Contacts of the helix formed by residues 463 - 479 (chain A) in PDB entry 4MXP
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 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A LYS 3.9 2.6 + - - -
462A VAL* 1.3 73.2 - - - +
464A LYS* 1.3 64.8 + - - -
465A SER* 3.3 4.3 - - - -
466A LYS* 3.1 28.6 + - - +
467A ILE* 3.1 15.4 + - - +
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Residues in contact with LYS 464 (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 SER* 5.5 3.4 - - - +
412A ALA* 4.3 23.2 - - + +
415A ASP* 3.7 24.5 + - - +
462A VAL 3.4 6.5 + - - +
463A GLY* 1.3 71.0 - - - -
465A SER* 1.3 58.6 + - - +
467A ILE* 3.2 8.2 + - - +
468A LEU* 2.9 48.7 + - + +
512A ASP* 4.3 19.6 + - - +
515A LEU* 4.2 23.3 - - + +
519A LEU* 5.6 3.4 - - - +
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Residues in contact with SER 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A GLY* 4.9 1.6 - - - -
464A LYS* 1.3 77.9 - - - +
466A LYS* 1.3 61.9 + - - +
468A LEU* 3.5 7.7 + - - +
469A VAL* 3.1 34.7 + - - +
501A ILE* 3.6 19.2 - - - +
505A GLU* 2.5 36.5 + - - +
510A VAL* 4.2 21.1 - - - +
515A LEU* 4.6 4.3 - - - +
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Residues in contact with LYS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 4.6 6.2 - - + +
462A VAL* 6.2 0.2 - - + -
463A GLY* 3.1 23.2 + - - +
465A SER* 1.3 76.7 + - - +
467A ILE* 1.3 63.6 + - + +
469A VAL* 3.5 13.3 + - - +
470A GLY* 3.0 24.3 + - - -
502A GLN* 5.8 4.6 - - - +
505A GLU* 3.2 35.0 + - - +
638A SER* 5.9 1.4 + - - -
642A GLN* 4.4 30.9 + - - +
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Residues in contact with ILE 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 3.5 33.7 - - + +
405A ILE* 4.3 9.6 - - + +
408A SER* 4.3 10.5 - - - -
409A LEU* 3.7 26.9 - - + +
412A ALA* 3.6 24.9 - - + -
462A VAL* 3.6 27.1 - - + -
463A GLY 3.1 14.5 + - - +
464A LYS* 3.5 9.6 - - - +
466A LYS* 1.3 78.6 - - + +
468A LEU* 1.3 62.3 + - - +
470A GLY* 3.1 3.5 + - - -
471A ILE* 3.0 23.2 + - + +
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Residues in contact with LEU 468 (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 ALA* 3.9 33.7 - - + +
415A ASP* 6.2 0.2 - - + -
416A TYR* 4.0 21.3 - - + -
464A LYS* 2.9 29.3 + - + +
465A SER* 3.9 4.0 - - - +
467A ILE* 1.3 76.8 - - - +
469A VAL* 1.3 62.2 + - - +
471A ILE* 3.2 7.7 + - + +
472A MET* 3.0 29.0 + - + +
501A ILE* 4.0 12.3 - - + -
515A LEU* 3.9 34.8 - - + -
519A LEU* 4.0 27.6 - - + -
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Residues in contact with VAL 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A SER 3.1 18.9 + - - +
466A LYS* 3.8 14.1 - - - +
468A LEU* 1.3 74.8 - - - +
470A GLY* 1.3 59.4 + - - +
472A MET* 3.2 9.8 + - - +
473A GLN* 2.8 50.4 + - + +
498A ILE* 4.0 29.8 - - + +
501A ILE* 3.8 26.7 - - + -
502A GLN* 4.9 10.5 - - + +
505A GLU* 5.3 2.5 - - - +
639A GLN* 5.3 0.9 - - + -
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Residues in contact with GLY 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 3.7 24.5 - - - -
366A SER* 3.8 6.6 - - - -
466A LYS 3.0 14.8 + - - -
467A ILE 3.1 5.1 + - - -
469A VAL* 1.3 77.2 - - - +
471A ILE* 1.3 55.7 + - - +
473A GLN* 3.3 16.2 + - - +
474A PHE* 3.0 27.9 + - - +
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Residues in contact with ILE 471 (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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365A ILE* 4.1 0.2 - - - +
369A LEU* 4.2 12.6 - - + -
409A LEU* 3.9 28.7 - - + -
413A ALA* 4.1 31.2 - - + +
416A TYR* 3.9 22.4 - - + -
433A VAL* 4.3 7.9 - - + -
436A VAL* 4.4 15.5 - - + -
467A ILE* 3.0 22.2 + - + +
468A LEU* 3.2 19.3 + - + +
470A GLY* 1.3 75.6 - - - +
472A MET* 1.3 58.5 + - - +
474A PHE* 3.3 4.3 + - - +
475A ILE* 2.9 35.6 + - + +
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Residues in contact with MET 472 (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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416A TYR* 3.8 26.0 - - + +
468A LEU 3.0 15.4 + - - +
469A VAL* 3.6 6.5 - - - +
471A ILE* 1.3 76.9 - - - +
473A GLN* 1.3 55.3 + - - +
475A ILE* 3.3 3.6 + - - +
476A LYS* 3.0 30.8 + - - +
494A MET* 3.7 19.4 - - - +
497A LYS* 3.6 34.5 - - + -
498A ILE* 3.7 27.6 - - + -
501A ILE* 3.7 20.4 - - + -
518A VAL* 4.6 0.4 - - + -
519A LEU* 3.6 31.2 - - + -
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Residues in contact with GLN 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A SER* 3.8 19.3 + - - +
469A VAL* 2.8 27.5 + - - +
470A GLY* 3.3 19.3 + - - +
472A MET* 1.3 72.1 - - - +
474A PHE* 1.3 65.0 + - - +
476A LYS* 3.2 12.5 + - + +
477A ASP* 3.0 31.0 + - - +
498A ILE* 4.2 8.1 - - + -
639A GLN* 2.8 46.5 - - - +
642A GLN* 6.0 3.7 - - - +
646A ILE* 5.8 3.8 - - - +
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Residues in contact with PHE 474 (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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366A SER* 4.0 8.0 - - - -
369A LEU* 3.5 44.9 - - + -
370A LYS* 3.9 13.2 - - + -
373A ASN* 4.1 8.1 - - - -
432A LEU* 4.9 6.5 - - + -
435A ALA* 5.8 1.1 - - + -
436A VAL* 3.8 29.4 - - + -
439A MET* 3.7 24.2 - - + -
470A GLY 3.0 12.3 + - - +
471A ILE 3.3 8.9 + - - +
473A GLN* 1.3 76.5 - - - +
475A ILE* 1.3 68.9 + - + +
477A ASP* 3.0 13.3 + - + +
478A VAL* 2.9 56.3 + - + +
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Residues in contact with ILE 475 (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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416A TYR* 4.2 5.4 - - - +
429A GLU* 5.1 2.7 - - + +
432A LEU* 3.8 42.4 - - + -
433A VAL* 4.0 27.6 - - + +
436A VAL* 5.7 0.2 - - + -
471A ILE* 2.9 25.2 + - + +
472A MET 3.5 7.6 - - - +
473A GLN 3.3 0.2 - - - -
474A PHE* 1.3 82.3 - - + +
476A LYS* 1.3 64.1 + - - +
478A VAL* 3.5 6.8 - - - +
479A ALA* 3.0 29.2 + - + +
490A THR* 3.9 11.4 - - + -
494A MET* 3.7 33.0 - - + -
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Residues in contact with LYS 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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472A MET 3.0 9.2 + - - +
473A GLN* 3.4 13.0 - - + +
474A PHE 3.2 0.2 - - - -
475A ILE* 1.3 80.1 - - - +
477A ASP* 1.3 65.2 - - - +
479A ALA* 3.6 7.6 + - - +
491A LYS* 3.3 49.4 + - - +
494A MET* 3.5 25.8 - - + -
495A ASN* 2.7 36.9 + - - +
498A ILE* 4.2 13.2 - - + +
580A ALA 4.5 9.8 + - - -
582A ALA 4.9 7.1 + - - -
639A GLN* 5.1 11.3 + - - +
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Residues in contact with ASP 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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366A SER* 4.2 17.0 + - - +
370A LYS* 5.5 16.5 - - + +
473A GLN* 3.0 23.9 + - - +
474A PHE* 3.0 11.1 + - + +
476A LYS* 1.3 80.0 - - - +
478A VAL* 1.3 64.4 + - + +
479A ALA 3.7 2.4 + - - +
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Residues in contact with VAL 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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370A LYS* 6.2 1.1 - - + -
373A ASN* 4.4 10.3 - - - +
432A LEU* 4.3 19.3 - - + -
474A PHE* 2.9 59.6 + - + +
475A ILE* 3.5 11.9 - - - +
477A ASP* 1.3 80.6 - - + +
479A ALA* 1.3 66.0 + - - +
480A ASP 3.7 1.2 + - - -
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Residues in contact with ALA 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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432A LEU* 6.0 4.3 - - + -
475A ILE* 3.0 17.9 + - + +
476A LYS 4.0 11.7 - - - +
477A ASP 3.4 3.4 - - - +
478A VAL* 1.3 79.9 - - + +
480A ASP* 1.3 66.4 + - - +
481A PRO* 3.5 5.0 - - - +
483A SER* 3.8 13.9 - - - +
490A THR* 3.9 19.5 - - + -
491A LYS* 4.3 12.3 + - + +
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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