Contacts of the helix formed by residues 452 - 463 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418C VAL* 4.9 0.3 - - - +
422C VAL* 4.0 15.7 - - - +
448C ALA 3.1 15.5 + - - -
449C THR* 3.6 9.4 - - - +
450C LYS 3.6 0.4 - - - -
451C TRP* 1.3 97.3 - - - +
453C PRO* 1.3 64.0 - - - +
454C GLU* 3.7 11.1 + - - +
455C LEU* 3.3 25.3 + - - +
456C ALA 3.0 16.5 + - - -
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Residues in contact with PRO 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C TRP* 3.5 24.2 - - + -
449C THR 5.0 0.4 - - - +
451C TRP 3.4 11.9 - - - +
452C SER* 1.3 84.2 - - - +
454C GLU* 1.3 77.9 + - - +
456C ALA* 3.6 8.8 - - + +
457C ALA* 3.1 18.4 + - - +
2U LYS* 3.8 27.6 - - + +
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Residues in contact with GLU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C HIS* 2.8 26.0 + - - -
411C TRP* 3.9 19.7 - - + -
415C PRO* 3.8 36.1 - - + +
418C VAL* 3.9 21.1 - - + +
419C ALA* 3.6 4.9 - - - +
452C SER* 3.8 9.5 + - - +
453C PRO* 1.3 95.1 - - - +
455C LEU* 1.3 62.8 + - - +
458C ALA 3.3 5.7 + - - -
2U LYS* 4.4 10.9 - - - +
3U VAL 6.2 0.2 - - - -
4U TRP* 4.0 28.4 - - + -
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Residues in contact with LEU 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C VAL* 3.7 23.8 - - + -
419C ALA* 3.6 29.1 - - - +
422C VAL* 4.2 11.0 - - + -
423C ALA* 4.0 12.1 - - + -
445C ILE* 3.9 16.6 - - + +
448C ALA* 3.5 35.7 - - + -
449C THR* 4.0 2.2 - - + +
452C SER* 3.2 19.1 + - - +
454C GLU* 1.3 77.8 - - - +
456C ALA* 1.3 66.0 + - - +
458C ALA* 3.1 1.7 + - - +
459C CYS* 2.9 36.2 + - - -
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Residues in contact with ALA 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C THR* 3.8 29.8 - - - +
452C SER 3.0 13.6 + - - +
453C PRO* 3.6 11.9 - - + +
454C GLU 3.3 0.2 - - - -
455C LEU* 1.3 77.8 - - - +
457C ALA* 1.3 64.2 + - - +
459C CYS* 3.3 2.6 + - - +
460C GLU* 3.1 24.1 + - - +
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Residues in contact with ALA 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C HIS* 3.9 17.7 - - + -
410C PRO* 4.1 8.9 - - + +
411C TRP* 3.9 21.1 - - + +
453C PRO 3.1 15.1 + - - +
454C GLU 3.8 4.7 - - - +
455C LEU 3.2 0.2 - - - -
456C ALA* 1.3 79.4 - - - +
458C ALA* 1.3 60.7 + - - +
460C GLU* 3.6 10.4 + - - +
461C VAL* 3.3 26.5 + - - +
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Residues in contact with ALA 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C VAL* 4.2 11.4 - - + +
409C HIS* 3.7 24.7 + - + -
410C PRO* 5.0 0.7 - - - -
419C ALA* 4.0 12.6 - - + -
454C GLU 3.3 5.1 + - - +
455C LEU 3.1 9.0 + - - +
457C ALA* 1.3 78.3 - - - +
459C CYS* 1.3 65.1 + - - +
461C VAL* 3.2 13.3 + - - +
462C TRP* 3.3 38.4 + - + +
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Residues in contact with CYS 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C VAL* 4.0 7.4 - - - -
385C TRP* 3.0 42.5 + - + +
445C ILE* 3.5 31.6 - - - -
449C THR* 3.7 17.3 - - + -
455C LEU* 2.9 29.6 + - - +
456C ALA* 3.7 5.2 - - - +
458C ALA* 1.3 76.4 - - - +
460C GLU* 1.3 61.8 + - - +
463C LYS* 3.1 16.0 + - - +
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Residues in contact with GLU 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456C ALA 3.1 16.9 + - - +
457C ALA* 3.6 9.9 - - - +
458C ALA 3.2 0.4 - - - -
459C CYS* 1.3 78.0 - - - +
461C VAL* 1.3 65.2 + - + +
463C LYS* 3.5 34.8 - - - +
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Residues in contact with VAL 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C GLY 5.0 4.9 - - - +
410C PRO* 3.9 26.0 - - + -
457C ALA 3.3 16.2 - - - +
458C ALA* 3.2 8.1 + - - +
460C GLU* 1.3 83.3 - - + +
462C TRP* 1.3 88.0 + - + +
463C LYS* 4.0 0.5 + - - +
464C GLU* 5.4 1.0 + - - +
465C ILE* 4.6 5.2 - - - +
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Residues in contact with TRP 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C HIS* 3.5 53.9 + + + +
384C VAL* 4.6 7.4 - - + -
385C TRP* 3.9 5.2 - - + -
404C GLY 3.8 13.0 - - - -
405C GLY* 3.6 33.2 - - - -
408C GLY* 3.7 30.5 - - - -
409C HIS* 4.0 7.2 - + - -
458C ALA* 3.3 42.1 + - + +
461C VAL* 1.3 96.8 - - + +
463C LYS* 1.3 65.5 + - - +
464C GLU 3.2 3.8 - - - -
465C ILE* 3.1 30.3 + - + -
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Residues in contact with LYS 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385C TRP* 3.4 27.6 - - + +
459C CYS 3.1 13.9 + - - +
460C GLU* 3.5 32.7 - - - +
461C VAL 3.6 0.8 - - - +
462C TRP* 1.3 75.8 - - - +
464C GLU* 1.3 82.3 + - + +
465C ILE 3.8 0.3 + - - +
466C LYS* 3.5 15.9 + - - -
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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