Contacts of the helix formed by residues 460 - 474 (chain M) in PDB entry 6D6Q
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 LEU 460 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431M LEU* 6.1 0.7 - - + -
438M LEU* 3.3 33.9 - - + -
440M GLN* 4.0 6.8 + - - +
441M VAL* 5.0 3.4 - - + -
459M LEU* 1.3 75.5 - - - +
461M PRO* 1.3 74.0 - - + +
462M ILE* 3.0 8.8 + - + +
463M LEU* 3.1 30.5 + - + +
464M LYS* 3.2 9.1 + - - +
979M PHE* 4.1 16.8 - - + -
990M GLU* 3.4 22.4 - - + +
994M ILE* 4.3 16.4 - - + -
1034M ILE* 3.7 29.2 - - + -
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Residues in contact with PRO 461 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459M LEU 3.7 5.5 - - - +
460M LEU* 1.3 87.2 - - + +
462M ILE* 1.3 67.6 + - + +
464M LYS* 3.3 21.9 - - + +
465M GLU* 2.9 35.7 + - + +
991M GLY* 5.8 0.2 - - - -
994M ILE* 4.7 14.1 - - + -
998M ARG* 3.6 33.2 - - - +
1034M ILE* 5.6 5.4 - - + +
1037M ALA* 6.5 0.9 - - + -
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Residues in contact with ILE 462 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427M ALA 5.0 6.3 - - - +
428M ILE* 4.1 26.0 - - + -
430M CYS* 4.9 5.6 - - - -
431M LEU* 3.5 41.1 - - + -
460M LEU* 3.0 5.8 + - + +
461M PRO* 1.3 82.9 - - + +
463M LEU* 1.3 65.2 + - + +
465M GLU* 3.3 2.3 + - - -
466M THR* 2.9 27.2 + - - +
1034M ILE* 3.9 19.1 - - + +
1037M ALA* 4.1 16.8 - - + -
1038M ALA 4.9 8.1 - - - +
1040M LEU* 3.6 22.2 - - + +
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Residues in contact with LEU 463 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424M PHE* 3.6 34.8 - - + -
428M ILE* 4.8 8.3 - - + -
440M GLN* 4.5 19.7 - - + +
441M VAL* 4.4 32.1 - - + +
444M VAL* 5.1 13.7 - - + -
448M LEU* 5.7 2.7 - - + -
459M LEU* 4.5 15.9 - - + -
460M LEU* 3.1 19.6 + - + +
462M ILE* 1.3 81.0 - - + +
464M LYS* 1.3 56.8 + - - +
466M THR* 3.5 6.3 - - - +
467M ILE* 2.9 42.2 + - + +
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Residues in contact with LYS 464 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455M HIS* 3.0 48.4 + - + +
456M HIS 4.3 8.3 - - - -
457M GLY* 4.5 12.1 - - - -
459M LEU* 5.0 16.5 + - + +
460M LEU 3.2 5.8 + - - +
461M PRO* 3.1 26.6 + - + +
462M ILE 3.1 0.8 - - - -
463M LEU* 1.3 76.3 - - - +
465M GLU* 1.3 60.5 + - + +
467M ILE* 3.3 7.4 + - - +
468M GLU* 2.9 39.5 + - - +
484M THR* 5.3 2.8 + - + +
995M ARG* 4.2 19.6 - - - +
20O C 4.7 5.3 + - - -
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Residues in contact with GLU 465 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193M ALA* 5.4 8.0 - - + +
196M ASN* 4.8 1.7 + - - -
461M PRO* 2.9 25.4 + - + +
462M ILE* 3.8 4.1 - - - +
464M LYS* 1.3 74.7 - - + +
466M THR* 1.3 67.6 + - - +
468M GLU* 3.2 5.5 + - - +
469M ILE* 2.9 30.6 + - - +
1038M ALA 4.5 1.0 - - - +
1039M SER* 2.3 31.4 + - - -
1040M LEU* 2.3 42.7 + - + +
1041M TYR* 3.5 29.6 + - + -
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Residues in contact with THR 466 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423M VAL* 5.7 1.3 - - + -
424M PHE* 4.3 29.4 - - + +
427M ALA* 4.1 10.2 - - + +
428M ILE* 5.2 2.4 - - - +
448M LEU* 4.9 4.7 - - + -
462M ILE* 2.9 20.2 + - - +
463M LEU* 3.5 12.6 - - - +
465M GLU* 1.3 77.8 - - - +
467M ILE* 1.3 56.8 + - - +
469M ILE* 3.3 5.9 + - - +
470M LEU* 2.9 53.1 + - + +
1040M LEU* 3.4 16.0 - - - +
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Residues in contact with ILE 467 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444M VAL* 5.0 8.7 - - + -
448M LEU* 3.9 35.2 - - + -
453M GLY* 5.0 1.1 - - - -
454M ILE* 3.1 32.5 - - + +
455M HIS* 4.9 7.0 - - + -
459M LEU* 4.5 9.4 - - + -
463M LEU* 2.9 27.8 + - + +
464M LYS* 3.8 5.4 - - - +
466M THR* 1.3 74.1 - - - +
468M GLU* 1.3 67.6 + - - +
470M LEU* 3.4 6.9 + - - +
471M PHE* 2.9 23.7 + - - +
476M ILE* 4.9 5.1 - - + +
479M LEU* 3.9 31.2 - - + -
485M PHE* 5.1 1.1 - - + -
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Residues in contact with GLU 468 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193M ALA* 5.2 10.5 - - - +
197M GLN* 3.7 8.0 + - - -
455M HIS* 3.3 22.2 - - - +
464M LYS* 2.9 27.7 + - - +
465M GLU* 3.2 3.4 + - - +
467M ILE* 1.3 77.7 - - - +
469M ILE* 1.3 60.5 + - - +
471M PHE* 3.4 3.0 + - - +
472M SER* 3.0 25.2 + - - -
484M THR* 4.6 4.0 - - - +
485M PHE* 3.9 30.2 - - + -
489M ILE* 4.1 18.3 - - + +
491M MET* 4.4 7.7 - - + +
1041M TYR* 3.1 34.3 + - - +
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Residues in contact with ILE 469 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L LEU* 3.4 34.5 - - + -
16L MET* 4.1 28.5 - - + -
18L PHE* 4.4 10.3 - - + -
465M GLU 2.9 25.0 + - - +
466M THR* 3.6 7.0 - - - +
468M GLU* 1.3 72.9 - - - +
470M LEU* 1.3 70.4 + - + +
472M SER* 2.9 21.0 + - - -
473M GLU* 2.9 11.8 + - - +
1040M LEU* 4.4 15.9 - - + -
1041M TYR* 3.4 27.1 - - + +
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Residues in contact with LEU 470 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L LEU* 5.7 2.2 - - + -
420M VAL* 4.5 15.7 - - + -
423M VAL* 3.7 25.1 - - + -
424M PHE* 6.0 0.7 - - + -
448M LEU* 4.4 23.3 - - + -
466M THR* 2.9 41.6 + - + +
467M ILE* 3.7 6.5 - - - +
469M ILE* 1.3 80.3 - - + +
471M PHE* 1.3 58.5 + - - +
473M GLU* 3.1 8.0 + - + +
474M GLY 2.8 24.6 + - - -
475M LEU* 3.2 39.1 + - + -
476M ILE* 4.5 11.0 - - + -
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Residues in contact with PHE 471 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388M PRO* 4.3 10.3 - - + -
389M VAL 4.6 1.1 - - - -
390M ILE* 4.0 15.9 - - + -
467M ILE 2.9 18.1 + - - +
468M GLU* 3.7 5.6 - - - +
469M ILE 3.1 0.2 - - - -
470M LEU* 1.3 72.9 - - - +
472M SER* 1.3 66.3 + - - +
473M GLU 3.2 0.9 + - - -
474M GLY* 3.3 11.7 + - - +
476M ILE* 3.4 41.2 - - + +
477M LYS 4.2 13.5 - - - -
479M LEU* 4.3 14.6 - - + -
485M PHE* 4.8 8.7 - + + -
491M MET* 3.1 41.7 - - + -
492M PRO 3.6 6.7 - - - -
493M ALA* 3.8 24.7 - - + -
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Residues in contact with SER 472 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468M GLU 3.0 7.9 + - - -
469M ILE* 2.9 13.5 + - - -
471M PHE* 1.3 76.9 - - - +
473M GLU* 1.3 66.3 + - - +
491M MET* 2.9 47.0 - - - +
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Residues in contact with GLU 473 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L LYS* 4.5 22.5 + - - +
9L LEU* 4.4 4.9 - - + +
10L SER* 3.2 40.3 + - - -
13L LEU* 3.1 41.0 + - + +
469M ILE* 2.9 12.8 + - + +
470M LEU* 3.3 9.2 - - - +
471M PHE 3.7 0.2 - - - -
472M SER* 1.3 83.4 - - - +
474M GLY* 1.3 59.7 + - - +
475M LEU* 4.2 19.1 - - + -
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Residues in contact with GLY 474 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L LYS* 5.6 5.9 - - - +
470M LEU 2.8 8.8 + - - -
471M PHE 3.3 8.8 + - - -
473M GLU* 1.3 74.5 - - - +
475M LEU* 1.3 60.7 + - - +
476M ILE 3.1 15.7 + - - +
477M LYS* 2.8 29.9 + - - +
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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
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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