Contacts of the helix formed by residues 446 - 458 (chain A) in PDB entry 2FBW
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 GLY 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A LEU* 4.2 12.9 - - - +
192A ILE* 3.7 19.9 - - - +
444A ASN 3.1 0.8 + - - -
445A ALA* 1.3 72.7 - - - +
447A GLU* 1.3 64.8 + - - +
448A GLU 3.2 3.4 - - - -
449A SER* 2.9 25.1 + - - -
450A VAL* 3.3 8.8 + - - +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ASN* 2.6 53.3 + - + +
445A ALA 3.4 0.4 - - - -
446A GLY* 1.3 78.2 - - - +
448A GLU* 1.3 68.1 + - + +
450A VAL* 3.1 10.3 + - - +
451A ALA* 2.8 29.4 + - - +
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A GLY 3.2 0.8 - - - -
447A GLU* 1.3 87.7 - - + +
449A SER* 1.3 57.3 + - - +
451A ALA* 3.8 7.4 - - - +
452A ASN* 2.9 29.1 + - - +
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Residues in contact with SER 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 4.2 17.5 - - - +
180A ASP* 2.7 40.0 + - - +
192A ILE* 3.8 18.8 - - - +
446A GLY* 2.9 14.6 + - - -
448A GLU* 1.3 79.8 - - - +
450A VAL* 1.3 57.7 + - - +
452A ASN* 3.3 8.1 + - - +
453A LEU* 2.9 28.2 + - - +
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.5 37.7 - - + -
14A VAL* 6.0 3.1 - - + -
179A LEU* 5.6 0.4 - - + -
192A ILE* 4.0 6.5 - - + -
201A ILE* 3.9 35.4 - - + -
446A GLY 3.3 10.9 + - - +
447A GLU* 3.1 10.8 + - - +
449A SER* 1.3 76.3 - - - +
451A ALA* 1.3 58.9 + - - +
453A LEU* 3.2 9.5 + - + +
454A ASP* 2.9 27.3 + - + +
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Residues in contact with ALA 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A GLU 2.8 17.5 + - - +
448A GLU* 3.8 8.3 - - - +
450A VAL* 1.3 77.7 - - - +
452A ASN* 1.3 61.7 + - - +
454A ASP* 3.1 7.8 + - - +
455A LYS* 2.9 37.8 + - - +
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Residues in contact with ASN 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A GLU 2.9 18.6 + - - +
449A SER* 3.7 6.7 + - - +
451A ALA* 1.3 75.3 - - - +
453A LEU* 1.3 65.3 + - - +
455A LYS* 3.1 21.0 + - - +
456A LEU* 3.1 18.7 + - - +
523A LEU* 3.7 15.0 - - - +
526A GLN* 2.9 43.7 + - - -
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Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.6 34.5 - - + +
179A LEU* 4.2 18.4 - - + -
194A LEU* 4.0 27.1 - - + -
201A ILE* 4.1 22.0 - - + -
449A SER 2.9 14.6 + - - +
450A VAL* 3.2 9.8 + - + +
452A ASN* 1.3 80.2 - - - +
454A ASP* 1.3 58.4 + - - +
456A LEU* 3.5 0.4 + - - -
457A ARG* 3.1 24.4 + - + +
513A ILE* 4.6 2.9 - - + -
519A LEU* 3.8 25.4 - - + +
523A LEU* 4.8 12.6 - - + -
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Residues in contact with ASP 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 5.3 4.6 - - - +
12A TYR* 2.5 40.6 + - + +
450A VAL* 2.9 16.3 + - + +
451A ALA* 3.1 8.0 + - - +
453A LEU* 1.3 75.0 - - - +
455A LYS* 1.3 64.7 + - - +
457A ARG* 3.5 3.9 + - - -
458A PHE* 3.2 46.8 - - - +
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Residues in contact with LYS 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A ALA* 2.9 24.0 + - - +
452A ASN* 3.1 15.4 + - - +
454A ASP* 1.3 78.9 - - - +
456A LEU* 1.3 67.9 + - + +
458A PHE* 3.8 1.4 - - - +
459A ALA* 3.1 23.6 + - - +
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Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A ASN* 3.1 15.7 + - - +
455A LYS* 1.3 79.3 - - + +
457A ARG* 1.3 60.3 + - - +
458A PHE 3.3 0.3 + - - -
459A ALA* 3.3 10.0 + - + +
503A LEU 5.9 0.4 - - - +
506A LEU* 4.2 13.7 - - + -
508A THR* 2.8 30.5 + - - +
519A LEU* 3.8 14.3 - - + +
522A THR* 3.8 31.4 - - + -
523A LEU* 3.8 26.0 - - + +
526A GLN* 3.4 39.5 - - - +
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Residues in contact with ARG 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.2 37.7 + - - -
453A LEU 3.1 18.6 + - - +
454A ASP* 3.8 6.5 + - - +
455A LYS 3.3 0.4 - - - -
456A LEU* 1.3 78.6 - - - +
458A PHE* 1.3 76.3 + - + +
508A THR* 3.5 2.1 + - - -
510A ASP 3.5 6.3 - - - +
511A ARG* 2.7 57.1 + - - +
512A GLY* 3.3 22.5 + - - +
513A ILE* 3.8 27.8 - - - +
516A ASN* 4.7 1.8 - - - +
519A LEU* 3.7 18.3 - - + +
22B ASP* 5.9 0.6 - - - -
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Residues in contact with PHE 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A ASP* 3.2 51.5 + - - +
455A LYS 3.8 1.8 - - - +
456A LEU 3.2 0.2 - - - -
457A ARG* 1.3 111.7 - - + +
459A ALA* 1.3 64.9 + - - +
460A ASP* 3.4 7.1 + - - +
511A ARG* 3.3 39.4 + - + +
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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