Contacts of the helix formed by residues 418 - 424 (chain A) in PDB entry 4WTM
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 THR 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A TYR* 3.9 8.7 - - + -
384A LEU 3.6 21.5 - - - +
385A THR* 3.4 25.4 - - - +
415A TYR* 2.7 31.4 + - + +
416A ALA 3.9 0.2 - - - +
417A PRO* 1.3 77.3 - - + +
419A ILE* 1.3 60.4 + - - +
420A TRP* 3.3 19.8 + - - +
421A VAL* 3.1 21.8 + - - +
422A ARG* 3.1 30.7 + - - +
477A TYR* 3.9 0.2 - - - -
481A GLU* 4.8 0.7 - - - -
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Residues in contact with ILE 419 (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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383A TYR* 5.1 0.2 + - - -
418A THR* 1.3 73.5 - - - +
420A TRP* 1.3 60.5 + - + +
422A ARG* 4.6 3.4 - - + +
423A MET* 3.0 57.0 + - + +
477A TYR* 3.6 42.5 - - + -
481A GLU* 4.4 16.5 + - + +
482A LEU* 3.7 27.4 - - + -
485A VAL* 3.8 27.8 - - + -
497A LEU* 4.3 9.8 - - + +
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Residues in contact with TRP 420 (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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385A THR* 3.2 18.8 + - - -
386A ARG* 3.4 31.1 + - + -
388A PRO* 3.6 22.4 - - + -
391A PRO* 3.9 32.8 - - + -
392A LEU* 5.8 3.4 - - + -
411A ASN* 4.1 3.8 - - + -
415A TYR* 3.7 35.0 - + + -
418A THR* 3.3 17.3 + - - -
419A ILE* 1.3 79.0 - - - +
421A VAL* 1.3 83.2 + - + +
424A VAL* 3.2 31.6 + - + +
425A LEU* 3.2 19.3 + - + +
481A GLU* 3.7 13.9 - - - -
485A VAL* 3.9 31.2 - - + -
489A LEU* 6.4 0.9 - - + -
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Residues in contact with VAL 421 (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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411A ASN 3.6 19.5 - - - +
412A ILE* 3.7 26.2 - - + -
415A TYR* 3.2 24.0 - - + +
416A ALA* 3.9 4.5 - - - +
418A THR* 3.1 18.0 + - - +
420A TRP* 1.3 96.7 - - + +
422A ARG* 1.3 64.4 + - - +
425A LEU* 3.3 9.8 + - + -
426A MET* 2.8 51.0 + - + +
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Residues in contact with ARG 422 (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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416A ALA 3.1 22.2 - - - +
417A PRO 3.6 2.7 - - - -
418A THR 3.1 17.9 + - - +
419A ILE* 4.1 3.8 - - - +
421A VAL* 1.3 78.8 - - - +
423A MET* 1.3 63.2 + - + +
426A MET* 3.6 28.4 - - + +
427A THR* 3.7 1.7 + - - -
471A ALA 3.2 15.8 + - - -
472A PHE* 3.2 31.4 + - - +
473A SER* 3.7 1.8 - - - +
474A MET* 2.9 30.9 + - - +
477A TYR* 3.0 26.3 + - - -
524A TYR 5.7 0.4 + - - -
525A LEU 5.2 1.8 + - - +
526A PHE* 4.3 0.3 - - - -
528A TRP* 3.3 58.3 + - + +
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Residues in contact with MET 423 (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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419A ILE* 3.0 45.6 + - + +
422A ARG* 1.3 80.5 - - + +
424A VAL* 1.3 59.4 + - - +
427A THR* 2.7 23.1 + - - -
497A LEU* 3.4 52.3 - - + +
498A ARG* 5.4 0.2 - - - -
500A TRP* 3.3 15.5 - - + +
501A LYS* 4.2 9.6 - - + +
528A TRP* 3.6 42.0 - - + -
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Residues in contact with VAL 424 (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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30A LEU* 3.7 26.7 - - + -
392A LEU* 4.4 15.9 - - + -
420A TRP* 3.2 19.2 + - + +
423A MET* 1.3 82.1 - - + +
425A LEU* 1.3 68.5 + - + +
426A MET 3.4 0.4 - - - -
427A THR* 3.4 3.1 + - - -
428A HIS* 3.0 22.7 + - - +
485A VAL* 5.4 0.2 - - + -
489A LEU* 4.1 16.2 - - + -
497A LEU* 4.1 17.5 - - + -
500A TRP* 3.7 36.3 - - + +
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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