Contacts of the helix formed by residues 451 - 459 (chain A) in PDB entry 2W3C
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 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A GLN* 3.8 25.4 + - - +
400A GLN* 2.9 33.2 + - - +
448A LEU 2.9 19.9 + - - +
450A GLU* 1.3 78.2 - - - +
452A ALA* 1.3 62.7 + - - +
453A THR* 3.4 12.6 + - - -
454A GLN* 3.2 39.3 + - + +
455A LYS* 3.0 23.4 + - - +
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Residues in contact with ALA 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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450A GLU 4.0 1.6 + - - -
451A ASN* 1.3 74.1 - - - +
453A THR* 1.3 63.4 + - - +
455A LYS* 3.3 12.4 + - - +
456A GLU* 3.0 38.5 + - - +
504A ASN 4.8 12.8 - - - +
505A CYS* 4.6 4.9 - - - -
507A ILE* 6.5 0.2 - - + -
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Residues in contact with THR 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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451A ASN* 3.2 9.9 + - - -
452A ALA* 1.3 78.9 - - - +
454A GLN* 1.3 72.0 + - - +
456A GLU* 3.3 9.0 + - - +
457A GLN* 2.9 32.7 + - + +
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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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397A GLN 5.0 1.8 + - - -
400A GLN 4.3 3.4 - - - -
401A GLY* 3.4 33.8 - - - +
404A VAL* 3.4 28.0 - - + +
405A SER 4.9 0.5 + - - -
447A ALA 4.0 13.2 - - - +
448A LEU* 3.5 5.0 - - + +
451A ASN* 3.2 34.2 + - - +
453A THR* 1.3 88.1 - - - +
455A LYS* 1.3 58.9 + - - +
457A GLN* 3.7 12.1 - - - +
458A LEU* 2.8 32.1 + - - +
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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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448A LEU* 3.5 40.8 - - + +
449A GLN* 4.9 0.6 - - - +
450A GLU* 4.6 7.3 - - - +
451A ASN 3.0 19.9 + - - +
452A ALA* 3.5 12.3 - - - +
454A GLN* 1.3 77.3 - - - +
456A GLU* 1.3 60.8 + - - +
459A LEU* 3.5 15.3 + - - +
500A THR* 2.8 22.7 + - - +
501A TRP* 3.1 44.4 + - + +
503A SER* 2.6 27.9 + - - +
504A ASN* 4.7 5.7 - - - +
505A CYS* 3.8 22.4 - - + -
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Residues in contact with GLU 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 ALA* 3.0 26.5 + - - +
453A THR* 3.4 11.4 + - - +
455A LYS* 1.3 74.6 - - - +
457A GLN* 1.3 69.5 + - + +
459A LEU* 3.2 25.5 - - + +
460A ARG* 3.9 8.7 + - - +
505A CYS* 4.3 12.8 - - - -
507A ILE* 4.1 30.3 - - + +
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Residues in contact with GLN 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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404A VAL* 4.1 6.7 - - + -
408A LEU* 3.3 24.9 - - + +
453A THR* 2.9 27.8 + - + +
454A GLN* 3.3 23.8 + - - +
456A GLU* 1.3 78.4 - - - +
458A LEU* 1.3 62.3 + - - +
460A ARG* 3.0 59.7 + - - +
461A VAL 4.0 1.2 + - - -
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Residues in contact with LEU 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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404A VAL* 3.9 18.8 - - + +
407A LEU* 3.9 13.7 - - + -
444A LEU* 4.2 18.8 - - + -
448A LEU* 3.9 21.3 - - + -
454A GLN 2.8 18.2 + - - +
455A LYS 3.9 3.1 - - - +
456A GLU 3.3 0.2 - - - -
457A GLN* 1.3 75.8 - - - +
459A LEU* 1.3 60.8 + - - +
461A VAL* 3.2 32.8 + - + +
474A LEU* 3.8 20.8 - - + +
475A LEU 5.4 0.2 + - - -
497A LEU* 5.1 2.5 - - + -
501A TRP* 3.4 47.2 - - + +
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Residues in contact with LEU 459 (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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455A LYS 3.5 9.3 + - - +
456A GLU* 3.2 21.3 + - + +
457A GLN 3.1 0.6 - - - -
458A LEU* 1.3 80.0 - - - +
460A ARG* 1.3 58.5 + - + +
461A VAL 3.4 4.8 + - - +
473A SER* 4.8 8.3 - - - -
475A LEU* 4.3 16.0 - - + +
501A TRP* 3.3 35.9 - - + +
505A CYS* 5.1 0.2 - - - -
507A ILE* 4.1 13.7 - - + +
508A ALA* 3.7 37.7 - - + +
511A HIS* 4.2 31.8 - - + +
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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