Contacts of the helix formed by residues 436 - 450 (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 ASP 436 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392C GLU* 5.9 0.2 - - - +
434C GLY 3.9 1.8 + - - -
435C ARG* 1.3 67.9 - - - +
437C LEU* 1.3 55.9 + - - +
438C ALA* 2.9 21.7 + - - +
439C ARG* 3.1 40.3 + - + +
440C GLU* 2.7 52.5 + - - +
444C ILE* 5.1 0.2 - - - -
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Residues in contact with LEU 437 (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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388C PRO* 4.0 22.6 - - + +
389C ALA 5.3 0.2 + - - -
391C THR* 3.8 34.3 - - + -
392C GLU* 4.2 18.1 - - + +
427C CYS* 3.8 30.7 - - + +
430C ALA* 4.6 2.2 - - + -
431C ARG* 4.0 26.0 - - + +
435C ARG 3.4 4.4 + - - +
436C ASP* 1.3 73.9 + - - +
438C ALA* 1.3 59.1 + - - +
441C GLY* 3.0 26.5 + - - +
444C ILE* 3.7 24.7 - - + -
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Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ALA* 6.4 1.1 - - - +
392C GLU* 4.6 22.1 - - + +
436C ASP* 2.9 11.7 + - - +
437C LEU* 1.3 81.3 - - - +
439C ARG* 1.3 62.6 + - + +
441C GLY* 4.5 1.6 + - - -
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Residues in contact with ARG 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C ASP* 3.1 31.1 + - + +
438C ALA* 1.3 83.1 - - + +
440C GLU* 1.3 64.8 + - + +
441C GLY 3.5 0.8 + - - -
442C ASN 5.3 0.5 + - - -
443C THR* 5.4 0.3 + - - -
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Residues in contact with GLU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C ARG* 2.9 42.3 + - - +
436C ASP* 2.7 44.1 + - - +
439C ARG* 1.3 79.3 - - + +
441C GLY* 1.3 64.1 + - - +
442C ASN 3.4 2.2 - - - -
443C THR* 3.0 14.1 + - - +
444C ILE* 2.9 33.1 + - + +
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Residues in contact with GLY 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C PRO* 3.6 24.2 - - - +
437C LEU 3.0 21.6 + - - -
438C ALA 4.5 2.1 + - - -
439C ARG 3.5 2.4 - - - -
440C GLU* 1.3 77.4 - - - +
442C ASN* 1.3 62.9 + - - +
444C ILE* 3.2 8.6 + - - +
445C ILE* 3.1 24.8 + - - +
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Residues in contact with ASN 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C TRP* 3.8 32.6 + - - +
388C PRO* 5.9 0.2 - - - +
439C ARG 5.3 0.6 + - - -
440C GLU 3.4 0.6 - - - -
441C GLY* 1.3 73.1 - - - +
443C THR* 1.3 65.1 + - - +
445C ILE* 3.3 3.9 + - - +
446C ARG* 3.0 53.9 + - - +
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Residues in contact with THR 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C ARG* 4.2 8.3 - - - +
439C ARG 5.4 0.7 + - - -
440C GLU* 3.0 16.8 + - - -
442C ASN* 1.3 78.7 - - - +
444C ILE* 1.3 58.1 + - - +
446C ARG* 3.3 8.9 + - + +
447C GLU* 2.9 56.8 + - + +
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Residues in contact with ILE 444 (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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426C ALA* 3.7 32.6 - - + +
427C CYS* 4.4 10.8 - - - +
430C ALA* 3.5 23.3 - - + -
435C ARG* 3.8 27.8 - - + +
437C LEU* 3.7 22.4 - - + -
440C GLU* 2.9 31.8 + - + +
441C GLY* 3.6 6.5 - - - +
443C THR* 1.3 77.6 - - - +
445C ILE* 1.3 61.6 + - + +
447C GLU* 3.5 12.0 + - - +
448C ALA* 3.3 19.9 + - - +
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Residues in contact with ILE 445 (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 3.9 18.4 - - - +
385C TRP* 3.8 22.2 - - + -
387C MET* 4.5 0.2 - - + -
388C PRO* 3.8 23.3 - - + -
423C ALA* 4.1 24.0 - - + +
426C ALA* 5.6 1.6 - - + -
427C CYS* 4.2 11.9 - - - -
441C GLY 3.1 13.4 + - - +
442C ASN* 3.7 6.3 - - - +
444C ILE* 1.3 78.0 - - + +
446C ARG* 1.3 63.4 + - - +
448C ALA* 3.0 15.6 + - - +
449C THR* 3.1 12.4 + - + +
455C LEU* 4.5 5.8 - - + -
459C CYS* 3.5 30.3 - - - -
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Residues in contact with ARG 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C TRP* 3.5 29.6 - - + -
442C ASN* 3.0 45.8 + - - +
443C THR* 3.3 7.1 + - - +
445C ILE* 1.3 77.5 - - - +
447C GLU* 1.3 62.9 + - + +
449C THR* 2.5 29.2 + - + +
450C LYS* 3.7 18.5 + - - +
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Residues in contact with GLU 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C ARG* 3.0 41.5 + - - -
443C THR* 2.9 37.1 + - + +
444C ILE* 3.6 9.1 - - - +
445C ILE 3.2 0.2 - - - -
446C ARG* 1.3 76.2 - - + +
448C ALA* 1.3 61.1 + - - +
450C LYS* 3.3 26.4 + - - +
451C TRP* 3.8 9.3 + - - -
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Residues in contact with ALA 448 (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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422C VAL* 4.5 2.2 - - + -
426C ALA* 4.2 20.2 - - + -
444C ILE 3.3 9.0 + - - +
445C ILE* 3.0 10.8 + - + +
447C GLU* 1.3 77.2 - - - +
449C THR* 1.3 60.2 + - - +
450C LYS 3.0 5.9 + - - -
451C TRP* 3.3 26.0 + - + +
452C SER* 3.1 25.3 + - - -
455C LEU* 3.5 17.5 - - + -
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Residues in contact with THR 449 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C TRP* 5.7 0.4 - - + -
445C ILE 3.1 15.0 + - - +
446C ARG* 2.5 29.5 + - + +
448C ALA* 1.3 75.3 - - - +
450C LYS* 1.3 68.9 + - - +
451C TRP 3.3 0.6 + - - -
452C SER 3.6 19.6 + - - +
453C PRO* 4.7 0.9 - - - +
455C LEU* 4.0 9.4 - - + -
456C ALA* 3.8 23.4 - - - +
459C CYS* 3.7 30.1 - - + -
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Residues in contact with LYS 450 (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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446C ARG* 3.8 18.8 + - - +
447C GLU* 3.4 19.1 - - - +
448C ALA 3.0 0.6 - - - -
449C THR* 1.3 87.8 + - - +
451C TRP* 1.3 60.7 + - + +
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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