Contacts of the helix formed by residues 468 - 475 (chain B) in PDB entry 3N9V
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 468 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463B LEU* 3.1 31.3 + - + +
466B GLU* 3.3 8.2 + - + +
467B LYS* 1.3 73.4 - - - +
469B PHE* 1.3 60.7 + - - +
470B GLN* 4.0 6.4 + - - +
471B MET* 3.5 26.9 + - - +
472B LEU* 3.7 15.1 + - - +
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Residues in contact with PHE 469 (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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463B LEU 5.7 0.4 - - - -
464B ILE* 4.2 20.9 - - + -
467B LYS* 3.3 34.2 + - + -
468B ASP* 1.3 70.6 - - - +
470B GLN* 1.3 63.6 + - - +
471B MET 3.2 2.2 - - - -
472B LEU* 3.3 6.9 + - + -
473B TYR* 3.1 26.3 + - - +
496B LEU 3.5 19.7 - - - +
497B THR* 3.2 31.4 - - - -
498B PHE 4.5 0.2 - - - -
499B GLN* 3.5 38.4 - - + -
500B PRO* 4.1 5.8 - - + -
522B TRP* 3.8 22.3 - + + -
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Residues in contact with GLN 470 (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* 3.4 6.4 - - - +
469B PHE* 1.3 78.4 - - - +
471B MET* 1.3 59.5 - - - +
473B TYR* 3.8 8.0 + - - +
474B ALA* 3.8 14.9 + - - +
495B GLU* 5.2 10.5 - - - +
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Residues in contact with MET 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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455B LEU* 5.1 1.8 - - - +
463B LEU* 5.5 9.0 - - + -
468B ASP* 3.5 23.1 + - + +
469B PHE 3.2 0.4 - - - -
470B GLN* 1.3 76.3 - - - +
472B LEU* 1.3 64.3 + - - +
474B ALA* 3.7 17.7 - - - +
475B TYR* 4.2 11.6 - - - -
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Residues in contact with LEU 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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452B ILE* 4.2 29.0 - - + +
455B LEU* 5.1 10.8 - - + -
460B VAL* 4.6 15.9 - - + +
463B LEU* 5.1 12.5 - - + +
468B ASP 3.7 11.6 + - - +
469B PHE* 3.3 11.7 + - + +
471B MET* 1.3 78.8 - - - +
473B TYR* 1.3 58.8 + - - +
475B TYR* 3.0 22.3 + - - +
476B ASP* 3.6 8.3 + - - +
500B PRO* 5.7 6.1 - - + -
522B TRP* 4.1 13.5 - - + -
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Residues in contact with TYR 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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469B PHE 3.1 16.6 + - - +
470B GLN* 4.0 8.3 - - - +
471B MET 3.4 0.4 - - - -
472B LEU* 1.3 75.1 - - - +
474B ALA* 1.3 65.9 + - - +
476B ASP* 3.2 24.9 + - + +
479B LYS* 3.4 38.3 - - + +
493B GLU* 3.9 19.5 + - - +
494B GLY 5.5 3.5 + - - -
495B GLU* 6.6 0.4 - - - -
496B LEU* 3.4 36.1 - - + -
522B TRP* 3.9 10.3 - + + -
525B ARG* 4.6 0.2 - - - -
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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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470B GLN 3.8 8.8 + - - +
471B MET* 3.7 15.9 - - - +
472B LEU 3.2 0.4 - - - -
473B TYR* 1.3 81.9 - - - +
475B TYR* 1.3 67.7 + - + +
476B ASP 3.5 2.3 + - - -
479B LYS* 5.2 1.0 - - - +
480B ILE* 4.1 15.6 - - - +
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Residues in contact with TYR 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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452B ILE* 3.4 11.0 - - + +
453B GLU* 3.2 41.5 + - + +
454B GLU* 4.1 24.9 - - + -
455B LEU* 3.8 32.1 - - + -
471B MET 4.2 11.0 - - - -
472B LEU 3.0 11.7 + - - +
474B ALA* 1.3 85.2 - - + +
476B ASP* 1.3 57.2 + - - +
477B GLN 3.8 0.3 + - - -
480B ILE* 4.6 7.9 - - + -
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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