Contacts of the helix formed by residues 452 - 460 (chain D) in PDB entry 2W93
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 GLN 452 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448C GLN 2.9 30.7 + - - +
449C LEU 3.1 14.8 + - - -
450C THR 3.7 0.6 - - - +
451C VAL* 4.0 7.6 - - + +
452C GLN* 3.0 42.2 + - - +
493C TRP* 3.8 15.5 - - + -
49D ALA* 3.7 15.3 - - + +
50D ASN* 3.5 12.3 + - - +
53D ASN* 3.3 13.8 + - - +
450D THR* 2.9 12.4 + - - -
451D VAL* 1.3 79.8 - - - +
453D GLU* 1.3 56.9 + - - +
454D ILE 3.1 1.3 - - - -
455D SER* 3.0 30.6 + - - -
502D PHE* 4.0 11.2 - - - -
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Residues in contact with GLU 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ASN* 2.8 22.7 + - - +
49D ALA* 3.0 24.6 + - - +
53D ASN* 3.0 44.6 + - + +
419D THR* 4.2 13.0 - - + +
420D GLY* 4.4 10.8 - - - -
423D LEU* 3.8 16.7 - - + +
450D THR 3.0 9.7 + - - +
452D GLN* 1.3 76.3 - - - +
454D ILE* 1.3 64.3 + - - +
455D SER 3.1 0.4 - - - -
456D THR* 2.8 30.5 + - - -
457D MET* 3.4 17.1 + - - +
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Residues in contact with ILE 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D THR* 4.2 12.0 - - + +
447D LEU* 4.2 11.9 - - + -
451D VAL* 3.2 30.0 + - + +
452D GLN 3.1 0.8 - - - -
453D GLU* 1.3 77.1 - - - +
455D SER* 1.3 62.7 + - - +
457D MET* 3.1 13.7 + - + +
458D ILE* 3.0 26.5 + - + +
466D LEU* 4.1 17.7 - - + -
498D LEU* 4.5 4.9 - - + -
499D LEU* 3.5 33.7 - - + +
502D PHE* 4.0 9.9 - - + -
533D ILE* 4.7 1.8 - - + -
535D MET* 3.8 26.5 - - + -
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Residues in contact with SER 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448C GLN* 4.6 2.3 + - - -
491C GLN* 3.1 18.5 - - - +
493C TRP* 2.9 39.1 + - - -
49D ALA* 4.9 2.7 - - - +
452D GLN 3.0 17.3 + - - -
454D ILE* 1.3 78.9 - - - +
456D THR* 1.3 56.4 + - - +
458D ILE* 3.2 6.4 + - - +
459D ARG* 3.0 26.9 + - - +
502D PHE* 4.0 16.7 - - - -
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Residues in contact with THR 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ALA* 3.7 26.0 - - + +
47D GLY 3.6 16.1 + - - +
48D ASN* 4.2 2.9 - - - +
49D ALA* 3.7 9.0 + - - +
423D LEU* 3.7 25.5 - - + +
453D GLU* 2.8 32.7 + - - +
455D SER* 1.3 75.0 + - - +
457D MET* 1.3 67.4 + - - +
459D ARG* 3.5 7.3 + - - +
460D TRP* 3.4 27.1 + - + +
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Residues in contact with MET 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D THR* 3.2 40.8 - - + +
422D THR* 4.1 9.2 - - + -
423D LEU* 3.6 30.9 - - + +
426D ALA* 5.8 0.2 - - + -
453D GLU 3.4 14.8 + - - +
454D ILE* 3.1 17.9 + - + +
456D THR* 1.3 78.9 - - - +
458D ILE* 1.3 59.3 + - - +
460D TRP 3.4 0.5 + - - -
461D GLY 3.2 2.9 + - - -
462D LEU* 2.9 41.1 + - + +
464D PRO* 3.8 24.0 - - + -
466D LEU* 4.2 12.6 - - + -
533D ILE* 3.8 17.5 - - + -
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Residues in contact with ILE 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491C GLN* 3.4 22.0 - - - +
454D ILE* 3.0 15.7 + - + +
455D SER* 3.4 6.3 - - - +
457D MET* 1.3 73.5 - - - +
459D ARG* 1.3 64.8 + - - +
461D GLY* 3.0 15.2 + - - +
462D LEU 5.3 0.9 - - - -
499D LEU* 3.7 35.7 - - + +
502D PHE* 3.7 30.5 - - + +
503D GLY 4.1 1.3 - - - +
504D ALA* 3.7 29.4 - - + -
505D LYS 5.1 0.9 - - - +
533D ILE* 4.6 10.1 - - + -
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Residues in contact with ARG 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486C GLN* 3.4 22.6 + - - +
489C GLU* 2.7 40.5 + - - +
490C ILE* 3.7 11.9 - - - +
491C GLN* 3.4 34.1 - - + +
45D TRP 6.1 0.4 - - - -
46D ALA 4.3 3.4 - - - -
47D GLY* 3.3 37.2 + - - -
455D SER 3.0 15.6 + - - +
456D THR* 3.6 9.6 - - - +
458D ILE* 1.3 77.3 - - - +
460D TRP* 1.3 78.7 + - + +
461D GLY 3.8 0.2 + - - -
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Residues in contact with TRP 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ARG* 3.7 44.4 - - + +
45D TRP 3.3 21.3 - - - -
46D ALA* 2.7 25.6 + - - +
427D PHE* 3.5 34.1 - + + -
430D GLU* 4.2 10.2 - - - +
456D THR* 3.4 15.4 + - + +
457D MET 3.4 1.8 + - - -
458D ILE 3.1 0.6 - - - -
459D ARG* 1.3 92.5 - - + +
461D GLY* 1.3 63.6 + - - +
462D LEU* 3.2 11.3 + - + +
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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