Contacts of the helix formed by residues 432 - 450 (chain C) in PDB entry 1M7X
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 ASN 432 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C HIS* 5.7 1.2 + - - -
374C ILE* 3.8 26.9 - - - +
377C TYR* 5.1 7.3 - - - -
410C MET 3.5 17.2 + - - +
411C ILE 2.4 25.4 + - - +
412C TYR* 4.3 6.5 - - - +
430C ARG 4.3 0.2 + - - -
431C GLU* 1.3 69.8 - - - +
433C LEU* 1.3 63.0 + - - +
434C GLU* 3.1 17.2 + - - +
435C ALA* 2.7 39.2 + - - +
436C ILE* 3.1 17.0 + - - +
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Residues in contact with LEU 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C GLU* 3.5 19.6 + - + +
432C ASN* 1.3 71.3 - - - +
434C GLU* 1.3 62.3 + - + +
436C ILE* 3.5 23.1 + - + +
437C GLU* 3.2 24.8 + - - +
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Residues in contact with GLU 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C HIS* 3.1 31.6 + - - -
376C ASN* 4.2 9.6 - - - +
377C TYR* 4.2 8.1 - - + +
378C GLY* 4.3 31.9 + - - +
432C ASN* 3.1 10.5 + - - +
433C LEU* 1.3 76.8 - - + +
435C ALA* 1.3 64.9 + - - +
437C GLU* 4.3 3.9 - - - +
438C PHE* 3.1 23.2 + - - +
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Residues in contact with ALA 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C TYR* 4.2 16.4 - - + -
410C MET* 3.2 40.8 - - + +
411C ILE* 3.8 5.8 - - + +
432C ASN* 2.7 23.7 + - + +
434C GLU* 1.3 69.4 - - - +
436C ILE* 1.3 62.7 + - - +
438C PHE* 3.0 8.9 + - - +
439C LEU* 2.9 32.4 + - - +
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Residues in contact with ILE 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ILE* 3.5 28.9 - - + -
431C GLU* 4.3 13.9 - - + +
432C ASN 3.1 12.9 + - - +
433C LEU* 3.6 28.9 - - + +
435C ALA* 1.3 80.0 - - - +
437C GLU* 1.3 63.0 + - - +
439C LEU* 3.4 3.1 + - - +
440C ARG* 3.1 63.4 + - - +
463C PHE* 3.7 28.3 - - + -
475C LEU* 4.1 5.8 - - + +
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Residues in contact with GLU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C LEU 3.2 14.7 + - - +
434C GLU* 4.3 4.0 - - - +
436C ILE* 1.3 79.0 - - - +
438C PHE* 1.3 56.6 + - - +
440C ARG* 2.9 37.1 + - - +
441C ASN* 2.4 59.7 + - - +
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Residues in contact with PHE 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C TRP* 4.7 5.4 - + - -
338C PRO* 3.9 15.9 - - + -
377C TYR* 3.3 45.1 - + + +
383C SER* 4.1 17.3 - - - -
386C LEU* 3.3 40.8 - - + -
387C VAL* 4.1 11.9 - - + -
410C MET* 3.8 16.4 - - + -
434C GLU 3.1 16.9 + - - +
435C ALA 3.1 7.6 - - - +
437C GLU* 1.3 76.4 - - - +
439C LEU* 1.3 65.2 + - + +
441C ASN* 3.4 4.3 + - - +
442C THR* 2.6 47.9 + - - -
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Residues in contact with LEU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C TRP* 5.9 3.6 - - + -
338C PRO* 5.9 1.3 - - + -
404C VAL* 4.8 8.1 - - + -
407C VAL* 3.9 24.9 - - + -
410C MET* 3.4 35.2 - - + -
411C ILE* 4.1 12.6 - - + -
435C ALA 2.9 15.2 + - - +
436C ILE 3.8 0.4 - - - +
438C PHE* 1.3 83.8 - - + +
440C ARG* 1.3 61.3 + - - +
442C THR* 3.8 6.2 - - - +
443C ASN* 3.1 31.9 + - - +
475C LEU* 3.7 31.9 - - + -
477C PHE* 4.0 24.5 - - + -
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Residues in contact with ARG 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C ILE* 3.1 36.6 + - - +
437C GLU* 2.9 40.9 + - - +
439C LEU* 1.3 77.4 - - - +
441C ASN* 1.3 64.2 + - - +
444C ARG* 3.2 9.4 + - - +
463C PHE* 5.0 9.5 - - - -
470C GLN* 3.1 41.1 + - + +
473C GLY 3.0 23.8 + - - -
474C GLY* 3.2 15.2 - - - -
475C LEU* 3.1 25.4 - - - +
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Residues in contact with ASN 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C SER* 6.0 0.9 - - - +
387C VAL* 5.8 2.9 - - + -
437C GLU* 2.4 57.7 + - - +
438C PHE* 4.1 4.9 - - - +
440C ARG* 1.3 71.4 - - - +
442C THR* 1.3 58.1 + - - +
444C ARG* 3.0 39.8 + - - +
445C ILE* 2.8 43.0 + - + +
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Residues in contact with THR 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C TRP* 3.7 33.2 - - + -
387C VAL* 3.7 26.6 - - + +
438C PHE* 2.6 35.5 + - - -
439C LEU* 3.8 9.3 - - + -
441C ASN* 1.3 77.8 - - - +
443C ASN* 1.3 61.2 + - - +
445C ILE* 3.3 0.5 + - - -
446C LEU* 2.9 55.4 + - + +
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Residues in contact with ASN 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU 3.1 13.4 + - - +
442C THR* 1.3 84.6 - - - +
444C ARG* 1.3 52.2 + - - +
446C LEU* 4.3 4.9 - - - +
447C GLY* 2.8 29.6 + - - -
455C THR* 2.5 36.1 + - - +
470C GLN* 3.8 8.5 - - - +
475C LEU 2.8 28.4 + - - +
476C GLY 3.8 11.4 - - - +
477C PHE* 3.3 32.7 - - - +
478C TRP* 3.5 10.4 - - + -
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Residues in contact with ARG 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C ARG 3.2 15.3 + - - +
441C ASN* 3.0 38.2 + - - +
443C ASN* 1.3 75.4 - - - +
445C ILE* 1.3 88.1 + - - +
447C GLY* 3.0 2.6 + - - -
448C GLU* 2.8 71.1 + - + +
470C GLN* 3.6 11.9 + - + +
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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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119C LEU* 3.7 33.7 - - + -
387C VAL* 3.8 33.9 - - + -
391C LEU* 4.4 9.2 - - + -
441C ASN* 2.8 22.8 + - + +
442C THR 3.9 2.9 - - - +
444C ARG* 1.3 104.5 - - - +
446C LEU* 1.3 52.9 + - - +
448C GLU* 4.4 6.1 - - - +
449C GLN* 2.6 53.5 + - + +
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Residues in contact with LEU 446 (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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336C TRP* 5.7 0.4 - - + -
387C VAL* 4.3 4.5 - - + -
390C ALA* 4.1 8.5 - - + -
391C LEU* 3.6 27.1 - - + -
394C ILE* 4.8 4.9 - - + -
402C LEU* 3.8 24.0 - - + -
442C THR* 2.9 47.1 + - + +
443C ASN* 3.9 4.9 - - - +
445C ILE* 1.3 74.4 - - - +
447C GLY* 1.3 60.7 + - - +
449C GLN* 4.9 0.4 - - - -
450C VAL* 2.8 55.9 + - + +
453C ALA 5.2 1.6 - - - +
455C THR* 3.5 31.0 - - + -
478C TRP* 4.9 1.3 - - + -
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Residues in contact with GLY 447 (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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443C ASN 2.8 19.4 + - - -
444C ARG* 3.0 2.7 + - - -
446C LEU* 1.3 77.0 - - - +
448C GLU* 1.3 59.0 + - - +
450C VAL 5.0 0.4 - - - -
451C SER* 3.4 25.2 - - - -
478C TRP* 3.8 20.4 - - - -
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Residues in contact with GLU 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ARG* 2.8 57.9 + - + +
445C ILE* 3.9 5.8 - - - +
447C GLY* 1.3 81.4 - - - +
449C GLN* 1.3 70.3 + - + +
451C SER* 4.6 5.8 + - - -
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Residues in contact with GLN 449 (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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119C LEU* 4.8 10.0 - - + +
120C ARG* 3.0 37.1 + - - +
391C LEU* 4.2 11.7 - - + -
395C GLU* 4.4 3.3 - - - +
445C ILE* 2.6 38.0 + - + +
446C LEU* 4.9 0.2 - - - -
448C GLU* 1.3 81.9 + - + +
450C VAL* 1.3 63.5 + - + +
451C SER 3.8 0.7 - - - -
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Residues in contact with VAL 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C LEU* 4.7 7.4 - - + -
394C ILE* 4.1 25.1 - - + -
395C GLU* 3.6 32.5 - - + +
446C LEU* 2.8 56.3 + - + +
449C GLN* 1.3 81.5 - - + +
451C SER* 1.3 65.8 + - - +
453C ALA* 3.2 27.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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