Contacts of the helix formed by residues 474 - 481 (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 TYR 474 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C LEU* 4.1 18.8 - - + +
26C PRO* 3.5 22.5 - - + +
48C ASN 4.4 7.8 + - - -
49C ALA* 5.8 0.3 - - - -
415D ILE* 4.9 1.8 - - + -
445D GLY* 3.5 26.8 + - - -
448D GLN* 4.9 3.5 + - - -
449D LEU* 4.8 2.6 - - - +
473D GLY* 1.3 70.9 - - - -
475D THR* 1.3 63.2 + - - +
476D ILE 3.4 1.6 - - - -
477D GLN* 3.2 26.7 + - + -
478D LYS* 3.1 24.3 + - - +
487D TYR 3.6 15.9 - - - -
488D ASN* 3.0 18.8 + - - +
489D GLU 4.8 0.9 - - - -
490D ILE* 3.5 26.4 - - + +
600D TPP 3.3 43.5 - - + -
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Residues in contact with THR 475 (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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390D THR* 3.8 5.9 - - - +
471D ASN* 3.2 40.6 - - + +
473D GLY 4.1 1.6 - - - +
474D TYR* 1.3 67.8 - - - +
476D ILE* 1.3 66.5 + - - +
478D LYS* 3.0 23.0 + - + +
479D LEU* 3.1 16.3 + - - +
541D PRO 4.7 0.2 - - - +
542D VAL 2.7 30.3 + - - +
543D PHE* 4.5 4.7 - - - -
544D ASP 3.8 13.9 + - - -
545D ALA* 4.5 3.3 - - - +
600D TPP 2.9 16.9 + - - -
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Residues in contact with ILE 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D PHE* 5.4 3.4 - - + -
389D GLY* 3.6 27.6 - - - +
390D THR* 4.5 0.2 - - - +
393D PHE* 3.9 12.3 - - + -
475D THR* 1.3 73.0 + - - +
477D GLN* 1.3 65.1 + - - +
479D LEU* 3.3 13.8 + - - +
480D ILE* 3.3 19.3 + - + +
549D LEU* 3.7 40.2 - - + -
553D ALA* 4.6 0.7 - - - +
600D TPP 2.8 58.9 + - + +
602D PY0 3.9 24.5 - - + +
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Residues in contact with GLN 477 (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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26C PRO* 3.3 26.1 - - - +
27C GLY* 3.3 19.9 - - - -
31C LEU* 4.1 11.7 - - + +
474D TYR* 3.2 13.9 + - + +
475D THR 3.1 0.8 - - - -
476D ILE* 1.3 72.9 - - - +
478D LYS* 1.3 58.6 + - - +
479D LEU 3.0 2.0 - - - -
480D ILE* 2.8 26.3 + - - +
481D HIS 2.9 17.3 + - - +
488D ASN* 2.8 35.3 + - - +
600D TPP 3.1 39.6 + - + +
602D PY0 3.4 17.9 + - - +
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Residues in contact with LYS 478 (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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471D ASN 4.7 0.2 + - - -
472D ASP 3.0 19.0 + - - -
473D GLY* 4.2 1.4 - - - -
474D TYR 3.1 16.9 + - - +
475D THR* 3.0 12.6 + - - +
477D GLN* 1.3 74.5 - - - +
479D LEU* 1.3 63.3 + - - +
481D HIS 4.0 4.1 + - - -
482D GLY 4.1 0.2 - - - -
483D PRO* 3.5 48.5 - - + +
488D ASN* 3.5 34.3 + - + +
489D GLU* 2.8 38.9 + - - -
542D VAL* 3.4 29.4 - - + +
543D PHE* 4.0 12.0 - - + -
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Residues in contact with LEU 479 (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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475D THR* 3.1 15.5 + - - +
476D ILE* 3.6 7.0 - - - +
477D GLN 3.0 0.8 - - - -
478D LYS* 1.3 80.0 - - - +
480D ILE* 1.3 61.6 + - - +
543D PHE* 4.2 32.8 - - + +
545D ALA* 3.5 31.6 - - + -
549D LEU* 4.4 12.3 - - + -
550D VAL* 4.0 28.3 - - + +
553D ALA* 3.6 20.5 - - + +
554D LYS* 4.8 9.0 + - - +
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Residues in contact with ILE 480 (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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28C ASP* 4.1 17.9 - - + +
31C LEU* 4.2 14.1 - - + -
292D PHE* 5.7 2.5 - - + -
476D ILE* 3.4 19.5 - - + +
477D GLN* 2.8 9.0 + - - +
479D LEU* 1.3 79.0 - - - +
481D HIS* 1.3 65.9 + - + +
549D LEU* 6.1 0.2 - - + -
553D ALA* 3.7 26.9 - - + +
556D THR* 4.6 7.6 - - + -
557D ALA* 3.6 36.7 - - + +
560D ASN* 5.4 0.7 - - - +
602D PY0 3.4 36.1 - - - +
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Residues in contact with HIS 481 (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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31C LEU* 3.8 33.4 - - + +
32C SER* 4.2 12.7 - - - -
35C ASP* 2.5 28.8 + - - -
477D GLN 2.9 6.7 + - - +
478D LYS 4.2 1.8 - - - -
479D LEU 3.6 1.4 - - - -
480D ILE* 1.3 84.8 + - + +
482D GLY* 1.3 63.3 + - - +
483D PRO* 3.9 1.1 - - - -
487D TYR* 3.2 26.8 + - - -
488D ASN* 3.0 20.3 + - - -
557D ALA* 5.5 1.7 - - + +
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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