A MET 5.1 3.1 - - - +
454A ALA* 1.3 76.5 - - - +
456A PRO* 1.3 69.8 - - - +
457A GLU* 3.6 8.7 + - - +
458A GLN* 2.8 57.5 + - - +
459A VAL* 3.1 12.5 + - - +
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Residues in contact with PRO 456 (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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454A ALA 4.3 3.1 - - - +
455A THR* 1.3 87.3 - - - +
457A GLU* 1.3 61.0 + - - +
459A VAL* 4.0 9.8 - - + +
460A GLY* 3.1 17.8 + - - -
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Residues in contact with GLU 457 (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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455A THR* 2.9 10.1 + - - +
456A PRO* 1.3 80.4 - - - +
458A GLN* 1.3 62.5 + - + +
460A GLY* 3.4 3.1 + - - -
461A LYS* 3.2 16.7 + - + +
528A LEU* 2.9 38.6 - - + +
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Residues in contact with GLN 458 (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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454A ALA* 3.5 1.9 - - + -
455A THR* 2.8 43.6 + - - +
457A GLU* 1.3 74.5 - - + +
459A VAL* 1.3 67.4 + - - +
460A GLY 2.9 1.1 - - - -
461A LYS* 2.8 15.4 + - - +
462A MET* 3.0 11.4 + - - +
525A PHE* 4.3 2.1 - - + -
528A LEU* 2.4 46.3 + - + +
529A VAL* 3.8 7.1 - - + +
375B VAL* 3.1 32.1 - - - +
379B SER* 3.8 17.5 - - - +
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Residues in contact with VAL 459 (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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454A ALA* 4.3 11.2 - - + +
455A THR 3.1 14.8 + - - +
456A PRO* 4.0 8.1 - - + +
458A GLN* 1.3 74.9 - - - +
460A GLY* 1.3 51.9 + - - +
462A MET* 3.1 2.6 + - - +
463A LYS* 2.8 59.0 + - - +
379B SER* 4.2 20.4 - - - +
382B HIS* 3.7 25.6 - - + +
383B ALA* 4.0 17.7 - - - +
386B ASP* 4.7 3.1 - - - +
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Residues in contact with GLY 460 (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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456A PRO 3.1 13.6 + - - -
457A GLU* 3.6 5.8 - - - -
458A GLN 2.9 2.2 - - - -
459A VAL* 1.3 78.9 - - - +
461A LYS* 1.3 62.0 + - - -
463A LYS* 3.1 22.3 + - - +
464A ALA* 3.1 12.4 + - - +
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Residues in contact with LYS 461 (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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457A GLU* 3.2 5.1 + - + +
458A GLN 2.8 11.0 + - - +
460A GLY* 1.3 71.3 - - - -
462A MET* 1.3 62.6 + - - +
464A ALA* 3.4 6.9 + - + +
465A ILE* 3.2 26.9 + - - +
521A LEU* 4.2 19.3 - - + +
524A GLU* 2.6 57.2 + - + +
525A PHE* 4.0 15.0 - - + +
528A LEU* 3.1 31.2 - - + -
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Residues in contact with MET 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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458A GLN 3.0 4.9 + - - -
459A VAL 3.6 6.7 - - - +
461A LYS* 1.3 73.2 - - - +
463A LYS* 1.3 67.6 + - - +
465A ILE* 3.0 20.8 + - + +
466A VAL* 2.8 28.2 + - + +
525A PHE* 3.3 43.9 - - + -
253B ILE* 4.5 10.1 - - + -
257B LEU* 3.9 16.8 - - + -
259B ILE* 5.0 3.8 - - + -
345B PHE* 5.6 0.2 - - - -
376B ALA 4.7 2.0 - - - +
379B SER* 3.7 16.8 - - - -
380B LEU* 3.3 47.3 - - + +
383B ALA* 3.7 7.9 - - + -
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Residues in contact with LYS 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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459A VAL* 2.8 30.6 + - - +
460A GLY* 3.1 13.0 + - - +
462A MET* 1.3 76.2 - - - +
464A ALA* 1.3 63.8 + - - +
466A VAL* 3.0 4.2 + - - +
467A GLU* 3.0 30.6 + - - +
383B ALA* 3.9 14.3 - - - +
386B ASP* 2.6 44.2 + - - +
387B LEU* 4.0 29.8 - - + -
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Residues in contact with ALA 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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460A GLY 3.1 8.2 + - - +
461A LYS* 3.5 12.3 - - + +
463A LYS* 1.3 79.4 - - - +
465A ILE* 1.3 62.4 + - - +
467A GLU* 3.2 10.6 + - - +
468A LYS* 3.2 30.8 + - - +
521A LEU* 3.8 25.1 - - + -
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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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461A LYS 3.2 14.8 - - - +
462A MET* 3.0 22.9 + - - +
464A ALA* 1.3 73.1 - - - +
466A VAL* 1.3 68.8 + - - +
468A LYS* 3.3 10.2 + - - +
469A LEU* 3.3 24.8 + - + +
518A LEU* 3.4 19.3 - - + -
521A LEU* 3.9 32.8 - - + +
522A VAL* 4.6 4.5 - - + +
525A PHE* 4.0 24.5 - - + -
253B ILE* 4.3 13.0 - - + -
257B LEU* 4.1 17.5 - - + -
345B PHE* 5.2 0.9 - - + -
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Residues in contact with VAL 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 MET* 2.8 24.9 + - + +
463A LYS 3.4 7.4 - - - +
465A ILE* 1.3 73.4 - - - +
467A GLU* 1.3 61.6 + - - +
469A LEU* 3.2 13.0 + - - -
470A ARG* 3.3 9.5 + - - +
345B PHE* 3.6 53.1 - - + +
380B LEU* 4.3 9.2 - - + -
383B ALA* 4.4 4.3 - - + -
384B LEU* 4.0 14.8 - - + -
387B LEU* 3.5 24.5 - - + -
389B MET* 3.7 12.6 - - - -
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Residues in contact with GLU 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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463A LYS* 3.0 19.3 + - - +
464A ALA* 3.8 8.1 + - - +
465A ILE 3.2 0.2 - - - -
466A VAL* 1.3 73.0 - - - +
468A LYS* 1.3 69.0 + - + +
469A LEU 3.0 2.5 + - - -
470A ARG* 3.2 46.9 + - - +
517A ARG* 4.3 2.6 + - - -
387B LEU* 3.3 30.6 - - + +
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Residues in contact with LYS 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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464A ALA* 3.2 21.5 + - - +
465A ILE 3.3 5.6 + - - +
467A GLU* 1.3 81.0 - - + +
469A LEU* 1.3 59.6 + - - +
470A ARG 3.4 3.3 + - - +
517A ARG* 2.6 65.8 + - + +
518A LEU* 4.1 9.0 - - + -
521A LEU* 3.6 25.8 - - + -
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Residues in contact with LEU 469 (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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465A ILE* 3.4 19.5 - - + +
466A VAL 3.2 6.0 + - - -
467A GLU 3.0 0.8 - - - -
468A LYS* 1.3 83.2 - - + +
470A ARG* 1.3 64.4 + - - +
471A PHE* 4.0 1.2 - - - -
514A MET* 4.0 42.8 - - + +
517A ARG* 5.0 4.7 - - + -
518A LEU* 4.0 14.1 - - + -
253B ILE* 3.5 32.3 - - + -
343B LEU 5.4 0.7 - - - +
344B GLY* 3.5 10.7 - - - -
345B PHE* 3.0 44.1 + - + -
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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