Contacts of the helix formed by residues 404 - 416 (chain A) in PDB entry 1MWT
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 THR 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A PRO* 2.7 40.4 + - - +
403A SER* 1.3 72.0 - - - +
405A GLN* 1.3 62.0 + - - +
406A LYS 3.2 0.5 + - - -
407A ILE 3.4 4.3 + - - -
408A LEU* 3.6 9.4 - - - +
531A ILE* 3.8 10.8 - - - +
535A TYR* 2.8 30.8 + - - -
597A LYS* 4.3 7.9 - - - +
598A SER 4.6 7.2 - - - +
616A TRP* 3.5 35.2 - - + -
618A ILE* 3.9 20.9 - - + -
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Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A PRO* 3.8 9.6 - - + -
402A GLY 3.0 16.1 + - - +
404A THR* 1.3 83.1 + - - +
406A LYS* 1.3 52.8 + - - +
408A LEU* 2.7 48.3 + - - +
409A THR* 3.0 27.4 + - - +
479A PHE* 4.0 4.6 - - - -
483A MET* 3.4 29.1 - - - +
517A SER 3.1 22.9 + - - +
518A GLY 4.0 0.2 - - - +
520A GLY* 3.6 12.6 - - - +
524A ILE* 3.4 21.7 - - + +
526A ILE* 4.3 4.0 - - - +
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A SER* 3.3 25.5 + - - +
404A THR 3.1 0.4 - - - -
405A GLN* 1.3 79.1 - - - +
407A ILE* 1.3 59.1 + - + +
409A THR* 3.2 3.5 + - - -
410A ALA* 2.8 29.3 + - - +
459A ILE* 6.1 0.2 - - + -
462A SER* 2.7 53.8 + - - +
463A ASP 3.4 4.8 - - - +
464A ASN* 3.1 13.6 + - - -
467A PHE* 3.3 42.1 - - + -
518A GLY 4.0 8.1 - - - -
519A TYR* 3.5 31.6 - - - -
597A LYS* 4.1 11.2 - - - -
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Residues in contact with ILE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A THR 3.4 1.0 + - - -
405A GLN 3.1 1.0 + - - -
406A LYS* 1.3 78.0 - - - +
408A LEU* 1.3 62.6 + - + +
410A ALA* 3.4 4.3 + - + +
411A MET* 3.0 42.6 + - + +
459A ILE* 4.4 20.9 - - + -
535A TYR* 3.0 52.9 - - + +
538A LEU* 4.8 5.6 - - + -
571A LEU* 4.2 21.3 - - + -
575A MET* 4.0 26.2 - - + -
597A LYS* 4.3 15.3 - - + -
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Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A PRO* 6.4 0.4 - - + -
404A THR* 3.6 19.1 - - - +
405A GLN* 2.7 40.9 + - - +
407A ILE* 1.3 68.6 - - - +
409A THR* 1.3 62.7 + - - +
411A MET* 3.0 15.1 + - - +
412A ILE* 3.1 19.7 + - - +
483A MET* 4.3 3.1 - - - -
486A LEU* 3.3 20.1 - - + +
488A VAL* 4.6 5.8 - - + -
526A ILE* 5.1 7.0 - - + -
531A ILE* 5.1 6.3 - - + -
534A ILE* 3.3 48.5 - - + -
535A TYR* 3.9 19.3 - - + -
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Residues in contact with THR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLN* 3.0 19.8 + - - +
406A LYS* 3.4 8.3 - - - -
408A LEU* 1.3 75.6 - - - +
410A ALA* 1.3 62.9 + - - +
412A ILE* 3.2 12.3 + - - +
413A GLY* 3.0 19.6 + - - -
467A PHE* 4.0 13.2 - - + +
470A VAL* 3.6 30.6 - - + +
471A ALA 4.6 1.6 - - - +
474A LEU* 4.2 1.3 - - + +
479A PHE* 4.0 10.0 - - + -
518A GLY* 2.5 37.9 + - - +
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Residues in contact with ALA 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A LYS 2.8 17.4 + - - +
407A ILE* 3.6 7.2 - - + +
409A THR* 1.3 76.0 - - - +
411A MET* 1.3 59.7 + - - +
413A GLY* 3.3 0.7 + - - -
414A LEU* 2.8 39.1 + - + +
419A LEU* 4.1 16.3 - - + +
455A LEU* 4.4 2.2 - - + -
459A ILE* 5.5 0.2 - - + -
467A PHE* 4.3 12.8 - - + -
571A LEU* 3.7 26.7 - - + -
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Residues in contact with MET 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ILE* 3.0 28.5 + - + +
408A LEU* 3.0 8.6 + - - +
410A ALA* 1.3 75.6 - - - +
412A ILE* 1.3 58.5 + - - +
414A LEU* 3.6 8.9 - - - +
415A ASN* 2.8 30.8 + - - +
486A LEU* 3.9 15.0 - - + -
534A ILE* 3.5 44.6 - - + +
537A ALA* 4.3 5.2 - - + -
538A LEU* 4.1 26.7 - - + -
562A ILE* 3.8 32.6 - - + +
563A ILE* 4.3 11.7 - - + +
571A LEU* 4.2 9.0 - - + -
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Residues in contact with ILE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A LEU 3.1 17.7 + - - +
409A THR 3.5 5.4 - - - +
411A MET* 1.3 75.7 - - - +
413A GLY* 1.3 57.9 + - - +
415A ASN* 3.1 6.5 + - - +
416A ASN* 2.9 41.3 + - - +
474A LEU* 3.7 16.6 - - + -
478A LYS 3.6 23.6 - - - +
479A PHE* 3.9 17.0 - - + +
482A GLY* 3.7 17.9 - - - +
483A MET* 3.6 43.5 - - + +
486A LEU* 3.9 8.1 - - + -
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Residues in contact with GLY 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A THR 3.0 13.8 + - - -
410A ALA 3.8 1.8 - - - -
412A ILE* 1.3 75.7 - - - +
414A LEU* 1.3 57.8 + - - +
416A ASN 3.4 0.3 + - - -
417A LYS 3.0 8.0 + - - -
418A THR* 3.0 42.4 + - - -
419A LEU* 3.2 15.3 + - - -
470A VAL* 4.5 3.6 - - - -
474A LEU* 3.9 10.5 - - - +
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A ALA* 2.8 32.8 + - + +
411A MET* 3.6 4.3 - - - +
413A GLY* 1.3 76.8 - - - +
415A ASN* 1.3 62.5 + - - +
417A LYS* 3.5 13.0 + - - +
419A LEU* 3.2 31.9 - - + +
420A ASP* 4.2 1.6 - - - -
455A LEU* 4.6 2.0 - - + -
563A ILE* 4.2 5.8 - - + -
567A ASN* 3.6 52.5 + - + +
570A LEU* 4.0 18.8 - - + -
571A LEU* 3.9 32.3 - - + -
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Residues in contact with ASN 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A MET 2.8 18.0 + - - +
412A ILE* 3.4 7.3 - - - +
414A LEU* 1.3 76.3 - - - +
416A ASN* 1.3 71.3 + - - +
417A LYS* 3.1 15.2 + - - +
482A GLY* 5.4 3.0 - - - -
485A LYS* 3.4 43.5 + - - +
561A ASN 5.2 0.7 - - - +
562A ILE 5.0 9.0 - - - +
563A ILE* 6.4 0.9 - - - +
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Residues in contact with ASN 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ILE* 2.9 41.2 + - - +
413A GLY 4.3 0.4 - - - +
415A ASN* 1.3 85.8 + - - +
417A LYS* 1.3 61.5 + - - +
418A THR* 2.8 22.2 + - + +
474A LEU* 3.9 15.2 - - + +
478A LYS* 3.9 39.8 + - + +
482A GLY* 5.0 1.6 - - - -
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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