Contacts of the helix formed by residues 470 - 487 (chain B) in PDB entry 3QMK
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 ASN 470 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399B LEU* 6.2 3.6 - - + -
466B LEU 5.6 0.4 - - - +
467B LEU* 3.3 12.8 + - + +
468B ASP 3.0 1.6 - - - -
469B GLN* 1.3 81.5 - - - +
471B PRO* 1.3 56.8 - - - +
472B HIS 3.4 2.5 - - - -
473B LEU* 3.2 23.4 + - + -
474B ALA* 2.8 32.7 + - - +
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Residues in contact with PRO 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B ASP* 4.3 9.1 - - - +
469B GLN 3.8 5.6 - - - +
470B ASN* 1.3 84.8 - - - +
472B HIS* 1.3 57.7 + - - +
474B ALA* 3.5 6.7 - - + +
475B GLN* 2.6 38.7 + - - +
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Residues in contact with HIS 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B ASN 3.4 1.2 - - - -
471B PRO* 1.3 78.6 - - - +
473B LEU* 1.3 53.8 + - - +
475B GLN* 3.0 5.8 + - - +
476B GLU* 2.7 41.7 + - - +
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Residues in contact with LEU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B LEU* 4.5 6.3 - - + +
404B PRO* 4.1 22.4 - - + +
406B ALA* 3.4 42.6 - - + +
409B VAL* 4.0 22.2 - - + -
467B LEU* 4.1 19.7 - - + -
470B ASN* 3.2 21.6 + - + +
472B HIS* 1.3 77.3 - - - +
474B ALA* 1.3 58.1 + - - +
476B GLU* 3.1 11.5 + - - +
477B LEU* 2.8 38.6 + - + +
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Residues in contact with ALA 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B LEU* 3.5 31.8 + - + +
468B ASP* 4.2 17.0 - - - +
470B ASN 2.8 19.9 + - - +
471B PRO* 3.5 8.5 - - + +
473B LEU* 1.3 74.0 - - - +
475B GLN* 1.3 54.4 + - - +
476B GLU 3.1 0.2 + - - -
477B LEU 3.6 0.2 - - - -
478B ARG* 2.7 37.6 + - - +
481B ILE* 5.2 1.0 - - - +
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Residues in contact with GLN 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B PRO 2.6 22.3 + - - +
472B HIS* 3.4 6.3 - - - +
474B ALA* 1.3 73.6 - - - +
476B GLU* 1.3 63.2 + - - +
478B ARG* 3.5 16.4 - - - +
479B PRO* 3.8 4.3 - - - +
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Residues in contact with GLU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ALA* 3.4 26.4 - - + +
472B HIS* 2.7 19.6 + - - +
473B LEU* 3.2 16.7 + - - +
475B GLN* 1.3 75.8 - - - +
477B LEU* 1.3 62.9 + - + +
478B ARG 3.5 0.2 + - - -
479B PRO* 3.7 12.3 - - - +
480B GLN* 4.1 6.8 + - - +
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B ALA* 3.4 41.5 - - + +
409B VAL* 3.7 27.4 - - + -
410B LEU* 3.8 20.0 - - + +
413B LEU* 5.8 0.7 - - + -
467B LEU* 4.6 8.3 - - + -
473B LEU* 2.8 28.5 + - + +
474B ALA 4.2 0.7 - - - +
476B GLU* 1.3 76.0 - - + +
478B ARG* 1.3 66.4 + - - +
479B PRO* 3.4 0.7 - - - -
480B GLN* 2.9 27.8 + - - +
481B ILE* 2.8 36.2 + - + +
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Residues in contact with ARG 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B ALA 2.7 21.6 + - - +
475B GLN* 3.5 11.0 - - - +
477B LEU* 1.3 71.1 - - - +
479B PRO* 1.3 73.3 - - + +
481B ILE* 3.1 8.8 + - - +
482B GLN* 3.0 33.9 + - + +
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Residues in contact with PRO 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B GLN 3.8 4.5 - - - +
476B GLU 3.7 14.1 - - - +
477B LEU 3.6 1.1 - - - -
478B ARG* 1.3 96.2 - - + +
480B GLN* 1.3 64.9 + - + +
482B GLN* 3.6 9.3 + - + +
483B GLU* 3.4 19.4 + - - +
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Residues in contact with GLN 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 3.6 27.1 - - + +
476B GLU* 4.1 6.7 + - - +
477B LEU* 2.9 37.6 + - - +
479B PRO* 1.3 80.3 - - + +
481B ILE* 1.3 65.4 + - - +
483B GLU* 3.4 8.4 + - - +
484B LEU* 3.3 25.0 + - - +
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Residues in contact with ILE 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU* 4.3 5.4 - - + -
413B LEU* 3.6 23.6 - - + -
417B LEU* 5.0 2.9 - - + -
464B LEU* 4.3 10.3 - - + -
467B LEU* 3.0 36.8 - - + -
474B ALA 5.2 0.7 - - - +
477B LEU* 2.8 32.6 + - + +
478B ARG* 3.5 9.9 - - - +
480B GLN* 1.3 72.8 - - - +
482B GLN* 1.3 65.6 + - - +
484B LEU* 2.9 11.9 + - - +
485B LEU* 2.8 48.0 + - + +
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Residues in contact with GLN 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B ARG* 3.0 24.5 + - + +
479B PRO* 3.7 10.3 - - + +
481B ILE* 1.3 80.5 - - - +
483B GLU* 1.3 57.1 + - - +
485B LEU* 3.7 17.9 - - - +
486B HIS* 2.8 34.5 + - - +
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Residues in contact with GLU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B PRO 3.4 10.1 + - - +
480B GLN* 3.6 11.2 - - - +
481B ILE 3.2 0.6 - - - -
482B GLN* 1.3 78.8 - - - +
484B LEU* 1.3 63.1 + - + +
486B HIS* 3.9 4.6 - - - +
487B SER* 3.2 21.1 + - - -
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU* 4.0 20.0 - - + -
413B LEU* 4.8 3.6 - - + -
414B ARG* 3.6 59.5 - - + +
417B LEU* 4.0 22.1 - - + +
480B GLN 3.4 14.4 - - - +
481B ILE* 2.9 16.5 + - - +
483B GLU* 1.3 79.3 - - + +
485B LEU* 1.3 61.6 - - - +
487B SER* 3.2 20.4 - - - -
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Residues in contact with LEU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B LEU* 3.8 28.7 - - + -
460B VAL* 4.2 8.1 - - + -
464B LEU* 3.7 31.6 - - + -
481B ILE* 2.8 31.2 + - + +
482B GLN* 3.9 19.1 - - - +
484B LEU* 1.3 78.2 - - - +
486B HIS* 1.3 60.6 + - - +
487B SER* 3.1 4.2 + - - -
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Residues in contact with HIS 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B GLN 2.8 22.4 + - - +
483B GLU* 3.9 5.4 - - - +
485B LEU* 1.3 71.1 - - - +
487B SER* 1.3 65.5 + - - +
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Residues in contact with SER 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B GLU 3.2 11.6 + - - -
484B LEU* 3.2 18.6 - - - -
485B LEU 3.1 5.4 - - - -
486B HIS* 1.3 82.6 - - - +
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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