Contacts of the helix formed by residues 475 - 486 (chain B) in PDB entry 6QX2
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 475 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458B ARG* 6.0 1.3 - - - -
461B ILE* 5.1 0.2 - - - +
462B LEU* 3.4 33.1 - - + +
471B ARG* 2.9 12.7 + - + +
472B ILE 3.3 14.3 + - - +
474B ASN* 1.3 74.9 - - - +
476B ASN* 1.3 57.2 + - - +
477B GLU* 2.9 34.8 + - - +
478B ILE* 3.1 21.3 + - + +
479B ARG* 3.1 31.5 + - - +
2013F G 5.4 0.4 + - - -
2014F T 4.1 18.8 + - - -
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Residues in contact with ASN 476 (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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458B ARG* 4.2 15.4 - - - +
474B ASN 3.5 5.3 + - - +
475B ASN* 1.3 71.8 + - - +
477B GLU* 1.3 75.4 + - - +
479B ARG* 3.4 8.3 + - - +
480B GLN* 3.0 52.2 + - - +
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Residues in contact with GLU 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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456B PRO 5.0 2.3 - - - +
457B LEU* 4.4 17.3 - - + +
458B ARG* 2.9 69.8 + - + +
459B GLY 5.9 0.2 - - - +
460B LYS 6.2 0.2 - - - +
461B ILE* 4.0 20.6 - - + -
475B ASN* 2.9 9.7 + - - +
476B ASN* 1.3 79.3 + - - +
478B ILE* 1.3 64.1 + - - +
480B GLN* 3.5 22.9 + - - +
481B MET* 3.3 29.2 + - - +
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Residues in contact with ILE 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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461B ILE* 4.2 12.3 - - + -
462B LEU* 4.6 9.0 - - + +
464B VAL* 4.2 11.7 - - + -
472B ILE* 3.5 32.3 - - + +
473B LEU* 5.3 1.6 - - + -
475B ASN* 3.1 24.2 + - + +
477B GLU* 1.3 73.5 - - - +
479B ARG* 1.3 63.6 + - - +
481B MET* 3.3 19.0 + - + +
482B ILE* 3.1 35.5 + - + +
523B PHE* 3.7 43.4 - - + -
527B PHE* 6.2 0.2 - - + -
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Residues in contact with ARG 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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472B ILE 5.4 0.2 - - - +
473B LEU* 3.1 29.5 + - - +
474B ASN* 4.1 15.4 + - - +
475B ASN 3.1 19.5 + - - +
476B ASN* 3.6 9.4 - - - +
477B GLU 3.3 0.2 - - - -
478B ILE* 1.3 76.1 - - - +
480B GLN* 1.3 56.6 + - - +
482B ILE* 3.3 13.0 + - + +
483B THR* 2.9 35.0 + - - +
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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
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417B LYS* 3.5 31.1 + - - +
418B LEU* 4.8 1.2 + - - +
455B LEU* 3.7 25.3 - - + +
456B PRO 5.1 1.0 - - - +
457B LEU* 6.3 0.7 - - + -
476B ASN* 3.0 47.1 + - - +
477B GLU* 3.9 18.9 + - - +
478B ILE 3.4 0.2 - - - -
479B ARG* 1.3 74.8 - - + +
481B MET* 1.3 58.2 + - - +
483B THR* 3.5 7.0 + - - -
484B ALA* 3.0 29.6 + - - +
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Residues in contact with MET 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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433B LEU* 4.4 13.0 - - + -
455B LEU* 3.7 23.6 - - + -
457B LEU* 4.2 8.5 - - + -
461B ILE* 3.3 31.0 - - + -
477B GLU 3.3 13.1 + - - +
478B ILE* 3.7 12.8 - - + +
479B ARG 3.2 0.6 - - - -
480B GLN* 1.3 75.2 - - - +
482B ILE* 1.3 64.5 + - - +
484B ALA* 3.3 2.1 + - - +
485B PHE* 3.1 44.7 + - + -
520B LEU* 3.6 22.4 - - + -
523B PHE* 3.6 33.2 - - + -
524B PHE* 4.5 5.4 - - - -
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Residues in contact with ILE 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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473B LEU* 5.3 4.9 - - + -
478B ILE* 3.1 35.8 + - + +
479B ARG* 3.6 12.8 - - + +
481B MET* 1.3 75.6 - - - +
483B THR* 1.3 59.2 + - - +
485B PHE* 3.5 1.2 + - - +
486B GLY* 2.9 27.9 + - - -
487B THR 4.1 2.3 + - - -
488B GLY* 4.3 22.2 + - - +
489B ILE* 3.7 39.5 - - + -
523B PHE* 4.0 4.9 - - + -
528B MET* 3.9 14.6 - - + -
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Residues in contact with THR 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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418B LEU* 6.4 0.7 - - + -
479B ARG* 2.9 20.9 + - - +
480B GLN* 3.7 7.1 - - - -
482B ILE* 1.3 76.7 - - - +
484B ALA* 1.3 63.6 + - - +
486B GLY* 3.4 12.3 + - - +
499B ARG* 3.9 12.0 + - - +
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Residues in contact with ALA 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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418B LEU* 3.9 20.2 - - + -
431B ILE* 3.9 21.3 - - + -
455B LEU* 4.3 8.5 - - + -
480B GLN 3.0 17.8 + - - +
481B MET* 3.3 6.5 + - - +
483B THR* 1.3 76.3 - - - +
485B PHE* 1.3 61.2 + - + +
499B ARG* 3.0 35.4 + - - +
500B TYR* 3.2 12.0 - - - -
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Residues in contact with PHE 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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431B ILE* 3.8 24.5 - - + -
433B LEU* 4.4 8.3 - - + -
481B MET* 3.1 33.7 + - + +
482B ILE 4.1 2.0 - - - +
484B ALA* 1.3 80.2 - - + +
486B GLY* 1.3 63.6 + - - +
487B THR* 3.4 16.7 + - + +
497B LYS 3.6 0.2 - - - +
498B ALA* 3.5 5.2 - - + -
499B ARG* 3.0 27.5 + - - +
500B TYR* 4.5 8.1 - + - -
503B ILE* 3.6 43.1 - - + -
524B PHE* 3.4 30.3 - + - -
528B MET* 3.7 23.3 - - + -
531B LEU* 4.7 6.7 - - + -
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Residues in contact with GLY 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 ILE 2.9 14.2 + - - -
483B THR* 3.8 9.0 - - - -
484B ALA 3.4 1.8 - - - -
485B PHE* 1.3 76.5 - - - +
487B THR* 1.3 57.7 + - - +
488B GLY 3.6 1.8 - - - -
497B LYS* 3.3 25.7 - - - +
499B ARG* 5.4 2.9 - - - -
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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