Contacts of the helix formed by residues 475 - 487 (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 GLY 475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A ALA 3.0 8.8 + - - -
472A LEU 3.5 8.7 + - - -
473A GLU 3.3 3.1 - - - -
474A LEU* 1.3 78.6 - - - +
476A SER* 1.3 67.8 + - - -
477A LYS* 2.9 6.0 + - - -
478A LYS 3.1 3.4 + - - -
479A PHE* 2.9 22.4 + - - +
514A LEU* 4.8 0.9 - - - -
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Residues in contact with SER 476 (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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475A GLY* 1.3 70.1 - - - -
477A LYS* 1.3 64.1 + - - +
479A PHE* 3.6 0.7 - - - +
480A GLU* 3.2 33.2 + - - +
508A LEU* 2.9 41.1 + - - +
509A ASP* 4.5 7.9 + - - -
514A LEU* 4.2 20.7 - - - +
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Residues in contact with LYS 477 (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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475A GLY* 2.9 2.6 + - - -
476A SER* 1.3 79.4 + - - +
478A LYS* 1.3 65.8 + - + +
479A PHE 3.1 1.6 - - - -
480A GLU* 4.0 7.1 - - - +
481A LYS* 3.1 60.0 + - + +
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Residues in contact with LYS 478 (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* 3.6 8.1 - - - +
416A ASN* 3.9 38.5 + - + +
418A THR* 5.1 10.9 - - + +
474A LEU* 3.4 30.1 - - + +
475A GLY 3.1 2.4 + - - -
477A LYS* 1.3 79.7 - - + +
479A PHE* 1.3 57.7 + - - +
481A LYS* 3.8 10.6 - - + +
482A GLY* 2.8 24.5 + - - -
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Residues in contact with PHE 479 (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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405A GLN* 4.0 13.5 - - - -
409A THR* 4.0 14.1 - - + -
412A ILE* 3.9 15.7 - - + +
471A ALA* 4.2 15.7 - - + -
474A LEU* 3.9 24.4 - - + +
475A GLY 2.9 16.4 + - - +
476A SER 3.6 6.1 - - - +
478A LYS* 1.3 74.5 - - - +
480A GLU* 1.3 60.8 + - - +
482A GLY* 2.8 2.6 + - - -
483A MET* 2.8 47.5 + - + +
503A ILE* 4.7 2.7 - - + -
508A LEU* 3.3 24.2 - - + -
514A LEU* 3.9 13.0 - - + -
517A SER* 3.9 41.1 - - - -
524A ILE* 4.5 6.1 - - + -
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Residues in contact with GLU 480 (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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476A SER* 3.2 17.1 + - - +
477A LYS* 4.0 6.2 - - - +
479A PHE* 1.3 78.5 - - - +
481A LYS* 1.3 57.2 + - - +
483A MET* 3.4 1.1 + - - +
484A LYS* 3.0 61.7 + - - +
503A ILE* 4.3 15.9 - - + +
504A SER* 4.6 2.4 + - - -
506A LYS 4.8 1.4 - - - +
507A ASN* 3.9 14.1 - - - +
508A LEU* 3.3 44.0 + - + +
509A ASP* 5.8 0.2 - - - +
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Residues in contact with LYS 481 (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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477A LYS* 3.1 56.3 + - + +
478A LYS* 3.9 9.9 - - + +
480A GLU* 1.3 77.3 - - - +
482A GLY* 1.3 57.4 + - - +
484A LYS* 4.0 11.2 - - + +
485A LYS* 3.0 30.8 + - - +
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Residues in contact with GLY 482 (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* 3.7 24.4 - - - +
415A ASN* 5.4 1.6 - - - -
416A ASN* 5.0 3.1 - - - -
478A LYS 2.8 17.2 + - - -
479A PHE 2.8 4.0 + - - -
481A LYS* 1.3 77.0 - - - +
483A MET* 1.3 61.5 + - - +
485A LYS* 3.3 12.8 - - - +
486A LEU* 3.1 25.3 + - - +
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Residues in contact with MET 483 (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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405A GLN* 3.4 21.5 - - - +
408A LEU* 4.3 7.6 - - - -
412A ILE* 3.7 18.6 - - + -
479A PHE* 2.8 29.1 + - + +
482A GLY* 1.3 69.7 - - - +
484A LYS* 1.3 61.5 + - - +
486A LEU* 2.8 26.8 + - - +
487A GLY 2.9 8.1 + - - -
488A VAL* 3.0 30.7 + - + +
503A ILE* 3.4 35.0 - - + -
524A ILE* 3.3 44.0 - - + -
526A ILE* 4.8 0.9 - - + -
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Residues in contact with LYS 484 (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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480A GLU* 3.0 49.4 + - - +
481A LYS* 4.2 10.4 - - + +
483A MET* 1.3 75.2 - - - +
485A LYS* 1.3 57.5 + - - +
487A GLY 2.9 13.0 + - - -
488A VAL 3.8 13.9 - - - +
490A GLU* 3.1 24.7 - - + +
503A ILE* 3.7 17.3 - - + -
559A LYS* 4.0 1.4 + - - -
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Residues in contact with LYS 485 (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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415A ASN* 3.4 39.4 + - - +
481A LYS 3.0 20.7 + - - +
482A GLY* 3.3 9.0 - - - +
484A LYS* 1.3 77.9 - - - +
486A LEU* 1.3 60.6 + - + +
487A GLY 3.1 0.6 + - - -
559A LYS* 3.7 14.9 - - - +
560A LYS 4.5 4.2 + - - +
561A ASN* 3.0 28.7 + - - +
562A ILE* 3.4 21.7 + - + +
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Residues in contact with LEU 486 (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* 3.3 36.8 - - + +
411A MET* 3.9 15.9 - - + -
412A ILE* 3.9 22.4 - - + -
482A GLY 3.1 17.5 + - - +
483A MET* 2.8 14.0 + - - +
485A LYS* 1.3 77.4 - - + +
487A GLY* 1.3 58.2 + - - +
488A VAL* 4.4 1.1 - - + -
530A GLN* 4.9 1.4 + - - -
534A ILE* 3.9 21.1 - - + +
544A ILE* 3.8 19.6 - - - +
558A TRP* 5.3 2.3 - - - -
559A LYS* 3.9 5.9 - - - +
562A ILE* 3.6 39.9 - - + +
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Residues in contact with GLY 487 (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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484A LYS 2.9 15.4 + - - -
485A LYS 3.1 0.6 - - - -
486A LEU* 1.3 79.9 - - - +
488A VAL* 1.3 64.0 + - - +
489A GLY 3.2 2.8 + - - -
490A GLU* 3.3 22.1 + - - +
530A GLN* 3.0 18.0 + - - -
558A TRP* 4.0 5.8 - - - -
559A LYS* 3.6 17.7 - - - -
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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