Contacts of the helix formed by residues 440 - 449 (chain A) in PDB entry 2WFD
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 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A SER* 3.5 28.3 - - - -
428A PRO* 3.9 26.2 - - + +
430A PRO* 3.9 29.8 - - + -
437A PHE 4.4 0.4 + - - -
439A ASN* 1.3 81.2 - - + +
441A SER* 1.3 58.6 - - - +
442A ALA 3.3 2.5 - - - -
443A VAL* 3.8 21.5 - - + -
444A THR* 2.8 40.0 + - + +
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Residues in contact with SER 441 (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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394A SER 3.2 1.2 + - - -
395A ASP* 3.4 21.7 + - - -
432A ILE 4.0 1.7 + - - -
434A ILE* 3.5 30.7 - - - +
437A PHE* 3.7 21.0 - - - +
438A GLY 3.5 15.2 + - - -
439A ASN 3.2 3.6 + - - -
440A LEU* 1.3 71.4 - - - +
442A ALA* 1.3 68.6 + - - +
444A THR* 3.6 2.3 + - - -
445A ILE* 3.4 25.1 + - - +
467A ILE* 4.1 5.8 - - - +
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Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A SER 3.0 15.9 + - - +
395A ASP* 3.2 29.4 - - - +
396A SER 3.3 5.6 - - - +
397A PRO* 3.8 2.5 - - + -
400A ILE* 3.3 20.6 - - + -
441A SER* 1.3 81.5 + - - +
443A VAL* 1.3 65.1 + - - +
445A ILE* 3.2 14.2 - - - +
446A CYS* 2.9 20.8 - - - -
467A ILE* 5.0 4.0 - - - +
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A PRO 3.8 7.2 - - - +
394A SER 4.6 0.2 - - - +
400A ILE* 3.4 30.3 - - + +
404A ARG* 3.7 22.4 + - - +
428A PRO* 4.4 13.2 - - + -
440A LEU* 3.4 30.7 + - + +
441A SER 3.3 0.2 - - - -
442A ALA* 1.3 79.0 - - - +
444A THR* 1.3 64.4 + - + +
445A ILE 3.3 0.7 + - - -
446A CYS* 3.3 8.5 + - - +
447A ASP* 3.3 26.7 + - - +
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Residues in contact with THR 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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437A PHE* 3.5 39.2 + - - +
440A LEU* 2.8 28.3 + - + +
441A SER 3.6 2.3 + - - -
442A ALA 3.3 0.4 - - - -
443A VAL* 1.3 79.5 - - + +
445A ILE* 1.3 61.2 + - - +
447A ASP* 3.7 13.3 - - - +
448A GLU* 3.4 26.2 + - - +
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Residues in contact with ILE 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A PRO* 4.8 2.9 - - + -
437A PHE* 3.9 33.2 - - + -
441A SER 3.4 11.6 + - - +
442A ALA 3.2 15.5 - - - +
444A THR* 1.3 77.1 + - - +
446A CYS* 1.3 52.7 + - - +
447A ASP 2.9 4.7 - - - -
448A GLU* 2.8 13.2 + - - +
449A LEU* 2.7 42.2 + - + +
463A ALA* 3.3 39.7 - - + +
466A LYS* 5.1 8.7 - - + -
467A ILE* 3.3 34.5 - - + -
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Residues in contact with CYS 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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397A PRO* 4.2 19.1 - - - +
400A ILE* 3.7 27.4 - - - -
401A ALA* 5.6 2.5 - - + -
404A ARG* 4.6 9.8 + - - +
442A ALA 2.9 20.4 - - - -
443A VAL 3.7 4.7 - - - +
445A ILE* 1.3 78.2 - - - +
447A ASP* 1.3 58.6 + - - +
449A LEU* 4.4 1.8 - - - +
450A LYS* 2.9 5.0 + - - -
451A ILE* 2.9 61.2 + - + +
463A ALA* 5.6 0.4 - - + -
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Residues in contact with ASP 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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404A ARG* 2.7 38.7 + - - -
443A VAL* 3.3 14.8 + - - +
444A THR* 3.7 13.7 - - - +
445A ILE 2.9 0.2 - - - -
446A CYS* 1.3 76.4 - - - +
448A GLU* 1.3 66.0 + - + +
450A LYS* 3.1 20.5 + - - +
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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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437A PHE* 4.1 29.0 - - - -
444A THR* 3.4 16.4 + - - +
445A ILE* 2.8 19.2 + - - +
447A ASP* 1.3 76.6 - - + +
449A LEU* 1.3 69.0 + - + +
450A LYS* 3.5 17.2 - - - +
466A LYS* 5.2 8.5 + - - +
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ILE* 2.7 26.3 + - + +
446A CYS* 4.4 0.2 - - - -
448A GLU* 1.3 77.8 - - + +
450A LYS* 1.3 73.2 + - - +
451A ILE* 4.2 12.3 - - + -
459A LYS* 3.3 45.5 + - + +
462A GLU* 4.1 26.9 - - + +
463A ALA* 3.7 28.9 - - + +
466A LYS* 5.4 10.1 - - + +
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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