Contacts of the helix formed by residues 436 - 452 (chain C) in PDB entry 1M1D
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 GLY 436 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C VAL 3.7 0.6 - - - -
435C ARG* 1.3 78.4 - - - +
437C TYR* 1.3 58.4 + - - +
439C THR* 3.5 6.7 + - - -
440C ARG* 3.0 40.1 + - - +
314D LYX 3.0 21.4 + - - -
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Residues in contact with TYR 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C LEU* 3.7 28.4 - - + +
351C PHE* 4.9 1.0 - - - -
399C ILE* 3.9 18.9 - - + +
407C ILE* 4.1 12.6 - - + -
428C VAL* 4.5 4.5 - - + -
432C GLU* 3.1 55.4 + - + -
435C ARG* 4.0 23.5 - - + +
436C GLY* 1.3 74.7 - - - +
438C GLY* 1.3 58.4 + - - +
440C ARG* 3.0 28.1 + - - +
441C LEU* 2.7 36.0 + - - +
314D LYX 3.8 5.6 + - - +
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Residues in contact with GLY 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C LEU* 5.2 2.7 - - - +
428C VAL* 3.7 11.8 - - - +
437C TYR* 1.3 72.1 - - - +
439C THR* 1.3 57.3 + - - +
441C LEU* 3.2 9.7 + - - +
442C MET* 2.9 27.7 + - - +
468C TYR* 3.2 11.2 + - - -
314D LYX 2.8 37.4 + - - -
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Residues in contact with THR 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C GLY* 3.5 9.5 + - - -
437C TYR 3.2 0.8 - - - -
438C GLY* 1.3 72.1 - - - +
440C ARG* 1.3 61.1 + - + +
442C MET* 3.3 4.9 + - - +
443C ASN* 3.0 41.6 + - - +
468C TYR* 3.1 12.7 + - - -
472C GLN* 3.7 22.1 + - - +
314D LYX 3.3 26.3 + - - -
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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
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349C LEU* 3.6 41.5 + - - +
351C PHE* 4.1 21.2 - - + -
435C ARG 5.4 1.5 + - - -
436C GLY* 3.0 32.0 + - - +
437C TYR* 3.6 19.9 - - - +
439C THR* 1.3 76.1 - - + +
441C LEU* 1.3 59.0 + - - +
443C ASN* 3.4 8.2 + - - +
444C LYS* 2.9 31.0 + - - +
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Residues in contact with LEU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C PHE* 3.8 10.9 - - + -
397C MET* 3.9 38.6 - - + +
399C ILE* 3.6 27.4 - - + -
409C GLY* 3.5 36.1 - - - +
410C ILE* 4.0 10.3 - - + +
426C LEU* 3.7 18.6 - - + -
427C ALA 4.7 1.8 - - - +
428C VAL* 5.3 0.4 - - + -
437C TYR 2.7 16.7 + - - +
438C GLY* 3.3 9.6 - - - +
440C ARG* 1.3 74.3 - - - +
442C MET* 1.3 57.9 + - - +
444C LYS* 3.2 2.4 + - - +
445C PHE* 2.9 26.7 + - - +
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Residues in contact with MET 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C ILE* 4.2 12.6 - - + -
423C VAL* 5.6 0.7 - - + -
426C LEU* 3.9 28.9 - - + -
438C GLY 2.9 15.2 + - - +
439C THR* 3.7 5.4 - - - +
441C LEU* 1.3 77.7 - - - +
443C ASN* 1.3 58.9 + - - +
445C PHE* 3.3 22.3 + - - +
446C LYS* 2.9 46.0 + - - +
457C LEU* 4.6 4.0 - - - -
468C TYR* 4.8 1.1 - - + +
469C PHE* 4.2 9.0 - - + -
472C GLN* 3.9 30.3 - - + +
474C PHE* 4.2 26.5 - - + -
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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 THR* 3.0 35.7 + - - +
440C ARG* 3.8 7.8 - - - +
441C LEU 3.2 0.2 - - - -
442C MET* 1.3 73.8 - - - +
444C LYS* 1.3 65.5 + - - +
446C LYS* 3.3 20.2 + - - +
447C ASP* 3.1 18.7 + - - +
472C GLN* 5.0 3.8 - - - +
508C TYR* 3.6 36.5 - - - +
510C ARG* 4.4 24.2 + - - +
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Residues in contact with LYS 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C PHE* 3.8 43.7 - - + -
397C MET* 3.9 13.2 - - + +
440C ARG 2.9 17.1 + - - +
441C LEU 3.6 4.7 - - - +
443C ASN* 1.3 76.7 - - - +
445C PHE* 1.3 64.0 + - - +
447C ASP* 3.2 15.1 + - + +
448C HIS* 3.0 21.8 + - - +
509C GLY* 5.8 7.6 - - - -
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Residues in contact with PHE 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C MET* 3.7 19.9 - - + -
410C ILE* 3.7 28.7 - - + -
412C PHE* 3.5 50.3 - + + -
421C ALA* 4.8 1.6 - - + -
423C VAL* 3.9 13.9 - - + -
441C LEU 2.9 17.0 + - - +
442C MET* 3.5 12.1 - - - +
443C ASN 3.2 0.2 - - - -
444C LYS* 1.3 75.9 - - - +
446C LYS* 1.3 57.2 - - - +
448C HIS* 3.3 1.4 + - + +
449C MET* 2.8 59.3 + - + +
457C LEU* 3.4 41.5 - - + -
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Residues in contact with LYS 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C MET* 2.9 34.9 + - + +
443C ASN* 3.6 18.3 + - - +
444C LYS 3.3 0.2 - - - -
445C PHE* 1.3 73.8 - - - +
447C ASP* 1.3 56.4 + - - +
449C MET* 3.2 8.6 + - - +
450C GLN* 2.8 34.7 + - - +
457C LEU* 4.5 8.5 - - + -
472C GLN* 2.8 33.9 + - - +
473C GLY* 4.9 0.8 - - - -
474C PHE* 5.2 0.2 - - - -
500C CYS* 4.1 11.0 - - - -
502C ILE* 3.5 28.7 - - + +
508C TYR* 3.5 37.5 - - + -
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Residues in contact with ASP 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ASN 3.1 13.8 + - - +
444C LYS* 3.2 19.6 + - + +
446C LYS* 1.3 75.2 - - - +
448C HIS* 1.3 65.1 + - - +
450C GLN* 3.1 16.3 + - - +
451C LYS* 3.0 53.6 + - - +
508C TYR* 4.1 18.3 + - + +
509C GLY* 4.6 8.7 + - - -
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Residues in contact with HIS 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ILE* 3.1 34.8 - - + +
395C GLU* 4.7 13.0 - - - -
397C MET* 3.9 12.4 - - + +
412C PHE* 4.6 5.8 - + - -
414C GLN* 4.7 2.9 - - - -
444C LYS 3.0 12.4 + - - +
445C PHE* 3.6 7.6 - - - +
447C ASP* 1.3 80.2 + - - +
449C MET* 1.3 82.4 + - + +
451C LYS* 2.9 14.4 + - + +
452C GLN* 2.9 58.0 + - + +
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Residues in contact with MET 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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412C PHE* 3.8 12.6 - - + -
414C GLN* 3.9 12.3 - - - +
421C ALA* 3.8 17.0 - - - -
445C PHE* 2.8 61.0 + - + +
446C LYS* 3.5 7.6 - - - +
448C HIS* 1.3 99.4 - - - +
450C GLN* 1.3 57.0 + - - +
452C GLN* 3.1 5.0 + - + -
453C ASN 3.1 3.8 + - - -
454C ILE* 2.8 61.4 + - + +
457C LEU* 3.8 8.3 - - + -
502C ILE* 4.8 4.9 - - + -
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Residues in contact with GLN 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 LYS 2.8 13.7 + - - +
447C ASP* 3.1 22.2 - - - +
448C HIS 3.0 0.2 - - - -
449C MET* 1.3 77.8 - - - +
451C LYS* 1.3 61.3 + - + +
453C ASN* 3.1 21.1 + - - +
454C ILE 4.6 1.6 - - - -
502C ILE* 4.3 9.8 - - + +
503C HIS 2.6 27.8 + - - +
504C PRO* 3.6 19.8 - - + +
505C TYR* 3.2 14.0 - - - +
506C VAL 3.0 29.5 + - - +
508C TYR* 3.6 13.2 + - - -
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Residues in contact with LYS 451 (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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447C ASP* 3.0 45.0 + - - +
448C HIS* 2.9 15.5 + - + +
450C GLN* 1.3 82.6 + - + +
452C GLN* 1.3 69.4 + - - +
453C ASN* 3.1 12.1 + - - -
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Residues in contact with GLN 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C GLN* 3.1 21.3 + - - +
416C LYS* 2.7 38.8 + - - +
448C HIS* 2.9 56.6 + - + +
449C MET* 3.6 9.2 - - + +
450C GLN 3.1 0.4 - - - -
451C LYS* 1.3 84.0 + - - +
453C ASN* 1.3 76.8 + - - +
454C ILE* 3.3 13.9 + - + +
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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
------------------------------------------------------------
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