Contacts of the helix formed by residues 452 - 463 (chain A) in PDB entry 1IR1
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 SER 452 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A VAL* 4.9 0.5 - - - +
422A VAL* 4.0 16.7 - - - +
448A ALA 3.1 15.3 + - - -
449A THR* 3.5 10.1 - - - +
450A LYS 3.6 1.4 - - - -
451A TRP* 1.3 96.7 - - - +
453A PRO* 1.4 60.4 - - - +
454A GLU* 3.9 9.4 + - - +
455A LEU* 3.3 24.0 + - - +
456A ALA 3.0 22.7 + - - -
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Residues in contact with PRO 453 (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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411A TRP* 3.7 22.8 - - + -
449A THR 5.1 0.4 - - - +
451A TRP 3.5 9.6 - - - +
452A SER* 1.4 82.9 - - - +
454A GLU* 1.3 76.2 + - - +
456A ALA* 3.6 8.2 - - + +
457A ALA* 3.0 24.6 + - - +
2S LYS* 4.1 23.6 - - + +
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Residues in contact with GLU 454 (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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409A HIS* 2.9 26.4 + - - -
411A TRP* 3.9 19.4 - - + -
415A PRO* 3.8 36.5 - - + +
418A VAL* 4.0 22.1 - - + +
419A ALA* 3.7 5.0 - - - +
452A SER* 3.9 6.5 + - - +
453A PRO* 1.3 94.3 - - - +
455A LEU* 1.3 61.3 + - - +
458A ALA 3.3 5.7 + - - -
2S LYS* 4.4 18.1 + - - +
3S VAL 6.1 0.3 - - - -
4S TRP* 4.0 26.3 - - + -
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Residues in contact with LEU 455 (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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384A VAL* 3.7 32.1 - - + -
419A ALA* 3.7 19.9 - - - +
422A VAL* 4.2 10.3 - - + -
423A ALA* 4.1 10.3 - - + -
445A ILE* 3.9 16.8 - - + +
448A ALA* 3.4 33.9 - - + -
449A THR* 4.0 5.8 - - + +
452A SER* 3.2 19.5 + - - +
454A GLU* 1.3 76.6 - - - +
456A ALA* 1.3 67.4 + - - +
458A ALA* 3.1 2.1 + - - +
459A CYS* 2.9 36.2 + - - -
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Residues in contact with ALA 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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449A THR* 3.8 30.0 - - - +
452A SER 3.0 16.5 + - - +
453A PRO* 3.6 10.1 - - + +
454A GLU 3.3 0.2 - - - -
455A LEU* 1.3 77.6 - - - +
457A ALA* 1.3 62.1 + - - +
459A CYS* 3.4 2.7 + - - +
460A GLU* 3.2 22.5 + - - +
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Residues in contact with ALA 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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409A HIS* 3.8 17.3 - - + -
410A PRO* 4.1 8.7 - - + +
411A TRP* 4.0 21.5 - - + +
453A PRO 3.0 16.8 + - - +
454A GLU 3.8 5.4 - - - +
455A LEU 3.2 0.2 - - - -
456A ALA* 1.3 76.7 - - - +
458A ALA* 1.3 61.8 + - - +
460A GLU* 3.6 8.4 + - - +
461A VAL* 3.3 26.3 + - - +
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Residues in contact with ALA 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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384A VAL* 4.2 13.0 - - + +
409A HIS* 3.7 24.8 + - + -
410A PRO* 5.0 0.7 - - - -
419A ALA* 3.9 12.3 - - + -
454A GLU 3.3 5.8 + - - +
455A LEU 3.1 7.7 + - - +
457A ALA* 1.3 76.9 - - - +
459A CYS* 1.3 65.1 + - - +
461A VAL* 3.3 11.8 + - - +
462A TRP* 3.4 38.0 + - + +
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Residues in contact with CYS 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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384A VAL* 4.1 7.4 - - - -
385A TRP* 2.9 42.0 + - + +
445A ILE* 3.6 31.2 - - - -
449A THR* 3.8 17.0 - - + -
455A LEU* 2.9 28.7 + - - +
456A ALA 3.7 5.6 - - - +
458A ALA* 1.3 76.4 - - - +
460A GLU* 1.3 62.5 + - - +
463A LYS* 3.1 15.6 + - - +
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Residues in contact with GLU 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 ALA 3.2 14.1 + - - +
457A ALA* 3.7 8.5 - - - +
458A ALA 3.3 0.2 - - - -
459A CYS* 1.3 77.9 - - - +
461A VAL* 1.3 72.0 + - - +
463A LYS* 4.0 20.4 - - + +
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Residues in contact with VAL 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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408A GLY 5.0 4.7 - - - +
410A PRO* 3.9 25.6 - - + -
457A ALA 3.3 16.4 - - - +
458A ALA 3.3 7.0 + - - +
460A GLU* 1.3 90.4 - - - +
462A TRP* 1.3 86.8 + - + +
463A LYS* 4.0 0.4 + - - -
464A GLU 5.3 0.3 + - - -
465A ILE* 4.6 4.7 - - - +
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Residues in contact with TRP 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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383A HIS* 3.5 53.3 + + + +
384A VAL* 4.5 6.3 - - + -
385A TRP* 3.8 5.2 - - + -
404A GLY 3.7 14.6 - - - -
405A GLY* 3.6 29.6 - - - -
408A GLY* 3.6 32.5 - - - -
409A HIS* 3.9 7.9 - + + -
410A PRO* 5.5 0.2 - - + -
458A ALA* 3.4 43.0 + - + +
461A VAL* 1.3 97.3 - - + +
463A LYS* 1.3 62.4 + - - +
464A GLU 3.3 3.1 - - - -
465A ILE* 3.2 29.3 + - + -
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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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383A HIS* 5.8 0.2 - - - -
385A TRP* 3.3 35.2 - - + +
446A ARG* 5.7 4.8 - - - +
459A CYS 3.1 15.3 + - - +
460A GLU* 4.0 20.2 - - + +
461A VAL 3.7 1.0 + - - -
462A TRP* 1.3 77.4 - - - +
464A GLU* 1.3 88.7 + - + +
465A ILE 3.4 1.3 + - - +
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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