Contacts of the helix formed by residues 441 - 450 (chain A) in PDB entry 2WP9
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 LEU 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.0 28.9 - - + -
167A LEU* 3.9 10.8 - - + -
181A THR* 3.9 21.8 - - + +
190A VAL* 3.8 24.9 - - + -
437A VAL* 4.0 10.3 - - + +
438A GLU* 2.9 31.3 + - - +
440A SER* 1.3 77.5 - - - +
442A ASP* 1.3 59.6 + - - +
443A ARG 3.3 2.5 - - - -
444A LEU* 3.1 14.4 + - + +
445A ASN* 2.9 42.6 + - - +
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Residues in contact with ASP 442 (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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438A GLU* 3.7 9.4 + - - +
439A ALA* 3.2 26.6 + - - +
440A SER 3.4 0.2 - - - -
441A LEU* 1.3 75.6 - - - +
443A ARG* 1.3 58.8 + - - +
445A ASN* 3.1 12.0 + - - +
446A ARG* 2.9 29.6 + - - +
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Residues in contact with ARG 443 (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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165A TYR* 4.5 5.5 - - - -
166A ALA 4.7 0.4 + - - -
167A LEU* 2.8 33.9 + - - +
168A ASP* 2.9 23.7 + - - +
228A ARG* 3.2 42.8 - - - +
439A ALA 4.9 0.2 + - - -
440A SER 4.7 1.1 + - - +
441A LEU 3.3 0.2 - - - -
442A ASP* 1.3 82.5 - - - +
444A LEU* 1.3 62.7 + - - +
446A ARG* 3.4 12.8 + - - +
447A TRP* 3.3 22.6 + - + +
514A LEU* 3.0 38.1 + - - +
517A ASP* 2.8 49.7 + - - +
518A ASN* 4.2 8.9 + - - +
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Residues in contact with LEU 444 (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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167A LEU* 3.9 28.5 - - + +
183A LEU* 5.2 4.0 - - + -
190A VAL* 3.9 28.3 - - + -
440A SER 5.1 0.8 + - - +
441A LEU* 3.1 20.2 + - + +
443A ARG* 1.3 78.0 - - - +
445A ASN* 1.3 67.2 + - - +
447A TRP* 3.2 6.4 + - + +
448A ASN* 3.1 34.4 + - - +
510A ARG* 3.8 30.5 - - + +
514A LEU* 4.2 21.4 - - + +
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Residues in contact with ASN 445 (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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438A GLU* 3.7 20.0 + - - -
441A LEU* 2.9 33.8 + - - +
442A ASP* 3.6 11.9 + - - +
444A LEU* 1.3 76.7 - - - +
446A ARG* 1.3 69.1 + - - +
448A ASN* 3.3 12.1 + - - +
449A ASN* 3.0 32.7 + - - +
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Residues in contact with ARG 446 (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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442A ASP 2.9 14.9 + - - +
443A ARG* 3.8 8.9 + - - +
444A LEU 3.3 0.2 - - - -
445A ASN* 1.3 77.0 - - - +
447A TRP* 1.3 102.3 + - - +
449A ASN* 2.9 14.3 + - - +
450A ASN* 3.0 32.1 + - + +
494A LEU 3.5 15.2 + - - -
495A LYS* 3.2 33.6 + - - +
497A ALA 3.1 28.3 + - - +
517A ASP* 5.0 1.2 + - - -
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Residues in contact with TRP 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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443A ARG 3.3 21.7 + - - -
444A LEU* 3.2 9.0 + - + +
446A ARG* 1.3 100.3 - - - +
448A ASN* 1.3 65.1 + - - +
449A ASN 3.1 1.0 + - - -
450A ASN* 3.3 11.9 + - - +
451A ARG* 4.2 0.7 + - - -
456A PRO* 4.4 5.8 - - + -
494A LEU* 3.9 11.7 - - + -
497A ALA* 3.5 35.2 - - + -
498A ARG 3.5 25.8 - - - -
499A LEU* 3.5 31.7 - - + +
510A ARG* 5.7 1.8 - - + -
513A CYS* 3.3 53.8 + - + -
514A LEU* 3.7 20.6 - - + +
516A LEU* 4.8 0.7 - - + -
517A ASP* 2.9 34.8 + - - -
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Residues in contact with ASN 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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444A LEU* 3.1 34.5 + - - +
445A ASN* 3.8 14.2 + - - +
446A ARG 3.2 0.2 - - - -
447A TRP* 1.3 76.8 - - - +
449A ASN* 1.3 65.8 + - - +
451A ARG* 3.2 22.5 + - - +
499A LEU* 3.8 8.1 - - - +
502A THR* 4.8 0.5 + - - -
510A ARG* 3.1 36.3 + - - +
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Residues in contact with ASN 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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445A ASN* 3.0 26.8 + - - +
446A ARG* 2.9 6.3 + - - +
448A ASN* 1.3 83.9 + - - +
450A ASN* 1.3 61.8 + - - +
451A ARG* 3.5 10.1 + - - +
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Residues in contact with ASN 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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446A ARG* 3.0 29.0 + - + +
447A TRP 3.3 4.9 + - - +
449A ASN* 1.3 74.5 - - - +
451A ARG* 1.3 66.0 + - - +
452A ASN 4.6 0.7 - - - -
453A GLY* 2.8 32.7 + - - -
495A LYS 4.9 0.2 + - - -
496A ASN* 3.5 22.8 + - - +
497A ALA 3.3 17.0 - - - +
498A ARG* 3.2 5.5 - - - -
499A LEU 3.0 24.9 + - - -
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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