Contacts of the helix formed by residues 475 - 486 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461K ILE* 5.1 0.3 - - - +
462K LEU* 3.4 32.4 - - + +
471K ARG* 2.9 13.0 + - + +
472K ILE 3.3 14.2 + - - +
474K ASN* 1.3 74.6 - - - +
476K ASN* 1.3 57.1 + - - +
477K GLU* 2.9 34.2 + - - +
478K ILE* 3.1 22.7 + - + +
479K ARG* 3.1 31.4 + - - +
13O G 5.5 0.6 + - - +
14O T 4.0 19.0 + - - -
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Residues in contact with ASN 476 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458K ARG* 3.8 14.5 - - - +
474K ASN 3.5 5.3 + - - +
475K ASN* 1.3 70.8 + - - +
477K GLU* 1.3 75.3 + - - +
479K ARG* 3.4 15.6 + - - +
480K GLN* 3.0 50.8 + - - +
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Residues in contact with GLU 477 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456K PRO 5.0 1.4 - - - +
457K LEU* 4.5 17.2 - - + +
458K ARG* 2.9 60.8 + - + +
459K GLY 5.8 0.7 - - - +
460K LYS 6.1 0.4 - - - +
461K ILE* 3.9 21.7 - - + +
475K ASN* 2.9 10.2 + - - +
476K ASN* 1.3 87.4 + - - +
478K ILE* 1.3 65.3 + - - +
480K GLN* 3.5 16.8 + - - +
481K MET* 3.3 29.1 + - - +
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Residues in contact with ILE 478 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461K ILE* 4.2 12.8 - - + -
462K LEU* 4.6 8.3 - - + +
464K VAL* 4.1 11.9 - - + -
472K ILE* 3.5 33.0 - - + +
473K LEU* 5.3 1.1 - - - -
475K ASN* 3.1 24.4 + - + +
477K GLU* 1.3 73.5 - - - +
479K ARG* 1.3 63.3 + - + +
481K MET* 3.3 19.0 + - + +
482K ILE* 3.1 35.9 + - + +
523K PHE* 3.7 42.8 - - + -
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Residues in contact with ARG 479 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473K LEU* 3.1 29.2 - - - +
474K ASN* 4.1 15.0 + - - +
475K ASN 3.1 18.8 + - - +
476K ASN* 3.6 15.6 + - - +
477K GLU 3.3 0.2 - - - -
478K ILE* 1.3 75.7 - - + +
480K GLN* 1.3 56.9 + - + +
482K ILE* 3.3 13.0 + - + +
483K THR* 2.9 34.9 + - - +
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Residues in contact with GLN 480 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416K GLY* 3.3 30.9 - - - +
417K LYS* 3.4 8.8 + - - +
418K LEU* 5.7 0.5 - - - +
455K LEU* 3.7 25.0 - - + +
456K PRO 5.0 2.4 - - - +
457K LEU* 6.3 0.9 - - + -
458K ARG* 3.0 30.0 + - - +
476K ASN* 3.0 38.5 + - - +
477K GLU* 3.9 15.2 + - - +
478K ILE 3.4 0.4 - - - -
479K ARG* 1.3 75.0 - - + +
481K MET* 1.3 56.9 + - - +
483K THR* 3.5 6.7 + - - -
484K ALA* 3.0 29.8 + - - +
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Residues in contact with MET 481 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433K LEU* 4.5 12.1 - - + -
455K LEU* 3.7 23.1 - - + -
457K LEU* 4.2 9.0 - - + -
461K ILE* 3.3 29.4 - - + -
477K GLU 3.3 11.5 + - - +
478K ILE* 3.7 13.7 - - + +
479K ARG 3.2 0.8 - - - -
480K GLN* 1.3 75.3 - - - +
482K ILE* 1.3 64.4 + - - +
484K ALA* 3.3 2.5 + - - +
485K PHE* 3.1 44.2 + - + -
520K LEU* 3.6 23.1 - - + -
523K PHE* 3.6 33.4 - - + -
524K PHE* 4.5 5.6 - - - -
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Residues in contact with ILE 482 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473K LEU* 5.2 6.5 - - + -
478K ILE* 3.1 33.4 + - + +
479K ARG* 3.6 11.7 - - + +
481K MET* 1.3 76.3 - - - +
483K THR* 1.3 58.9 + - - +
485K PHE* 3.9 1.4 - - - +
486K GLY* 2.9 27.9 + - - -
487K THR 4.2 1.9 + - - -
488K GLY* 4.4 21.8 - - - +
489K ILE* 3.7 39.7 - - + -
523K PHE* 4.0 5.2 - - + -
528K MET* 3.9 15.2 - - + +
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Residues in contact with THR 483 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418K LEU* 6.4 0.7 - - + -
479K ARG* 2.9 20.4 + - - +
480K GLN* 3.7 7.6 - - - -
481K MET 3.3 0.2 - - - -
482K ILE* 1.3 77.5 - - - +
484K ALA* 1.3 63.2 + - - +
486K GLY* 3.4 12.5 + - - -
499K ARG* 3.9 12.3 + - - +
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Residues in contact with ALA 484 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418K LEU* 3.9 15.7 - - + -
431K ILE* 3.9 24.9 - - + -
455K LEU* 4.3 9.4 - - + -
480K GLN 3.0 18.0 + - - +
481K MET 3.3 5.4 + - - +
483K THR* 1.3 76.6 - - - +
485K PHE* 1.3 59.4 + - + +
499K ARG* 3.0 35.1 + - - +
500K TYR* 3.1 12.6 - - - -
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Residues in contact with PHE 485 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431K ILE* 3.8 21.8 - - + -
433K LEU* 4.4 9.4 - - + -
455K LEU* 5.6 0.2 - - + -
481K MET* 3.1 33.0 + - + +
482K ILE 4.1 2.2 - - - +
484K ALA* 1.3 78.5 - - + +
486K GLY* 1.3 63.2 + - - +
487K THR* 3.3 16.6 + - + +
497K LYS 3.6 0.3 - - - +
498K ALA* 3.5 5.5 - - + -
499K ARG* 3.0 27.6 + - - +
500K TYR* 4.5 7.9 - + - +
503K ILE* 3.6 45.8 - - + -
523K PHE* 4.9 0.2 - + - -
524K PHE* 3.4 29.4 - + - -
528K MET* 3.6 24.2 - - + -
531K LEU* 4.7 6.1 - - + -
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Residues in contact with GLY 486 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482K ILE 2.9 13.2 + - - -
483K THR* 3.4 9.6 + - - -
484K ALA 3.4 2.0 - - - -
485K PHE* 1.3 76.5 - - - +
487K THR* 1.3 59.4 + - - +
488K GLY 3.6 2.5 - - - -
497K LYS* 3.3 25.3 - - - +
499K ARG* 5.4 3.1 - - - -
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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