Contacts of the helix formed by residues 449 - 454 (chain A) in PDB entry 2WKP
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 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A ASP* 2.9 36.2 + - - +
425A ASN* 4.0 16.2 + - - +
426A PRO* 4.1 2.0 - - - +
448A ARG* 1.3 74.4 + - - +
450A CYS* 1.3 59.2 + - - +
451A ARG* 2.9 66.1 + - + +
452A PHE* 3.0 23.4 + - - +
1725A FMN 2.8 30.4 + - - -
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Residues in contact with CYS 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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416A VAL* 4.4 4.3 - - - -
418A THR* 5.6 0.7 - - + -
425A ASN 5.1 1.4 + - - -
427A ILE* 4.0 18.9 - - + +
434A PHE* 3.9 18.6 - - - -
448A ARG 3.8 1.6 + - - -
449A ASN* 1.3 72.4 + - - +
451A ARG* 1.3 61.0 + - - +
452A PHE* 3.0 15.6 + - - -
453A LEU* 3.2 34.1 + - - +
1725A FMN 3.5 55.7 + - + +
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Residues in contact with ARG 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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424A ASP* 2.8 43.0 + - - -
449A ASN* 2.9 33.1 + - + +
450A CYS* 1.3 77.2 - - - +
452A PHE* 1.3 57.3 + - - +
453A LEU 3.0 1.6 - - - -
454A GLN* 2.9 44.6 + - - +
460A ARG* 6.4 0.4 - - - +
1725A FMN 2.7 58.4 + - - +
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Residues in contact with PHE 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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427A ILE* 3.9 17.7 - - + -
434A PHE* 4.4 6.5 - + - -
440A TYR* 3.7 38.9 + + - +
445A ILE* 3.5 28.3 - - + -
448A ARG* 3.6 40.8 - - + +
449A ASN 3.0 26.4 + - - -
450A CYS* 3.0 17.4 + - - -
451A ARG* 1.3 81.7 - - - +
453A LEU* 1.3 87.4 + - + +
454A GLN 3.2 7.3 + - - +
483A TYR* 4.8 2.3 - - - +
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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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434A PHE* 3.8 14.1 - - + -
438A THR* 3.8 22.7 - - + -
440A TYR* 4.4 1.8 - - + -
450A CYS* 3.6 21.1 - - - +
451A ARG 3.0 0.8 + - - -
452A PHE* 1.3 102.4 - - + +
454A GLN* 1.3 60.0 + - - +
482A ASN* 3.2 25.1 - - + +
483A TYR* 2.7 48.4 + - - +
490A PHE* 4.9 5.6 - - + -
492A ASN* 4.9 0.9 - - - +
513A GLN* 5.2 0.9 - - + -
1725A FMN 3.6 31.9 - - + +
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Residues in contact with GLN 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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451A ARG* 2.9 25.0 + - - +
452A PHE 3.7 7.6 - - - +
453A LEU* 1.3 82.4 - - - +
455A GLY* 1.3 58.9 + - - +
458A THR* 3.6 19.5 - - + +
460A ARG* 2.9 27.8 + - - +
463A VAL* 3.8 15.8 - - + +
466A ILE* 5.4 0.4 - - - +
480A LEU* 4.7 0.2 - - - +
482A ASN* 3.9 4.3 - - - +
483A TYR* 3.9 3.3 - - - +
1725A FMN 2.8 65.7 + - - +
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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