Contacts of the helix formed by residues 414 - 429 (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 ASP 414 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413M THR* 1.3 75.6 - - - +
415M GLU* 1.3 82.5 + - - +
416M GLU 3.3 1.3 - - - -
417M LYS* 3.1 12.6 + - + +
418M LYS* 2.9 42.9 + - - +
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Residues in contact with GLU 415 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L THR* 4.6 23.5 - - - +
413M THR* 3.5 5.1 + - - +
414M ASP* 1.3 89.9 + - - +
416M GLU* 1.3 64.9 + - + +
418M LYS* 3.2 29.3 + - - +
419M MET* 2.9 32.9 + - + +
422M GLU* 5.8 0.2 - - - +
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Residues in contact with GLU 416 (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* 2.9 38.3 + - - +
7L THR* 4.1 6.8 - - - +
412M ASN* 4.2 24.7 - - + +
413M THR* 3.1 26.8 + - + +
415M GLU* 1.3 79.3 - - - +
417M LYS* 1.3 57.6 + - - +
419M MET* 3.1 17.4 + - - +
420M VAL* 2.9 36.5 + - + +
475M LEU* 2.7 37.1 - - + +
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Residues in contact with LYS 417 (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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410M ASP* 4.0 27.8 + - - +
412M ASN* 4.0 13.2 + - + -
413M THR 3.0 20.8 - - - +
414M ASP* 3.1 14.2 + - + +
416M GLU* 1.3 75.1 - - - +
418M LYS* 1.3 65.6 + - + +
420M VAL* 3.3 6.5 + - - +
421M GLU* 2.9 31.8 + - - +
449M LYS* 3.3 51.8 - - + +
450M ARG* 4.5 5.6 - - - +
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Residues in contact with LYS 418 (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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414M ASP* 2.9 29.6 + - - +
415M GLU* 3.5 31.1 + - - +
417M LYS* 1.3 75.0 - - + +
419M MET* 1.3 57.8 + - - +
421M GLU* 3.3 17.1 + - - +
422M GLU* 2.9 38.2 + - + +
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Residues in contact with MET 419 (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* 3.5 14.4 - - - +
7L THR 4.1 17.7 - - - +
8L ARG* 4.6 0.2 - - - -
9L LEU* 3.2 46.9 - - + -
415M GLU* 2.9 20.2 + - + +
416M GLU* 3.1 32.8 - - - +
418M LYS* 1.3 74.7 - - - +
420M VAL* 1.3 59.6 + - - +
422M GLU* 3.2 16.6 + - - +
423M VAL* 2.9 34.3 + - + +
475M LEU* 3.4 20.9 - - + -
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Residues in contact with VAL 420 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412M ASN* 5.6 2.0 - - - +
416M GLU* 2.9 23.2 + - + +
417M LYS* 3.7 7.2 - - - +
419M MET* 1.3 73.9 - - - +
421M GLU* 1.3 61.5 + - - +
423M VAL* 3.1 8.5 - - - +
424M PHE* 2.9 34.1 + - + +
445M LEU* 5.0 9.0 - - + -
448M LEU* 4.3 38.4 - - + +
449M LYS* 4.6 4.5 - - + +
470M LEU* 4.5 14.6 - - + -
475M LEU* 3.8 36.1 - - + +
476M ILE* 6.1 0.2 - - + -
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Residues in contact with GLU 421 (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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417M LYS* 2.9 20.8 + - - +
418M LYS* 3.4 17.0 - - - +
420M VAL* 1.3 78.5 - - + +
422M GLU* 1.3 62.3 + - + +
424M PHE* 3.7 5.9 - - - +
425M SER* 2.9 26.3 + - - -
445M LEU* 4.7 10.3 - - + -
449M LYS* 3.2 37.4 + - + +
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Residues in contact with GLU 422 (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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9L LEU* 5.7 3.6 - - - +
19L MET* 6.3 0.2 - - - -
415M GLU* 5.8 0.2 - - - +
418M LYS* 2.9 24.8 + - + +
419M MET* 3.2 19.9 + - - +
421M GLU* 1.3 76.8 - - + +
423M VAL* 1.3 56.4 + - + +
425M SER* 3.3 4.5 + - - -
426M ASN* 2.6 43.1 + - - +
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Residues in contact with VAL 423 (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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9L LEU* 4.3 24.5 - - + -
13L LEU* 5.0 5.2 - - + -
18L PHE* 4.3 5.6 - - + -
19L MET* 3.7 26.7 - - + -
419M MET* 2.9 15.9 + - + +
420M VAL* 3.1 18.8 - - + +
422M GLU* 1.3 76.1 - - + +
424M PHE* 1.3 68.9 + - + +
426M ASN* 3.2 7.0 + - - +
427M ALA* 2.9 25.0 + - - +
466M THR* 5.7 2.9 - - + -
470M LEU* 3.7 27.8 - - + -
475M LEU* 5.3 1.6 - - + -
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Residues in contact with PHE 424 (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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420M VAL* 2.9 20.8 + - + +
421M GLU* 3.7 4.9 - - - +
423M VAL* 1.3 79.7 - - + +
425M SER* 1.3 58.7 + - - +
427M ALA* 3.2 6.4 + - - +
428M ILE* 2.9 60.4 + - + +
441M VAL* 3.7 33.9 - - + -
444M VAL* 6.2 0.4 - - + -
445M LEU* 3.5 39.0 - - + -
448M LEU* 4.5 10.8 - - + -
463M LEU* 3.6 26.0 - - + -
466M THR* 4.3 18.8 - - + -
470M LEU* 6.0 0.4 - - + -
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Residues in contact with SER 425 (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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421M GLU 2.9 17.9 + - - -
422M GLU* 3.7 4.5 - - - -
424M PHE* 1.3 75.1 - - - +
426M ASN* 1.3 67.0 + - - +
427M ALA 3.0 1.8 - - - -
428M ILE* 4.0 11.5 - - - +
429M ASP* 2.9 34.1 + - - +
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Residues in contact with ASN 426 (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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18L PHE* 3.0 46.5 + - + +
19L MET* 3.7 31.3 + - - +
21L ARG 4.9 9.1 - - - -
422M GLU* 2.6 33.7 + - - +
423M VAL 3.2 4.5 + - - +
425M SER* 1.3 76.3 + - - +
427M ALA* 1.3 57.9 + - - +
429M ASP* 4.3 8.8 + - - +
430M CYS 5.2 0.5 + - - -
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Residues in contact with ALA 427 (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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18L PHE* 3.5 22.9 - - + +
423M VAL 2.9 16.5 + - - +
424M PHE* 3.5 6.3 - - - +
425M SER 3.0 0.2 - - - -
426M ASN* 1.3 76.6 - - - +
428M ILE* 1.3 60.8 + - + +
429M ASP 3.2 5.6 + - - -
430M CYS* 3.1 26.0 + - - +
462M ILE* 5.0 1.2 - - - +
466M THR* 4.1 21.5 - - + +
1040M LEU* 4.1 17.0 - - + +
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Residues in contact with ILE 428 (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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424M PHE* 2.9 69.1 + - + +
425M SER* 4.0 9.2 - - - +
427M ALA* 1.3 73.7 - - + +
429M ASP* 1.3 61.6 + - - +
430M CYS* 3.2 6.3 - - - -
431M LEU* 3.4 23.3 + - + +
436M LYS* 3.1 42.1 - - + +
441M VAL* 5.6 6.1 - - + -
462M ILE* 4.1 20.6 - - + -
463M LEU* 4.8 4.9 - - + -
466M THR* 5.2 1.6 - - - +
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Residues in contact with ASP 429 (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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425M SER* 2.9 22.0 + - - +
426M ASN* 4.5 7.9 - - - +
427M ALA 3.2 1.0 - - - -
428M ILE* 1.3 75.1 - - - +
430M CYS* 1.3 57.6 + - - +
431M LEU 3.0 19.0 + - - +
436M LYS* 3.4 20.1 + - - +
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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