Contacts of the helix formed by residues 402 - 415 (chain C) in PDB entry 1XMI
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 402 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400C PHE* 3.6 17.2 - - - +
401C TRP* 1.3 89.2 + - + +
403C GLU* 1.3 65.5 + - - +
404C GLY 3.3 2.7 - - - +
405C PHE* 3.2 36.1 + - + -
406C GLY 3.2 15.9 + - - -
438C THR* 4.1 23.1 + - - +
440C VAL 5.7 0.2 + - - -
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Residues in contact with GLU 403 (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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400C PHE 5.5 1.1 - - - -
401C TRP 3.5 6.3 + - - +
402C GLU* 1.3 71.0 - - - +
404C GLY* 1.3 63.6 + - - +
406C GLY* 3.1 3.2 + - - +
407C GLU* 3.0 45.2 + - + +
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Residues in contact with GLY 404 (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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402C GLU* 3.3 2.6 - - - +
403C GLU* 1.3 78.5 - - - +
405C PHE* 1.3 60.6 + - - +
407C GLU* 3.8 5.2 + - - +
408C LEU* 3.2 28.3 + - - +
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Residues in contact with PHE 405 (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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400C PHE* 3.7 24.7 - - + -
402C GLU* 3.2 40.8 + - + +
404C GLY* 1.3 75.7 - - - +
406C GLY* 1.3 59.2 + - - +
408C LEU* 3.3 19.5 + - + +
409C PHE* 2.9 30.7 + - - +
434C SER* 5.0 3.6 - - - +
436C LEU* 3.6 25.6 - - + -
437C GLY* 3.5 29.4 - - - -
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Residues in contact with GLY 406 (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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400C PHE* 3.7 16.0 - - - +
402C GLU 3.2 7.8 + - - -
403C GLU* 3.1 7.5 + - - -
405C PHE* 1.3 77.1 - - - +
407C GLU* 1.3 60.9 + - - +
409C PHE* 3.4 1.7 + - - +
410C GLU* 3.3 22.1 + - - +
478C SER* 3.2 26.2 + - - -
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Residues in contact with GLU 407 (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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403C GLU* 3.0 35.6 + - + +
404C GLY* 4.1 4.7 - - - +
406C GLY* 1.3 72.3 - - - +
408C LEU* 1.3 60.3 + - - +
410C GLU* 3.4 12.1 + - - +
411C LYS* 3.0 37.3 + - + +
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Residues in contact with LEU 408 (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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404C GLY 3.2 19.7 + - - +
405C PHE* 3.5 23.8 - - + +
407C GLU* 1.3 74.1 - - - +
409C PHE* 1.3 63.0 + - - +
411C LYS* 3.5 8.6 + - + -
412C ALA* 3.1 28.6 + - + +
433C PHE* 3.7 50.3 - - + +
434C SER* 4.0 7.0 - - - -
436C LEU* 4.7 9.0 - - + -
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Residues in contact with PHE 409 (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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398C THR* 4.5 15.0 - - + -
400C PHE* 3.5 30.3 - + + -
405C PHE 2.9 16.6 + - - +
406C GLY 3.6 4.3 - - - +
407C GLU 3.3 0.2 - - - -
408C LEU* 1.3 76.9 - - - +
410C GLU* 1.3 59.4 + - - +
412C ALA* 3.8 1.7 + - - +
413C LYS* 3.2 29.5 + - + +
434C SER* 3.6 24.5 + - - -
439C PRO* 6.2 0.9 - - + -
478C SER* 3.8 19.7 - - - -
479C GLU* 4.0 42.0 - - + -
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Residues in contact with GLU 410 (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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406C GLY 3.3 20.0 + - - +
407C GLU* 3.8 10.1 - - - +
409C PHE* 1.3 77.9 - - + +
411C LYS* 1.3 63.1 + - + +
413C LYS* 3.4 18.0 + - - +
414C GLN* 3.6 11.1 + - - +
477C PRO 5.0 2.7 - - - +
478C SER* 3.4 38.3 + - - +
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Residues in contact with LYS 411 (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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407C GLU* 3.0 22.0 + - + +
408C LEU* 4.0 11.0 - - + +
410C GLU* 1.3 77.0 - - + +
412C ALA* 1.3 59.1 + - - +
413C LYS 3.3 0.2 - - - -
414C GLN* 3.4 18.6 - - - +
415C ASN* 2.9 31.8 + - - +
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Residues in contact with ALA 412 (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 LEU* 3.1 20.4 + - + +
409C PHE 4.0 2.5 - - - +
411C LYS* 1.3 76.0 - - - +
413C LYS* 1.3 62.3 + - - +
414C GLN 3.5 0.2 - - - -
415C ASN* 3.7 20.8 + - - +
431C SER 5.2 5.1 - - - +
432C ASN* 4.6 12.1 - - - +
433C PHE* 4.8 10.8 - - + +
434C SER* 4.5 18.4 - - - +
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Residues in contact with LYS 413 (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 PHE* 3.2 23.8 + - + +
410C GLU* 3.4 11.0 - - - +
412C ALA* 1.3 77.1 - - - +
414C GLN* 1.3 64.3 + - - +
415C ASN 3.6 6.4 - - - +
479C GLU* 4.9 12.1 - - - +
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Residues in contact with GLN 414 (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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410C GLU 3.6 8.9 + - - +
411C LYS* 3.4 24.0 - - - +
413C LYS* 1.3 78.9 - - - +
415C ASN* 1.3 94.8 + - - +
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Residues in contact with ASN 415 (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 LYS* 2.9 28.0 + - - +
412C ALA* 3.7 15.7 + - - +
413C LYS 3.3 8.2 - - - +
414C GLN* 1.3 107.6 + - - +
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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